Alexander D. MacKerell

发表

Molecular modeling and dynamics of neuropeptide Y

Alexander D. MacKerell, 1988, J. Comput. Aided Mol. Des..

Automated Selection of Compounds with Physicochemical Properties To Maximize Bioavailability and Druglikeness

Alexander D. MacKerell, Taiji Oashi, Ashley L. Ringer, 2011, J. Chem. Inf. Model..

All‐atom polarizable force field for DNA based on the classical drude oscillator model

Alexander D. MacKerell, Alexey Savelyev, A. Savelyev, 2014, J. Comput. Chem..

CHARMM force field parameters for simulation of reactive intermediates in native and thio‐substituted ribozymes

Alexander D. MacKerell, Darrin M. York, Evelyn Mayaan, 2007, J. Comput. Chem..

Estimation of relative free energies of binding using pre‐computed ensembles based on the single‐step free energy perturbation and the site‐identification by Ligand competitive saturation approaches

Alexander D. MacKerell, E. Prabhu Raman, Sirish Kaushik Lakkaraju, 2017, J. Comput. Chem..

Extending the treatment of backbone energetics in protein force fields: Limitations of gas‐phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations

Alexander D. MacKerell, Charles L. Brooks, Michael Feig, 2004, J. Comput. Chem..

Additive CHARMM force field for naturally occurring modified ribonucleotides

Alexander D. MacKerell, You Xu, Lennart Nilsson, 2016, J. Comput. Chem..

Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model

Alexander D. MacKerell, Benoît Roux, David van der Spoel, 2015, J. Comput. Chem..

Correction to Intrinsic Energy Landscapes of Amino Acid Side-Chains

Xiao Zhu, Alexander D. MacKerell, Pedro E. M. Lopes, 2012, J. Chem. Inf. Model..

Impact of Ribosomal Modification on the Binding of the Antibiotic Telithromycin Using a Combined Grand Canonical Monte Carlo/Molecular Dynamics Simulation Approach

Alexander D. MacKerell, Pedro E. M. Lopes, Meagan C. Small, 2013, PLoS Comput. Biol..

Binding Response: A Descriptor for Selecting Ligand Binding Site on Protein Surfaces

Alexander D. MacKerell, Shijun Zhong, Shijun Zhong, 2007, J. Chem. Inf. Model..

Glycan reader: Automated sugar identification and simulation preparation for carbohydrates and glycoproteins

Alexander D. MacKerell, Sunhwan Jo, Wonpil Im, 2011, J. Comput. Chem..

Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing

Alexander D. MacKerell, Kenno Vanommeslaeghe, K. Vanommeslaeghe, 2012, J. Chem. Inf. Model..

Protein Force Fields

Alexander D. MacKerell, 2002 .

Empirical force fields for biological macromolecules: Overview and issues

Alexander D. MacKerell, 2004, J. Comput. Chem..

Conformational Determinants of the Activity of Antiproliferative Factor Glycopeptide

Alexander D. MacKerell, Sairam S. Mallajosyula, Kristie M. Adams, 2013, J. Chem. Inf. Model..

CHARMM general force field: A force field for drug‐like molecules compatible with the CHARMM all‐atom additive biological force fields

Alexander D. MacKerell, Sibsankar Kundu, Chayan Acharya, 2009, J. Comput. Chem..

Impact of 2′‐hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all‐atom additive force field for RNA

Alexander D. MacKerell, Lennart Nilsson, U. Deva Priyakumar, 2011, J. Comput. Chem..

Polarizable empirical force field for nitrogen‐containing heteroaromatic compounds based on the classical Drude oscillator

Alexander D. MacKerell, Pedro E. M. Lopes, Guillaume Lamoureux, 2009, J. Comput. Chem..

Impact of Substrate Protonation and Tautomerization States on Interactions with the Active Site of Arginase I

Alexander D. MacKerell, Shanthi Nagagarajan, Fengtian Xue, 2013, J. Chem. Inf. Model..

POSE SCALING: GEOMETRICAL ASSESSMENT OF LIGAND BINDING POSES

Alexander D. MacKerell, Shijun Zhong, 2008 .

Polarizable empirical force field for sulfur‐containing compounds based on the classical Drude oscillator model

Xiao Zhu, Alexander D. MacKerell, Xiao Zhu, 2010, J. Comput. Chem..

DIRECT‐ID: An automated method to identify and quantify conformational variations—application to β2‐adrenergic GPCR

Alexander D. MacKerell, Jing Huang, Sirish Kaushik Lakkaraju, 2016, J. Comput. Chem..

Polarizable force field for RNA based on the classical drude oscillator

Alexander D. MacKerell, Justin A. Lemkul, 2018, J. Comput. Chem..

Mapping Functional Group Free Energy Patterns at Protein Occluded Sites: Nuclear Receptors and G-Protein Coupled Receptors

Alexander D. MacKerell, Lei Fang, Wenbo Yu, 2015, J. Chem. Inf. Model..

A molecular mechanics force field for NAD+ NADH, and the pyrophosphate groups of nucleotides

Alexander D. MacKerell, Jiali Gao, Joseph J. Pavelites, 1997, J. Comput. Chem..

Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks

Alexander D. MacKerell, Jing Huang, Justin A. Lemkul, 2018, J. Comput. Chem..

All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution

Alexander D. MacKerell, Nilesh K. Banavali, N. Banavali, 2000, J. Comput. Chem..

CH/π interactions involving aromatic amino acids: Refinement of the CHARMM tryptophan force field

Alexander D. MacKerell, Alba T. Macias, Alba T. Macias, 2005, J. Comput. Chem..

CHARMM‐GUI 10 years for biomolecular modeling and simulation

Alexander D. MacKerell, Xi Cheng, Sunhwan Jo, 2017, J. Comput. Chem..

Computational Fragment-Based Binding Site Identification by Ligand Competitive Saturation

Alexander D. MacKerell, Olgun Guvench, Olgun Guvench, 2009, PLoS Comput. Biol..

Extension of the CHARMM general force field to sulfonyl‐containing compounds and its utility in biomolecular simulations

Alexander D. MacKerell, Wenbo Yu, Kenno Vanommeslaeghe, 2012, J. Comput. Chem..

Combined ab initio/empirical approach for optimization of Lennard-Jones parameters

Alexander D. MacKerell, Daxu Yin, D. Yin, 1998, J. Comput. Chem..

Robustness in the fitting of molecular mechanics parameters

Alexander D. MacKerell, Kenno Vanommeslaeghe, Mingjun Yang, 2015, J. Comput. Chem..

Estimation of Ligand Efficacies of Metabotropic Glutamate Receptors from Conformational Forces Obtained from Molecular Dynamics Simulations

Alexander D. MacKerell, Sirish Kaushik Lakkaraju, Fengtian Xue, 2013, J. Chem. Inf. Model..

Use of Computer Aided Drug Design (CADD) to identify small molecule inhibitors of TLR2 signaling

Shannon Green, Alexander D. MacKerell, Ryan S. Schwarz, 2010 .

Additive empirical force field for hexopyranose monosaccharides

Alexander D. MacKerell, Ganesh Kamath, Olgun Guvench, 2008, J. Comput. Chem..

Appendix: Useful Internet Resources

Alexander D. MacKerell, Oren M. Becker, Benoît Roux, 2001 .

Combining the polarizable Drude force field with a continuum electrostatic Poisson–Boltzmann implicit solvation model

Alexander D. MacKerell, Benoît Roux, Fang-Yu Lin, 2018, J. Comput. Chem..

(Ala)4‐X‐(Ala)4 as a model system for the optimization of the χ1 and χ2 amino acid side‐chain dihedral empirical force field parameters

Xiao Zhu, Alexander D. MacKerell, Robert B. Best, 2013, J. Comput. Chem..

Reproducing Crystal Binding Modes of Ligand Functional Groups Using Site-Identification by Ligand Competitive Saturation (SILCS) Simulations

Alexander D. MacKerell, Wenbo Yu, E. Prabhu Raman, 2011, J. Chem. Inf. Model..

Intrinsic Energy Landscapes of Amino Acid Side-Chains

Xiao Zhu, Alexander D. MacKerell, Pedro E. M. Lopes, 2012, J. Chem. Inf. Model..

Inclusion of Multiple Fragment Types in the Site Identification by Ligand Competitive Saturation (SILCS) Approach

Alexander D. MacKerell, Wenbo Yu, E. Prabhu Raman, 2013, J. Chem. Inf. Model..

Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates

Alexander D. MacKerell, Fang-Yu Lin, Meagan C. Small, 2017, Journal of Computer-Aided Molecular Design.

Site-Identification by Ligand Competitive Saturation (SILCS) assisted pharmacophore modeling

Alexander D. MacKerell, Wenbo Yu, E. Prabhu Raman, 2014, J. Comput. Aided Mol. Des..

CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model

Alexander D. MacKerell, Charles L. Brooks, Sandeep Patel, 2004, J. Comput. Chem..

Balancing target flexibility and target denaturation in computational fragment‐based inhibitor discovery

Alexander D. MacKerell, Olgun Guvench, Theresa J. Foster, 2012, J. Comput. Chem..

Consideration of Molecular Weight during Compound Selection in Virtual Target-Based Database Screening

Alexander D. MacKerell, Yongping Pan, Niu Huang, 2003, J. Chem. Inf. Comput. Sci..

Pharmacophore Modeling Using Site-Identification by Ligand Competitive Saturation (SILCS) with Multiple Probe Molecules

Alexander D. MacKerell, Lei Fang, Wenbo Yu, 2015, J. Chem. Inf. Model..

New insights into the structure of abasic DNA from molecular dynamics simulations

Alexander D. MacKerell, Nicolas Foloppe, Daniel Barsky, 2000, Nucleic Acids Res..

Lead Validation and SAR Development via Chemical Similarity Searching; Application to Compounds Targeting the pY+3 Site of the SH2 Domain of p56lck

Alexander D. MacKerell, Jun Hayashi, Md. Younus Mia, 2005, J. Chem. Inf. Model..

Introduction of Polarized Embedding QMMM Technique in CHARMM with PSI4

Alexander D. MacKerell, Andrew C. Simmonett, Anmol Kumar, 2021 .

Enhanced Sampling of RNA Folding/Unfolding Configurations using Machine Learning/Grand Canonical Monte Carlo

Alexander D. MacKerell, Mert Y. Sengul, Abhishek A. Kognole, 2021 .

Identification of non-phosphate-containing small molecular weight inhibitors of the tyrosine kinase p56 Lck SH2 domain via in silico screening against the pY + 3 binding site.

Alexander D. MacKerell, N. Huang, A. Nagarsekar, 2004, Journal of medicinal chemistry.

All-atom empirical potential for molecular modeling and dynamics studies of proteins.

Alexander D. MacKerell, M. Karplus, D. Nguyen, 1998, The journal of physical chemistry. B.

All‐atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data

Alexander D. MacKerell, N. Foloppe, 2000 .

Importance of the CMAP correction to the CHARMM22 protein force field: dynamics of hen lysozyme.

Alexander D. MacKerell, M. Buck, S. Bouguet-Bonnet, 2006, Biophysical journal.

CHARMM: The Energy Function and Its Parameterization

Alexander D. MacKerell, M. Karplus, B. Brooks, 2002 .

Improved treatment of the protein backbone in empirical force fields.

Alexander D. MacKerell, C. Brooks, M. Feig, 2004, Journal of the American Chemical Society.

Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone φ, ψ and side-chain χ(1) and χ(2) dihedral angles.

Alexander D. MacKerell, Pedro E. M. Lopes, M. Feig, 2012, Journal of chemical theory and computation.

An Improved Empirical Potential Energy Function for Molecular Simulations of Phospholipids

Alexander D. MacKerell, S. Feller, 2000 .

An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer.

Alexander D. MacKerell, Jeffery B. Klauda, B. Brooks, 2005, The journal of physical chemistry. B.

Computational Biochemistry and Biophysics

Alexander D. MacKerell, Masakatsu Watanabe, B. Roux, 2001 .

All‐atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution

Alexander D. MacKerell, N. Banavali, 2000 .

Molecular dynamics simulations of nucleic acid-protein complexes.

Alexander D. MacKerell, L. Nilsson, 2008, Current opinion in structural biology.

Protein dynamics. A time-resolved fluorescence, energetic and molecular dynamics study of ribonuclease T1.

Alexander D. MacKerell, U. Hahn, L. Nilsson, 1987, Biophysical chemistry.

Protein-facilitated base flipping in DNA by cytosine-5-methyltransferase

Alexander D. MacKerell, Niu Huang, Alexander D MacKerell, 2002, Proceedings of the National Academy of Sciences of the United States of America.

Cooperative binding of DNA and CBFβ to the Runt domain of the CBFα studied via MD simulations

Alexander D. MacKerell, Victor M. Anisimov, B. Habtemariam, 2005, Nucleic acids research.

Specificity in protein-DNA interactions: energetic recognition by the (cytosine-C5)-methyltransferase from HhaI.

Alexander D. MacKerell, Niu Huang, Alexander D MacKerell, 2005, Journal of molecular biology.

A molecular mechanics force field for NAD+ NADH, and the pyrophosphate groups of nucleotides

Alexander D. MacKerell, Jiali Gao, Joseph J. Pavelites, 1997, J. Comput. Chem..

Force-Field Representation of Biomolecular Systems

Alexander D. MacKerell, Meagan C. Small, 2015 .

Development and current status of the CHARMM force field for nucleic acids

Alexander D. MacKerell, N. Foloppe, N. Banavali, 2000, Biopolymers.

An all-atom empirical energy function for the simulation of nucleic acids

Alexander D. MacKerell, M. Karplus, J. Wiórkiewicz-Kuczera, 1995 .

Influence of Magnesium Ions on Duplex DNA Structural, Dynamic, and Solvation Properties

Alexander D. MacKerell, 1997 .

Polarizable Force Field for DNA Based on the Classical Drude Oscillator: I. Refinement Using Quantum Mechanical Base Stacking and Conformational Energetics.

Alexander D. MacKerell, Justin A. Lemkul, Alexander D MacKerell, 2017, Journal of chemical theory and computation.

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

Alexander D. MacKerell, Justin A. Lemkul, Jeffery B. Klauda, 2015, Journal of chemical theory and computation.

Update of the CHARMM all-atom additive force field for lipids: validation on six lipid types.

Alexander D. MacKerell, Jeffery B. Klauda, D. Tobias, 2010, The journal of physical chemistry. B.

CHARMM all-atom additive force field for sphingomyelin: elucidation of hydrogen bonding and of positive curvature.

Alexander D. MacKerell, Huan Rui, Jeffery B. Klauda, 2014, Biophysical journal.

CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses.

Alexander D. MacKerell, Olgun Guvench, Alexander D Mackerell, 2009, Journal of chemical theory and computation.

CHARMM additive all-atom force field for carbohydrate derivatives and its utility in polysaccharide and carbohydrate-protein modeling.

Alexander D. MacKerell, Kenno Vanommeslaeghe, Olgun Guvench, 2011, Journal of chemical theory and computation.

Conformational Properties of α- or β-(1→6)-Linked Oligosaccharides: Hamiltonian Replica Exchange MD Simulations and NMR Experiments

Alexander D. MacKerell, Sairam S. Mallajosyula, Dhilon S. Patel, 2014, The journal of physical chemistry. B.

Molecular dynamics simulation of unsaturated lipid bilayers at low hydration: parameterization and comparison with diffraction studies.

Alexander D. MacKerell, R. Pastor, S. Feller, 1997, Biophysical journal.

CHARMM Additive All-Atom Force Field for Acyclic Carbohydrates and Inositol.

Alexander D. MacKerell, Ganesh Kamath, Olgun Guvench, 2008, Journal of chemical theory and computation.

CHARMM additive all-atom force field for glycosidic linkages in carbohydrates involving furanoses.

Alexander D. MacKerell, Olgun Guvench, Alexander D MacKerell, 2010, The journal of physical chemistry. B.

Optimization of the CHARMM additive force field for DNA: Improved treatment of the BI/BII conformational equilibrium.

Alexander D. MacKerell, Elizabeth J. Denning, N. Foloppe, 2012, Journal of chemical theory and computation.

Development of the CHARMM Force Field for Lipids.

Alexander D. MacKerell, R. Pastor, 2011, The journal of physical chemistry letters.

A piRNA-like small RNA interacts with and modulates p-ERM proteins in human somatic cells

Alexander D. MacKerell, David J Weber, M. Edelman, 2015, Nature Communications.

Influence of solvent and intramolecular hydrogen bonding on the conformational properties of o-linked glycopeptides.

Alexander D. MacKerell, Alexander D MacKerell, Sairam S. Mallajosyula, 2011, The journal of physical chemistry. B.

The BioFragment Database (BFDb): An open-data platform for computational chemistry analysis of noncovalent interactions.

Alexander D. MacKerell, Daniel G. A. Smith, K. Merz, 2017, The Journal of chemical physics.

Dispersion interactions between urea and nucleobases contribute to the destabilization of RNA by urea in aqueous solution.

Alexander D. MacKerell, U. D. Priyakumar, Koushik Kasavajhala, 2015, The journal of physical chemistry. B.

Combined ab initio/empirical approach for optimization of Lennard–Jones parameters

Alexander D. MacKerell, D. Yin, 1998 .

Molecular mechanics.

Alexander D. MacKerell, Olgun Guvench, K. Vanommeslaeghe, 2014, Current pharmaceutical design.

Recent advances in ligand-based drug design: relevance and utility of the conformationally sampled pharmacophore approach.

Alexander D. MacKerell, J. Polli, A. Coop, 2011, Current computer-aided drug design.

Comprehensive conformational studies of five tripeptides and a deduced method for efficient determinations of peptide structures.

Alexander D. MacKerell, X. Liu, Zijing Lin, 2012, The journal of physical chemistry. B.

Force field development and simulations of intrinsically disordered proteins.

Alexander D. MacKerell, Jing Huang, 2018, Current opinion in structural biology.

Inclusion of many-body effects in the additive CHARMM protein CMAP potential results in enhanced cooperativity of α-helix and β-hairpin formation.

Alexander D. MacKerell, M. Feig, R. Best, 2012, Biophysical journal.

An Empirical Potential Energy Function for Phospholipids: Criteria for Parameter Optimization and Applications

Alexander D. MacKerell, M. Karplus, J. Brickmann, 1996 .

Chapter 1 Considerations for Lipid Force Field Development

Alexander D. MacKerell, Jeffery B. Klauda, R. Pastor, 2008 .

Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model

Alexander D. MacKerell, Pedro E. M. Lopes, B. Roux, 2014, The journal of physical chemistry letters.

Molecular dynamics studies of polyethylene oxide and polyethylene glycol: hydrodynamic radius and shape anisotropy.

Alexander D. MacKerell, R. Pastor, R. Venable, 2008, Biophysical journal.

Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field.

Alexander D. MacKerell, Pedro E. M. Lopes, B. Roux, 2010, Journal of chemical theory and computation.

Balancing the Interactions of Ions, Water, and DNA in the Drude Polarizable Force Field

Alexander D. MacKerell, A. Savelyev, 2014, The journal of physical chemistry. B.

Current status of protein force fields for molecular dynamics simulations.

Alexander D. MacKerell, Pedro E. M. Lopes, Olgun Guvench, 2015, Methods in molecular biology.

Competition among Li(+), Na(+), K(+), and Rb(+) monovalent ions for DNA in molecular dynamics simulations using the additive CHARMM36 and Drude polarizable force fields.

Alexander D. MacKerell, A. Savelyev, 2015, The journal of physical chemistry. B.

A polarizable model of water for molecular dynamics simulations of biomolecules

Alexander D. MacKerell, Edward D Harder, B. Roux, 2006 .

Targeting NAD biosynthesis in bacterial pathogens: Structure-based development of inhibitors of nicotinate mononucleotide adenylyltransferase NadD.

Alexander D. MacKerell, A. Osterman, Yongping Pan, 2009, Chemistry & biology.

Development of extracellular signal-regulated kinase inhibitors.

Alexander D. MacKerell, P. Shapiro, R. Deshmukh, 2009, Current topics in medicinal chemistry.

Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields

Alexander D. MacKerell, O. Borodin, B. Roux, 2019, Chemical reviews.

CHARMM36: An Improved Force Field for Folded and Intrinsically Disordered Proteins

Alexander D. MacKerell, Helmut Grubmüller, Jing Huang, 2017 .

A simple polarizable model of water based on classical Drude oscillators

Alexander D. MacKerell, Benoît Roux, Guillaume Lamoureux, 2003 .

An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications

Alexander D. MacKerell, Benoît Roux, Jing Huang, 2016, Chemical reviews.

Turning Defense into Offense: Defensin Mimetics as Novel Antibiotics Targeting Lipid II

Alexander D. MacKerell, A. Bonvin, Jing Huang, 2013, PLoS pathogens.

Molecular-level organization of saturated and polyunsaturated fatty acids in a phosphatidylcholine bilayer containing cholesterol.

Alexander D. MacKerell, Frank Suits, Alexander D Mackerell, 2004, Biochemistry.

Computational approaches for the design of protein–protein interaction inhibitors

Alexander D. MacKerell, Olgun Guvench, Wenbo Yu, 2013 .

Pharmacophore Modeling using Site-Identification by Ligand Competitive Saturation (SILCS) Method with Multiple Probe Molecules

Lei Fang, Alexander D. MacKerell, E. Prabhu Raman, 2015 .

pH dependence of binding reactions from free energy simulations and macroscopic continuum electrostatic calculations: application to 2'GMP/3'GMP binding to ribonuclease T1 and implications for catalysis.

Alexander D. MacKerell, M Karplus, M. Karplus, 1995, Journal of molecular biology.

Inhibiting S100B in Malignant Melanoma

Alexander D. MacKerell, David J Weber, P. Wilder, 2013 .

Prospects of Modulating Protein–Protein Interactions

Alexander D. MacKerell, Taiji Oashi, Paul Shapiro, 2012 .

Ab Initio Calculations on the Use of Helium and Neon as Probes of the van der Waals Surfaces of Molecules

Alexander D. MacKerell, Daxu Yin, D. Yin, 1996 .

Altered structural fluctuations in duplex RNA versus DNA: a conformational switch involving base pair opening.

Alexander D. MacKerell, Yongping Pan, Yongping Pan, 2003, Nucleic acids research.

Structural modifications of (Z)-3-(2-aminoethyl)-5-(4-ethoxybenzylidene)thiazolidine-2,4-dione that improve selectivity for inhibiting the proliferation of melanoma cells containing active ERK signaling.

Alexander D. MacKerell, J. Yap, S. Fletcher, 2013, Organic & biomolecular chemistry.

Structure–activity exploration of a small-molecule Lipid II inhibitor

Alexander D. MacKerell, Jing Huang, S. Fletcher, 2015, Drug design, development and therapy.

Polarizable Empirical Force Field for Hexopyranose Monosaccharides Based on the Classical Drude Oscillator

Alexander D. MacKerell, Dhilon S. Patel, Xibing He, 2014, The journal of physical chemistry. B.

Differential Impact of the Monovalent Ions Li+, Na+, K+, and Rb+ on DNA Conformational Properties

Alexander D. MacKerell, Alexey Savelyev, A. Savelyev, 2014, The journal of physical chemistry letters.

Conformationally Sampled Pharmacophore for Peptidic δ Opioid Ligands

Alexander D. MacKerell, D. Bernard, A. Coop, 2005 .

An ab Initio Quantum Mechanical Study of Hydrogen-Bonded Complexes of Biological Interest

Alexander D. MacKerell, Niu Huang, 2002 .

Importance of attractive van der Waals contribution in empirical energy function models for the heat of vaporization of polar liquids

Alexander D. MacKerell, Martin Karplus, M. Karplus, 1991 .

Evaluating CHARMM Additive and Drude Polarizable Force Fields Through QM/MM Computations of the Vibrational Stark Effect

Alexander D. MacKerell, Ashley L. Ringer, 2011 .

Automation of the Charmm General Force Field for Drug-Like Molecules

Alexander D. MacKerell, Sudhakar Pamidighantam, Kenno Vanommeslaeghe, 2011 .

A Small Molecule Agonist of EphA2 Receptor Tyrosine Kinase Inhibits Tumor Cell Migration In Vitro and Prostate Cancer Metastasis In Vivo

Alexander D. MacKerell, Chayan Acharya, Jianxing Song, 2012, PloS one.

Identification and characterization of small molecule inhibitors of the calcium-dependent S100B-p53 tumor suppressor interaction.

Alexander D. MacKerell, Alexander D MacKerell, Ryan S. Udan, 2004, Journal of medicinal chemistry.

Computer-Aided Drug Design: Structure-Activity Relationships of Delta Opioid Ligands

Alexander D. MacKerell, D. Bernard, A. Coop, 2005 .

Induced Polarization Influences the Fundamental Forces in DNA Base Flipping

Alexander D. MacKerell, Alexey Savelyev, Justin A. Lemkul, 2014, The journal of physical chemistry letters.

Importance of domain closure for the autoactivation of ERK2.

Alexander D. MacKerell, Taiji Oashi, Paul Shapiro, 2011, Biochemistry.

Chapter 7 Empirical Force Fields for Proteins: Current Status and Future Directions

Alexander D. MacKerell, 2005 .

Contribution of the Phosphodiester Backbone and Glycosyl Linkage Intrinsic Torsional Energetics to DNA Structure and Dynamics

Alexander D. MacKerell, Nicolas Foloppe† and, N. F. And, 1999 .

Force field influence on the observation of π-helical protein structures in molecular dynamics simulations

Alexander D. MacKerell, Charles L. Brooks, Michael Feig, 2003 .

Quantifying the Binding Interaction between the Hypoxia-Inducible Transcription Factor and the von Hippel-Lindau Suppressor.

Alexander D. MacKerell, C. Domene, C. Schofield, 2015, Journal of chemical theory and computation.

Conformational Properties of the Deoxyribose and Ribose Moieties of Nucleic Acids: A Quantum Mechanical Study

Alexander D. MacKerell, Nicolas Foloppe, N. Foloppe, 1998 .

Base Flipping in a GCGC Containing DNA Dodecamer: A Comparative Study of the Performance of the Nucleic Acid Force Fields, CHARMM, AMBER, and BMS.

Alexander D. MacKerell, U. Deva Priyakumar, U. D. Priyakumar, 2006, Journal of chemical theory and computation.

Sampling of Organic Solutes in Aqueous and Heterogeneous Environments Using Oscillating Excess Chemical Potentials in Grand Canonical-like Monte Carlo-Molecular Dynamics Simulations

Alexander D. MacKerell, E. Prabhu Raman, Sirish Kaushik Lakkaraju, 2014, Journal of chemical theory and computation.

Lipid-linked oligosaccharides in membranes sample conformations that facilitate binding to oligosaccharyltransferase.

Alexander D. MacKerell, Jeffery B. Klauda, Nathan R Kern, 2014, Biophysical journal.

Formalisms for the Explicit Inclusion of Electronic Polarizability in Molecular Modeling and Dynamics Studies

Alexander D. MacKerell, Pedro E. M. Lopes, Edward D Harder, 2009 .

Use of oligodeoxyribonucleotides with conformationally constrained abasic sugar targets to probe the mechanism of base flipping by HhaI DNA (cytosine C5)-methyltransferase

Alexander D. MacKerell, Victor E. Marquez, Marc C. Nicklaus, 2000 .

Site Identification by Ligand Competitive Saturation (SILCS) simulations for fragment-based drug design.

Alexander D. MacKerell, Olgun Guvench, E. P. Raman, 2015, Methods in molecular biology.

Decoding the Signaling of a GPCR Heteromeric Complex Reveals a Unifying Mechanism of Action of Antipsychotic Drugs

Davide Provasi, Alexander D. MacKerell, Marta Filizola, 2011, Cell.

Small‐Molecule Inhibitors of the ERK Signaling Pathway: Towards Novel Anticancer Therapeutics

Alexander D. MacKerell, Paul Shapiro, Steven Fletcher, 2011, ChemMedChem.

Molecular Dynamics Simulation Analysis of a Sodium Dodecyl Sulfate Micelle in Aqueous Solution: Decreased Fluidity of the Micelle Hydrocarbon Interior

Alexander D. MacKerell, 1995 .

Characterization of Mg2+ Distributions around RNA in Solution

Alexander D. MacKerell, Sirish Kaushik Lakkaraju, Justin A. Lemkul, 2016, ACS omega.

Targeting Protein Tyrosine Phosphatase SHP2 for the Treatment of PTPN11-Associated Malignancies

Alexander D. MacKerell, M. Loh, Olgun Guvench, 2013, Molecular Cancer Therapeutics.

Small Molecule Therapeutics Targeting Protein Tyrosine Phosphatase SHP 2 for the Treatment of PTPN 11-Associated Malignancies

Alexander D. MacKerell, M. Loh, Olgun Guvench, 2013 .

The Future Of Opioid Analgesics

Alexander D. MacKerell, A. Coop, 2003 .

Empirical Force Fields

Alexander D. MacKerell, 2007 .

Differential Deformability of the DNA Minor Groove and Altered BI/BII Backbone Conformational Equilibrium by the Monovalent Ions Li(+), Na(+), K(+), and Rb(+) via Water-Mediated Hydrogen Bonding.

Alexander D. MacKerell, A. Savelyev, 2015, Journal of chemical theory and computation.

Delineating the conformational flexibility of trisaccharides from NMR spectroscopy experiments and computer simulations.

Alexander D. MacKerell, G. Widmalm, Madhurima Jana, 2016, Physical chemistry chemical physics : PCCP.

Synthesis and Characterization of a Novel Diels - Alder Adduct of Codeine.

Alexander D. MacKerell, A. Wilks, A. Coop, 2010, Helvetica chimica acta.

Using Caenorhabditis elegans as a model organism for evaluating extracellular signal-regulated kinase docking domain inhibitors

Alexander D. MacKerell, Yuan Luo, P. Shapiro, 2008, Journal of Cell Communication and Signaling.

Structure of the cell-binding component of the Clostridium difficile binary toxin reveals a novel macromolecular assembly

Alexander D. MacKerell, David J Weber, A. Grishaev, 2019, bioRxiv.

Enhanced Conformational Sampling Using Replica Exchange with Concurrent Solute Scaling and Hamiltonian Biasing Realized in One Dimension

Alexander D. MacKerell, Jing Huang, Mingjun Yang, 2015, Journal of chemical theory and computation.

Consensus 3D model of μ-opioid receptor ligand efficacy based on a quantitative Conformationally Sampled Pharmacophore.

Alexander D. MacKerell, Jihyun Shim, A. Coop, 2011, The journal of physical chemistry. B.

Thermodynamic analysis of the equilibrium, association and dissociation of 2'GMP and 3'GMP with ribonuclease T1 at pH 5.3.

Alexander D. MacKerell, U. Hahn, W. Saenger, 1991, Biochimica et biophysica acta.

Explicit Inclusion of Induced Polarization in Atomistic Force Fields Based on the Classical Drude Oscillator Model

Alexander D. MacKerell, B. Roux, A. Savelyev, 2016 .

CHARMM Additive All-Atom Force Field for Phosphate and Sulfate Linked to Carbohydrates.

Alexander D. MacKerell, Olgun Guvench, Sairam S. Mallajosyula, 2012, Journal of chemical theory and computation.

Molecular dynamics simulations of glycoproteins using CHARMM.

Alexander D. MacKerell, Sairam S. Mallajosyula, W. Im, 2015, Methods in molecular biology.

Perturbation of Long-Range Water Dynamics as the Mechanism for the Antifreeze Activity of Antifreeze Glycoprotein

Alexander D. MacKerell, Sairam S. Mallajosyula, K. Vanommeslaeghe, 2014, The journal of physical chemistry. B.

Structure-based design of N-substituted 1-hydroxy-4-sulfamoyl-2-naphthoates as selective inhibitors of the Mcl-1 oncoprotein.

Alexander D. MacKerell, P. Wilder, J. Yap, 2016, European journal of medicinal chemistry.

Polarizable empirical force field for acyclic polyalcohols based on the classical Drude oscillator.

Alexander D. MacKerell, Pedro E. M. Lopes, Xibing He, 2013, Biopolymers.

Impact of electronic polarizability on protein-functional group interactions.

Alexander D. MacKerell, Vincent D Ustach, Asaminew H. Aytenfisu, 2020, Physical chemistry chemical physics : PCCP.

Impact of branching on the conformational heterogeneity of the lipopolysaccharide from Klebsiella pneumoniae: Implications for vaccine design

Alexander D. MacKerell, Asaminew H. Aytenfisu, R. Simon, 2018, bioRxiv.

Many-body polarization effects and the membrane dipole potential.

Alexander D. MacKerell, Edward D Harder, B. Roux, 2009, Journal of the American Chemical Society.

Room temperature catalyst-free Knoevenagel condensation: facile access to isatinylidenerhodanines

Alexander D. MacKerell, F. Xue, Geoffrey A. Heinzl, 2013 .

Chemical substituent effect on pyridine permeability and mechanistic insight from computational molecular descriptors.

Alexander D. MacKerell, J. Polli, D. Yin, 2006, Molecular pharmaceutics.

hERG Blockade Prediction by Combining Site Identification by Ligand Competitive Saturation and Physicochemical Properties.

Alexander D. MacKerell, Himanshu Goel, Wenbo Yu, 2022, Chemistry.

Structure and thermodynamic insights on acetylaminofluorene-modified deletion DNA duplexes as models for frameshift mutagenesis.

Alexander D. MacKerell, B. Cho, Bin Lin, 2013, Chemical research in toxicology.

Active site of human liver aldehyde dehydrogenase.

Alexander D. MacKerell, R. Pietruszko, S. Stein, 1987, Biochemistry.

An Activating Mutation of the NSD2 Histone Methyltransferase Drives Oncogenic Reprogramming in Acute Lymphocytic Leukemia

Alexander D. MacKerell, N. Kelleher, J. Licht, 2018, Oncogene.

Conformational sampling of oligosaccharides using Hamiltonian replica exchange with two-dimensional dihedral biasing potentials and the weighted histogram analysis method (WHAM).

Alexander D. MacKerell, Mingjun Yang, 2015, Journal of chemical theory and computation.

Novel LRRK 2 GTP-binding inhibitors reduced degeneration in Parkinson ’ s disease cell and mouse models

Alexander D. MacKerell, Dejun Yang, Joseph M. Thomas, 2014 .

Novel LRRK2 GTP-binding inhibitors reduced degeneration in Parkinson's disease cell and mouse models.

Alexander D. MacKerell, Dejun Yang, Joseph M. Thomas, 2014, Human molecular genetics.

Structural and thermodynamic insight into Escherichia coli UvrABC-mediated incision of cluster diacetylaminofluorene adducts on the NarI sequence.

Alexander D. MacKerell, Y. Zou, Benjamin A. Hilton, 2013, Chemical research in toxicology.

The Expanding Role of the BCL6 Oncoprotein as a Cancer Therapeutic Target

Alexander D. MacKerell, A. Melnick, Wenbo Yu, 2016, Clinical Cancer Research.

Conformational Preference of Serogroup B Salmonella O Polysaccharide in Presence and Absence of the Monoclonal Antibody Se155-4.

Alexander D. MacKerell, R. Simon, Mingjun Yang, 2017, The journal of physical chemistry. B.

Iodobenzene-Catalyzed Synthesis of Phenanthridinones via Oxidative C-H Amidation.

Alexander D. MacKerell, J. Deschamps, Yue Li, 2017, The Journal of organic chemistry.

Characterization of ERK Docking Domain Inhibitors that Induce Apoptosis by Targeting Rsk-1 and Caspase-9

Alexander D. MacKerell, U. D. Priyakumar, P. Shapiro, 2011, BMC Cancer.

Solvation dynamics: improved reproduction of the time-dependent Stokes shift with polarizable empirical force field chromophore models.

Alexander D. MacKerell, Payal Chatterjee, C. Schröder, 2019, Physical chemistry chemical physics : PCCP.

Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields.

Alexander D. MacKerell, Pedro E. M. Lopes, B. Roux, 2013, The Journal of chemical physics.

Targeting of an interrupted polypurine:polypyrimidine sequence in mammalian cells by a triplex-forming oligonucleotide containing a novel base analogue.

Alexander D. MacKerell, J. Liu, E. Darian, 2010, Biochemistry.

CHARMM Drude Polarizable Force Field for Glycosidic Linkages Involving Pyranoses and Furanoses.

Alexander D. MacKerell, Asaminew H. Aytenfisu, Mingjun Yang, 2018, Journal of chemical theory and computation.

Semi-automated Optimization of the CHARMM36 Lipid Force Field to Include Explicit Treatment of Long-Range Dispersion.

Alexander D. MacKerell, Andrew C. Simmonett, Jeffery B. Klauda, 2020, Journal of chemical theory and computation.

Conformational Heterogeneity of Intracellular Loop 3 of the μ-opioid G-protein Coupled Receptor.

Alexander D. MacKerell, S. K. Lakkaraju, Jing Huang, 2016, The journal of physical chemistry. B.

Small-molecule inhibitors of ERK-mediated immediate early gene expression and proliferation of melanoma cells expressing mutated BRaf.

Alexander D. MacKerell, U. D. Priyakumar, S. Fletcher, 2015, The Biochemical journal.

Thiourea-Based Inhibitors of the B-Cell Lymphoma 6 (BCL6) BTB Domain via NMR-Based Fragment Screening and Computer-Aided Drug Design

Alexander D. MacKerell, A. Melnick, T. Cierpicki, 2019 .

The SKI complex is a broad-spectrum, host-directed antiviral drug target for coronaviruses, influenza, and filoviruses

Alexander D. MacKerell, P. Jahrling, Krystal L. Matthews, 2020, Proceedings of the National Academy of Sciences.

SILCS-RNA: Toward a Structure-Based Drug Design Approach for Targeting RNAs with Small Molecules.

Alexander D. MacKerell, A. A. Kognole, Anthony Hazel, 2022, Journal of chemical theory and computation.

Inhibition Requirements of the Human Apical Sodium-Dependent Bile Acid Transporter (hASBT) Using Aminopiperidine Conjugates of glutamyl-Bile Acids

Alexander D. MacKerell, J. Polli, C. Acharya, 2009, Pharmaceutical Research.

Synthesis, modeling, and pharmacological evaluation of UMB 425, a mixed μ agonist/δ antagonist opioid analgesic with reduced tolerance liabilities.

Alexander D. MacKerell, Jace W. Jones, Jihyun Shim, 2013, ACS chemical neuroscience.

Polarization Effects in Water-Mediated Selective Cation Transport across a Narrow Transmembrane Channel.

Alexander D. MacKerell, B. Roux, Hui Li, 2021, Journal of chemical theory and computation.

Molecular simulations of dodecyl-β-maltoside micelles in water: influence of the headgroup conformation and force field parameters.

Alexander D. MacKerell, M. Marchi, E. P. Raman, 2011, The journal of physical chemistry. B.

Small Molecule Inhibitors of Ca(2+)-S100B Reveal Two Protein Conformations.

Alexander D. MacKerell, M. I. Ansari, David J Weber, 2016, Journal of medicinal chemistry.

Mg2+ Impacts the Twister Ribozyme through Push-Pull Stabilization of Non-Sequential Phosphate Pairs

Alexander D. MacKerell, A. MacKerell, A. A. Kognole, 2019, bioRxiv.

Bromoacetophenone as an affinity reagent for human liver aldehyde dehydrogenase.

Alexander D. MacKerell, R. Pietruszko, R. Macwright, 1986, Biochemistry.

Human aldehyde dehydrogenase: kinetic identification of the isozyme for which biogenic aldehydes and acetaldehyde compete.

Alexander D. MacKerell, R. Pietruszko, E. Blatter, 1986, Alcoholism, clinical and experimental research.

Complexes of bacterial nicotinate mononucleotide adenylyltransferase with inhibitors: implication for structure-based drug design and improvement.

Alexander D. MacKerell, A. Osterman, Rohit Kolhatkar, 2010, Journal of medicinal chemistry.

Calculation of the Vibrational Stark Effect Using a First-Principles QM/MM Approach.

Alexander D. MacKerell, Ashley L. Ringer, 2011, The journal of physical chemistry letters.

Identification of novel nonsteroidal compounds as substrates or inhibitors of hASBT.

Alexander D. MacKerell, J. Polli, Vidula Kolhatkar, 2012, Journal of pharmaceutical sciences.

Targeting zymogen activation to control the matriptase-prostasin proteolytic cascade.

Alexander D. MacKerell, P. Wilder, Michael D. Johnson, 2011, Journal of medicinal chemistry.

Protonation of trimethylamine N-oxide (TMAO) is required for stabilization of RNA tertiary structure.

Alexander D. MacKerell, Elizabeth J. Denning, D. Thirumalai, 2013, Biophysical chemistry.

Free energy and structural pathways of base flipping in a DNA GCGC containing sequence.

Alexander D. MacKerell, Alexander D MacKerell, Nilesh K Banavali, 2002, Journal of molecular biology.

Facile one-step synthesis of 2,5-diketopiperazines

Alexander D. MacKerell, A. Faden, F. Xue, 2014 .

Desmethyl macrolides: synthesis and evaluation of 4-desmethyl telithromycin.

Alexander D. MacKerell, Meagan C. Small, D. Klepacki, 2014, ACS medicinal chemistry letters.

Desmethyl Macrolides: Synthesis and Evaluation of 4,8,10-Tridesmethyl Cethromycin.

Alexander D. MacKerell, Meagan C. Small, D. Klepacki, 2012, ACS medicinal chemistry letters.

Desmethyl Macrolides: Synthesis and Evaluation of 4,8-Didesmethyl Telithromycin.

Alexander D. MacKerell, Meagan C. Small, D. Klepacki, 2012, ACS medicinal chemistry letters.

Conformational, Aqueous Solvation, and pKa Contributions to the Binding and Activity of Cocaine, WIN 35 065-2, and the WIN Vinyl Analog

Alexander D. MacKerell, Biao Yang, Jeremy Wright, 1994 .

Influence of conformation on the EPR spectrum of 5,5-dimethyl-1-hydroperoxy-1-pyrrolidinyloxyl: a spin trapped adduct of superoxide.

Alexander D. MacKerell, H. Halpern, B. Robinson, 2004, The Journal of organic chemistry.

Optimized Lennard-Jones Parameters for Druglike Small Molecules.

Alexander D. MacKerell, B. Roux, E. Boulanger, 2018, Journal of chemical theory and computation.

Direct comparisons of experimental and calculated neutron structure factors of pure solvents as a method for force field validation.

Alexander D. MacKerell, D. Tobias, Jennie L. Thomas, 2007, The journal of physical chemistry. B.

Inhibition of the bacterial heme oxygenases from Pseudomonas aeruginosa and Neisseria meningitidis: novel antimicrobial targets.

Alexander D. MacKerell, Pedro E. M. Lopes, A. Wilks, 2007, Journal of medicinal chemistry.

Cyclopropyl-containing positive allosteric modulators of metabotropic glutamate receptor subtype 5.

Alexander D. MacKerell, S. K. Lakkaraju, B. Stoica, 2015, Bioorganic & medicinal chemistry letters.

Structure-Based Discovery of a Novel Pentamidine-Related Inhibitor of the Calcium-Binding Protein S100B.

Alexander D. MacKerell, David J Weber, R. Godoy-Ruiz, 2012, ACS medicinal chemistry letters.

(-)-3 beta-Substituted ecgonine methyl esters as inhibitors for cocaine binding and dopamine uptake.

Alexander D. MacKerell, M. Eldefrawi, S. Lieske, 1998, Journal of medicinal chemistry.

Quantitative conformationally sampled pharmacophore for delta opioid ligands: reevaluation of hydrophobic moieties essential for biological activity.

Alexander D. MacKerell, D. Bernard, A. Coop, 2007, Journal of medicinal chemistry.

Position of coordination of the lithium ion determines the regioselectivity of demethylations of 3,4-dimethoxymorphinans with L-selectride.

Alexander D. MacKerell, J. Deschamps, D. Bernard, 2005, Organic letters.

Design of Inhibitors for S100B.

Alexander D. MacKerell, David J Weber, J. Markowitz, 2005, Current topics in medicinal chemistry.

Small molecules bound to unique sites in the target protein binding cleft of calcium-bound S100B as characterized by nuclear magnetic resonance and X-ray crystallography.

Alexander D. MacKerell, David J Weber, P. Wilder, 2009, Biochemistry.

Divalent metal ion complexes of S100B in the absence and presence of pentamidine.

Alexander D. MacKerell, David J Weber, P. Wilder, 2008, Journal of molecular biology.

Deconstructing 14-phenylpropyloxymetopon: minimal requirements for binding to mu opioid receptors.

Alexander D. MacKerell, Jihyun Shim, A. Coop, 2012, Bioorganic & medicinal chemistry.

Facile Synthesis of Spirocyclic Lactams from β-Keto Carboxylic Acids.

Alexander D. MacKerell, Lauren A. Mitchell, J. Deschamps, 2015, Organic letters.

Acyl-2-aminobenzimidazoles: a novel class of neuroprotective agents targeting mGluR5.

Alexander D. MacKerell, Alexander D MacKerell, Fengtian Xue, 2015, Bioorganic & medicinal chemistry.

Small‐Molecule Inhibitors of the ERK Signaling Pathway: Towards Novel Anticancer Therapeutics

Alexander D. MacKerell, J. Yap, S. Fletcher, 2011, ChemMedChem.

CHARMM Drude Polarizable Force Field for Aldopentofuranoses and Methyl-aldopentofuranosides.

Alexander D. MacKerell, Alexander D MacKerell, Madhurima Jana, 2015, The journal of physical chemistry. B.

3-chloropropanoic acid (UMB66): a ligand for the gamma-hydroxybutyric acid receptor lacking a 4-hydroxyl group.

Alexander D. MacKerell, A. Coop, Alba T. Macias, 2004, Bioorganic & medicinal chemistry.

Intramolecular vibrational coupling of adsorbates probed using HREELS and ab initio calculations: Ethoxides adsorbed on Mo(11)

Alexander D. MacKerell, P. Uvdal, B. Wiegand, 1993 .

The structure of aqueous guanidinium chloride solutions.

Alexander D. MacKerell, Alexander D MacKerell, J. Brady, 2004, Journal of the American Chemical Society.

Relaxation of the rigid backbone of an oligoamide-foldamer-based α-helix mimetic: identification of potent Bcl-xL inhibitors.

Alexander D. MacKerell, P. Wilder, J. Yap, 2012, Organic & biomolecular chemistry.

Structure of Penta-Alanine Investigated by Two-Dimensional Infrared Spectroscopy and Molecular Dynamics Simulation.

Alexander D. MacKerell, Jing Huang, Nien-Hui Ge, 2016, The journal of physical chemistry. B.

Prediction of Membrane Permeation of Drug Molecules by Combining an Implicit Membrane Model with Machine Learning

Alexander D. MacKerell, Michael Feig, Alexander D MacKerell, 2018, J. Chem. Inf. Model..

A comparative Kirkwood-Buff study of aqueous methanol solutions modeled by the CHARMM additive and Drude polarizable force fields.

Alexander D. MacKerell, Xibing He, Bin Lin, 2013, The journal of physical chemistry. B.

Six-site polarizable model of water based on the classical Drude oscillator.

Alexander D. MacKerell, Benoît Roux, Pedro E. M. Lopes, 2013, The Journal of chemical physics.

Contribution of the intrinsic mechanical energy of the phosphodiester linkage to the relative stability of the A, BI, and BII forms of duplex DNA.

Alexander D. MacKerell, Alexander D MacKerell, 2009, The journal of physical chemistry. B.

Automated conformational energy fitting for force-field development

Alexander D. MacKerell, Olgun Guvench, 2008, Journal of molecular modeling.

Intrinsic conformational energetics associated with the glycosyl torsion in DNA: a quantum mechanical study.

Alexander D. MacKerell, Nicolas Foloppe, Lennart Nilsson, 2002, Biophysical journal.

Intrinsic conformational properties of deoxyribonucleosides: implicated role for cytosine in the equilibrium among the A, B, and Z forms of DNA.

Alexander D. MacKerell, N. Foloppe, A D MacKerell, 1999, Biophysical journal.

All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data

Alexander D. MacKerell, N. Foloppe, 2000, J. Comput. Chem..

Recent developments and applications of the CHARMM force fields

Xiao Zhu, Alexander D. MacKerell, Pedro E. M. Lopes, 2012, Wiley interdisciplinary reviews. Computational molecular science.

Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg2.

Alexander D. MacKerell, B. Roux, T. Simonson, 2018, The journal of physical chemistry. A.

Polarizability rescaling and atom-based Thole scaling in the CHARMM Drude polarizable force field for ethers

Alexander D. MacKerell, C. Baker, C. M. Baker, 2010, Journal of molecular modeling.

Urea destabilizes RNA by forming stacking interactions and multiple hydrogen bonds with nucleic acid bases.

Changbong Hyeon, Alexander D. MacKerell, U Deva Priyakumar, 2009, Journal of the American Chemical Society.

Conformational properties of methyl β-maltoside and methyl α- and β-cellobioside disaccharides.

Alexander D. MacKerell, Göran Widmalm, Alexander D MacKerell, 2011, The journal of physical chemistry. B.

Bifurcated hydrogen bonding and asymmetric fluctuations in a carbohydrate crystal studied via X-ray crystallography and computational analysis.

Alexander D. MacKerell, Elizabeth Hatcher, G. Widmalm, 2013, The journal of physical chemistry. B.

CHARMM additive all-atom force field for aldopentofuranoses, methyl-aldopentofuranosides, and fructofuranose.

Alexander D. MacKerell, Olgun Guvench, Alexander D Mackerell, 2009, The journal of physical chemistry. B.

INHIBITION OF (CYTOSINE C5)-METHYLTRANSFERASE BY OLIGONUCLEOTIDES CONTAINING FLEXIBLE (CYCLOPENTANE) AND CONFORMATIONALLY CONSTRAINED (BICYCLO[3.1.0]HEXANE) ABASIC SITES

Alexander D. MacKerell, M. Manoharan, N. Banavali, 2001, Nucleosides, nucleotides & nucleic acids.

Comparative molecular field analysis-based predictive model of structure-function relationships of polyamine transport inhibitors in L1210 cells.

Alexander D. MacKerell, M. Egorin, D. Rosen, 1997, Cancer research.

Ab initio conformational analysis of nucleic acid components: Intrinsic energetic contributions to nucleic acid structure and dynamics

Alexander D. MacKerell, N. Foloppe, L. Nilsson, 2001, Biopolymers.

Reevaluation of stereoelectronic contributions to the conformational properties of the phosphodiester and N3'-phosphoramidate moieties of nucleic acids.

Alexander D. MacKerell, N. Banavali, N K Banavali, 2001, Journal of the American Chemical Society.

Unusual sequence effects on nucleotide excision repair of arylamine lesions: DNA bending/distortion as a primary recognition factor

Alexander D. MacKerell, E. Darian, Y. Zou, 2012, Nucleic acids research.

Desmethyl Macrolide Analogues to Address Antibiotic Resistance: Total Synthesis and Biological Evaluation of 4,8,10-Tridesmethyl Telithromycin.

Alexander D. MacKerell, D. Klepacki, Olgun Guvench, 2011, ACS medicinal chemistry letters.

Drude Polarizable Force Field for Molecular Dynamics Simulations of Saturated and Unsaturated Zwitterionic Lipids.

Alexander D. MacKerell, Benoît Roux, Hui Li, 2017, Journal of chemical theory and computation.

DNA bending induced by carbocyclic sugar analogs constrained to the north conformation.

Alexander D. MacKerell, N. Banavali, Alba T. Macias, 2007, Biopolymers.

Human Aldehyde Dehydrogenase Catalytic Activity and Structural Interactions with Coenzyme Analogs

Alexander D. MacKerell, G. Izaguirre, R. Pietruszko, 2001, Journal of biomolecular structure & dynamics.

CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues.

Alexander D. MacKerell, Sunhwan Jo, Benoît Roux, 2014, Advances in protein chemistry and structural biology.

Re-examination of the intrinsic, dynamic and hydration properties of phosphoramidate DNA.

Alexander D. MacKerell, N. Banavali, 2001, Nucleic acids research.

Rational design of human DNA ligase inhibitors that target cellular DNA replication and repair.

Alexander D. MacKerell, X. Chen, G. M. Wilson, 2008, Cancer research.

Lesion processing by a repair enzyme is severely curtailed by residues needed to prevent aberrant activity on undamaged DNA

Alexander D. MacKerell, M. Noon, E. Pozharski, 2012, Proceedings of the National Academy of Sciences.

Structural mechanism associated with domain opening in gain‐of‐function mutations in SHP2 phosphatase

Alexander D. MacKerell, Olgun Guvench, Alexander D MacKerell, 2011, Proteins.

Identification of small molecular weight inhibitors of Src homology 2 domain-containing tyrosine phosphatase 2 (SHP-2) via in silico database screening combined with experimental assay.

Alexander D. MacKerell, Olgun Guvench, Alexander D Mackerell, 2008, Journal of medicinal chemistry.

Tyr66 acts as a conformational switch in the closed-to-open transition of the SHP-2 N-SH2-domain phosphotyrosine-peptide binding cleft

Alexander D. MacKerell, Olgun Guvench, C. Qu, 2007, BMC Structural Biology.

A hybrid mechanism of action for BCL6 in B cells defined by formation of functionally distinct complexes at enhancers and promoters.

Alexander D. MacKerell, Francine E. Garrett-Bakelman, Eugenia G. Giannopoulou, 2013, Cell reports.

Re-evaluation of the reported experimental values of the heat of vaporization of N-methylacetamide.

Alexander D. MacKerell, Alexander D Mackerell, Victor M Anisimov, 2008, Journal of chemical theory and computation.

A small-molecule inhibitor of BCL6 kills DLBCL cells in vitro and in vivo.

Alexander D. MacKerell, Jose M Polo, Alexander D Mackerell, 2010, Cancer cell.

TIT for TAT: the properties of inosine and adenosine in TATA box DNA.

Alexander D. MacKerell, H. Weinstein, N. Pastor, 1999, Journal of biomolecular structure & dynamics.

Identification of HIV-1 integrase inhibitors via three-dimensional database searching using ASV and HIV-1 integrases as targets.

Alexander D. MacKerell, M C Nicklaus, Y. Pommier, 2000, Bioorganic & medicinal chemistry.

Rationally designed BCL6 inhibitors target activated B cell diffuse large B cell lymphoma.

Alexander D. MacKerell, O. Elemento, J. Leonard, 2016, The Journal of clinical investigation.

RUNX2 and TAZ-dependent signaling pathways regulate soluble E-Cadherin levels and tumorsphere formation in breast cancer cells

Alexander D. MacKerell, A. Passaniti, M. Sudol, 2015, Oncotarget.

Identification of Thiourea-Based Inhibitors of the B-Cell Lymphoma 6 BTB Domain via NMR-Based Fragment Screening and Computer-Aided Drug Design.

Alexander D. MacKerell, A. Melnick, T. Cierpicki, 2018, Journal of medicinal chemistry.

Impact of geometry optimization on base-base stacking interaction energies in the canonical A- and B-forms of DNA.

Alexander D. MacKerell, Alexander D MacKerell, Elizabeth J. Denning, 2013, The journal of physical chemistry. A.

Characterizing Structural Transitions Using Localized Free Energy Landscape Analysis

Alexander D. MacKerell, N. Banavali, 2009, PloS one.

Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges

Alexander D. MacKerell, E. Prabhu Raman, K. Vanommeslaeghe, 2012, J. Chem. Inf. Model..

Putative Irreversible Inhibitors of the Human Sodium-Dependent Bile Acid Transporter (hASBT; SLC10A2) Support the Role of Transmembrane Domain 7 in Substrate Binding/Translocation

Alexander D. MacKerell, J. Polli, P. Swaan, 2012, Pharmaceutical Research.

Additive CHARMM36 Force Field for Nonstandard Amino Acids.

Alexander D. MacKerell, W. Im, Jumin Lee, 2021, Journal of chemical theory and computation.

Further Optimization and Validation of the Classical Drude Polarizable Protein Force Field.

Alexander D. MacKerell, B. Roux, Jing Huang, 2020, Journal of chemical theory and computation.

Force Field for Peptides and Proteins based on the Classical Drude Oscillator.

Alexander D. MacKerell, Pedro E. M. Lopes, B. Roux, 2013, Journal of chemical theory and computation.

Structure-Based Design of Potent Iminosugar Inhibitors of Endoplasmic Reticulum α-Glucosidase I with Anti-SARS-CoV-2 Activity.

Alexander D. MacKerell, R. Mariuzza, S. S. Karade, 2023, Journal of medicinal chemistry.

Do Halogen–Hydrogen Bond Donor Interactions Dominate the Favorable Contribution of Halogens to Ligand–Protein Binding?

Alexander D. MacKerell, Fang-Yu Lin, 2017, The journal of physical chemistry. B.

The novel BH3 α-helix mimetic JY-1-106 induces apoptosis in a subset of cancer cells (lung cancer, colon cancer and mesothelioma) by disrupting Bcl-xL and Mcl-1 protein–protein interactions with Bak

Alexander D. MacKerell, Xiaobo Cao, Kenno Vanommeslaeghe, 2013, Molecular Cancer.

Ab initio modeling of glycosyl torsions and anomeric effects in a model carbohydrate: 2-ethoxy tetrahydropyran.

Alexander D. MacKerell, Bernard R Brooks, H Lee Woodcock, 2007, Biophysical journal.

Comparison of protein force fields for molecular dynamics simulations.

Alexander D. MacKerell, Olgun Guvench, 2008, Methods in molecular biology.

Lipopolysaccharide membrane building and simulation.

Alexander D. MacKerell, Jeffery B. Klauda, W. Im, 2015, Methods in molecular biology.

Exploring protein‐protein interactions using the site‐identification by ligand competitive saturation methodology

Alexander D. MacKerell, Sirish Kaushik Lakkaraju, Sunhwan Jo, 2019, Proteins.

Identification and validation of human DNA ligase inhibitors using computer-aided drug design.

Alexander D. MacKerell, Alexander D MacKerell, Alan E Tomkinson, 2008, Journal of medicinal chemistry.

Specificity of Molecular Fragments Binding to S100B versus S100A1 as Identified by NMR and Site Identification by Ligand Competitive Saturation (SILCS)

Alexander D. MacKerell, David J Weber, Wenbo Yu, 2021, Molecules.

Computer-Aided Drug Design Methods.

Alexander D. MacKerell, Alexander D MacKerell, Wenbo Yu, 2017, Methods in molecular biology.

Predicting Partition Coefficients of Neutral and Charged Solutes in the Mixed SLES-Fatty Acids Micellar System.

Alexander D. MacKerell, M. Turchi, Q. Cai, 2020, The journal of physical chemistry. B.

Inhibiteurs du facteur de transcription runx2 et utilisations associées

Alexander D. MacKerell, Antonino Passaniti, 2016 .

Reconstruction of the (011) surface on α-quartz: A semiclassical Ab initio molecular dynamics study

Alexander D. MacKerell, Pedro E. M. Lopes, E. Demchuk, 2009 .

Computational ligand-based rational design: Role of conformational sampling and force fields in model development.

Alexander D. MacKerell, Jihyun Shim, 2011, MedChemComm.

Structural determinants for transport across the intestinal bile acid transporter using C-24 bile acid conjugates.

Alexander D. MacKerell, Chayan Acharya, Alexander D Mackerell, 2010, Molecular pharmaceutics.

Molecular switch controlling the binding of anionic bile acid conjugates to human apical sodium-dependent bile acid transporter.

Alexander D. MacKerell, Chayan Acharya, Alexander D Mackerell, 2010, Journal of medicinal chemistry.

Conformationally sampled pharmacophore for peptidic delta opioid ligands.

Alexander D. MacKerell, D. Bernard, A. Coop, 2005, Journal of medicinal chemistry.

2D conformationally sampled pharmacophore: a ligand-based pharmacophore to differentiate delta opioid agonists from antagonists.

Alexander D. MacKerell, Alexander D MacKerell, Andrew Coop, 2003, Journal of the American Chemical Society.

Drude Polarizable Force Field Parametrization of Carboxylate and N-acetyl Amine Carbohydrate Derivatives.

Alexander D. MacKerell, Sairam S. Mallajosyula, Asaminew H. Aytenfisu, 2019, Journal of chemical theory and computation.

Insight into Early-Stage Unfolding of GPI-Anchored Human Prion Protein.

Alexander D. MacKerell, Sairam S. Mallajosyula, Jeffery B. Klauda, 2015, Biophysical journal.

INTERACTION OF TATA-BOX BINDING PROTEIN (TBP) WITH DNA: A MOLECULAR DYNAMICS SIMULATION STUDY

Alexander D. MacKerell, S. J. Silva, 2003 .

Identification of novel extracellular signal-regulated kinase docking domain inhibitors.

Alexander D. MacKerell, Paul Shapiro, Alexander D Mackerell, 2005, Journal of medicinal chemistry.

Desmethyl Macrolides: Synthesis and Evaluation of 4,10-Didesmethyl Telithromycin.

Alexander D. MacKerell, Meagan C. Small, D. Klepacki, 2012, ACS medicinal chemistry letters.

Discovery of beta-lactamase CMY-10 inhibitors for combination therapy against multi-drug resistant Enterobacteriaceae

Alexander D. MacKerell, S. S. Azam, Wenbo Yu, 2021, PloS one.

Insights into Glucose-6-phosphate Allosteric Activation of β-Glucosidase A

Alexander D. MacKerell, S. K. Lakkaraju, B. Guimarães, 2021, J. Chem. Inf. Model..

Molecular dynamics simulations of ribonuclease T1

Alexander D. MacKerell, L. Nilsson, U. Heinemann, 1988, European Biophysics Journal.

Molecular modeling and dynamics of biologically active peptides: application to neuropeptide Y.

Alexander D. MacKerell, 1991, Methods in enzymology.

Analysis of structure-function relationships of neuropeptide Y using molecular dynamics simulations and pharmacological activity and binding measurements

Alexander D. MacKerell, J. Lacroix, J. Lundberg, 1989, Regulatory Peptides.

Molecular dynamics simulations of ribonuclease T1: Comparison of the free enzyme and 2′ GMP–enzyme complex

Alexander D. MacKerell, U Heinemann, L. Nilsson, 1989, Proteins.

Molecular dynamics simulations of ribonuclease T1: analysis of the effect of solvent on the structure, fluctuations, and active site of the free enzyme.

Alexander D. MacKerell, L. Nilsson, W. Saenger, 1988, Biochemistry.

Polyunsaturated fatty acids in lipid bilayers: intrinsic and environmental contributions to their unique physical properties.

Alexander D. MacKerell, Alexander D MacKerell, S. Feller, 2002, Journal of the American Chemical Society.

Extension of the CHARMM Classical Drude Polarizable Force Field to N- and O-Linked Glycopeptides and Glycoproteins.

Alexander D. MacKerell, Asaminew H. Aytenfisu, A. A. Kognole, 2022, The journal of physical chemistry. B.

Improving the Force Field Description of Tyrosine-Choline Cation-π Interactions: QM Investigation of Phenol-N(Me)4+ Interactions.

Alexander D. MacKerell, N. Reuter, Cédric Grauffel, 2016, Journal of chemical theory and computation.

Correlation of loss of activity of human aldehyde dehydrogenase with reaction of bromoacetophenone with glutamic acid-268 and cysteine-302 residues. Partial-sites reactivity of aldehyde dehydrogenase.

Alexander D. MacKerell, R. Pietruszko, D. Abriola, 1990, The Biochemical journal.

Intrinsic contribution of the 2'-hydroxyl to RNA conformational heterogeneity.

Alexander D. MacKerell, Alexander D MacKerell, Elizabeth J. Denning, 2012, Journal of the American Chemical Society.

Induced Dipole–Dipole Interactions Influence the Unfolding Pathways of Wild-Type and Mutant Amyloid β-Peptides

Alexander D. MacKerell, Justin A. Lemkul, Jing Huang, 2015, Journal of Physical Chemistry B.

Simulation study of ion pairing in concentrated aqueous salt solutions with a polarizable force field.

Alexander D. MacKerell, Wei Jiang, Yun Luo, 2013, Faraday discussions.

Molecular recognition of aldehydes by aldehyde dehydrogenase and mechanism of nucleophile activation

Alexander D. MacKerell, Troy Wymore, Hugh B Nicholas, 2004, Proteins.

Role of the adenine ligand on the stabilization of the secondary and tertiary interactions in the adenine riboswitch.

Alexander D. MacKerell, U Deva Priyakumar, Alexander D MacKerell, 2010, Journal of molecular biology.

Computational and Experimental Characterization of rDNA and rRNA G-Quadruplexes.

Alexander D. MacKerell, Amanda J. Pickard, A. Pickard, 2022, The journal of physical chemistry. B.

Amphipathic α-helix mimetics based on a 1,2-diphenylacetylene scaffold.

Alexander D. MacKerell, P. Wilder, J. Yap, 2013, Organic letters.

A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes

Alexander D. MacKerell, Bernard R Brooks, Walter Thiel, 2018, Molecules.

Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator

Alexander D. MacKerell, Benoît Roux, Fang-Yu Lin, 2018, J. Chem. Inf. Model..

Progress toward chemical accuracy in the computer simulation of condensed phase reactions.

Alexander D. MacKerell, D. Levine, P. Hallstrom, 1996, Proceedings of the National Academy of Sciences of the United States of America.

Additive and Classical Drude Polarizable Force Fields for Linear and Cyclic Ethers.

Alexander D. MacKerell, Adam Moser, Alexander D MacKerell, 2007, Journal of chemical theory and computation.

Characterization of Conformational Ensembles of Protonated N-glycans in the Gas-Phase

Alexander D. MacKerell, Y. Sugita, E. Muneyuki, 2018, Scientific Reports.

Fundamental, binary combination, and overtone modes in methoxy adsorbed on Cu(100): Infrared spectroscopy and ab initio calculations

Alexander D. MacKerell, M. Andersson, P. Uvdal, 2002 .

VIBRATIONAL SHIFTS INDUCED BY 13C ISOTOPIC SUBSTITUTIONS IN A SURFACE ADSORBATE DETERMINED BY INFRARED SPECTROSCOPY AND AB INITIO CALCULATIONS

Alexander D. MacKerell, P. Uvdal, R. Ásmundsson, 1999 .

Mapping the Drude polarizable force field onto a multipole and induced dipole model.

Alexander D. MacKerell, Andrew C Simmonett, Bernard R Brooks, 2017, The Journal of chemical physics.

High-performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD.

Klaus Schulten, Alexander D. MacKerell, James C. Phillips, 2011, The journal of physical chemistry letters.

Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field.

Alexander D. MacKerell, Benoît Roux, Guillaume Lamoureux, 2010, Journal of chemical theory and computation.

Development of an empirical force field for silica. Application to the quartz-water interface.

Alexander D. MacKerell, Pedro E. M. Lopes, Vladimir Murashov, 2006, The journal of physical chemistry. B.

Nucleic Acid Simulations

Alexander D. MacKerell, L. Nilsson, 2001 .

Inactivation of lactate dehydrogenase by UV radiation in the 300 nm wavelength region

Alexander D. MacKerell, P. Söderberg, E. Chen, 1993, Radiation and environmental biophysics.

Computational Characterization of Antibody-Excipient Interactions for Rational Excipient Selection using the Site Identification by Ligand Competitive Saturation (SILCS)-Biologics Approach.

Alexander D. MacKerell, Sunhwan Jo, Sandeep Somani, 2020, Molecular pharmaceutics.

Statistical mechanics of polarizable force fields based on classical Drude oscillators with dynamical propagation by the dual-thermostat extended Lagrangian.

Alexander D. MacKerell, B. Roux, G. Lamoureux, 2020, The Journal of chemical physics.

Rapid estimation of hydration thermodynamics of macromolecular regions.

Alexander D. MacKerell, Alexander D MacKerell, E Prabhu Raman, 2013, The Journal of chemical physics.

Human mitochondrial aldehyde dehydrogenase inhibition by diethyldithiocarbamic acid methanethiol mixed disulfide: a derivative of disulfiram

Alexander D. MacKerell, R. Pietruszko, R. C. Vallari, 1985, FEBS letters.

Balancing the Interactions of Mg2+ in Aqueous Solution and with Nucleic Acid Moieties For a Polarizable Force Field Based on the Classical Drude Oscillator Model.

Alexander D. MacKerell, Justin A. Lemkul, Alexander D MacKerell, 2016, The journal of physical chemistry. B.

Computational identification of inhibitors of protein-protein interactions.

Alexander D. MacKerell, Alexander D MacKerell, Shijun Zhong, 2007, Current topics in medicinal chemistry.

Caught in the act: visualization of an intermediate in the DNA base-flipping pathway induced by HhaI methyltransferase.

Alexander D. MacKerell, Xiaodong Cheng, N. Banavali, 2004, Nucleic acids research.

Computational approaches for investigating base flipping in oligonucleotides.

Alexander D. MacKerell, U Deva Priyakumar, Alexander D MacKerell, 2006, Chemical reviews.

Characterization of ATP-independent ERK inhibitors identified through in silico analysis of the active ERK2 structure.

Alexander D. MacKerell, Paul Shapiro, Alexander D MacKerell, 2006, Bioorganic & medicinal chemistry letters.

Molecular details of the activation of the μ opioid receptor.

Alexander D. MacKerell, Jihyun Shim, A. Coop, 2013, The journal of physical chemistry. B.

CHARMM Additive All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates and Inositol.

Alexander D. MacKerell, Olgun Guvench, Alexander D Mackerell, 2009, Journal of chemical theory and computation.

CHARMM‐GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field

Alexander D. MacKerell, Justin A. Lemkul, W. Im, 2021, J. Comput. Chem..

An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.

Alexander D. MacKerell, Andrew C Simmonett, Bernard R Brooks, 2017, Journal of chemical theory and computation.

Spatial requirements for ITAM signaling in an intracellular natural killer cell model membrane.

Alexander D. MacKerell, Gene Chong, 2022, Biochimica et biophysica acta. General subjects.

Polarizable Molecular Dynamics Simulations of Ionic Liquids and Electrolytes.

Alexander D. MacKerell, O. Borodin, B. Roux, 2018 .

Development of a polarizable intermolecular potential function (PIPF) for liquid amides and alkanes.

Alexander D. MacKerell, Jiali Gao, Jingzhi Pu, 2007, Journal of chemical theory and computation.

Development of a glycoconjugate vaccine to prevent invasive Salmonella Typhimurium infections in sub-Saharan Africa

Alexander D. MacKerell, M. Levine, G. Ramachandran, 2017, PLoS neglected tropical diseases.

Induction of peptide bond dipoles drives cooperative helix formation in the (AAQAA)3 peptide.

Alexander D. MacKerell, Jing Huang, 2014, Biophysical journal.

Cation-π Interactions between Methylated Ammonium Groups and Tryptophan in the CHARMM36 Additive Force Field.

Alexander D. MacKerell, N. Reuter, H. Khan, 2018, Journal of chemical theory and computation.

NMR imino proton exchange experiments on duplex DNA primarily monitor the opening of purine bases.

Alexander D. MacKerell, U Deva Priyakumar, Alexander D Mackerell, 2006, Journal of the American Chemical Society.

Contributions and competition of Mg2+ and K+ in folding and stabilization of the Twister ribozyme

Alexander D. MacKerell, A. A. Kognole, A. Kognole, 2020, bioRxiv.

Computational model for predicting chemical substituent effects on passive drug permeability across parallel artificial membranes.

Alexander D. MacKerell, J. Polli, Chayan Acharya, 2008, Molecular pharmaceutics.

Improved Modeling of Cation‐π and Anion‐Ring Interactions Using the Drude Polarizable Empirical Force Field for Proteins

Alexander D. MacKerell, Fang-Yu Lin, Alexander D MacKerell, 2019, J. Comput. Chem..

CHARMM additive and polarizable force fields for biophysics and computer-aided drug design.

Alexander D. MacKerell, K. Vanommeslaeghe, A D MacKerell, 2015, Biochimica et biophysica acta.

Putative Irreversible Inhibitors of the Human Sodium-Dependent Bile Acid Transporter (hASBT; SLC10A2) Support the Role of Transmembrane Domain 7 in Substrate Binding/Translocation

Alexander D. MacKerell, J. Polli, P. Swaan, 2012, Pharmaceutical Research.

Chemical modification of human aldehyde dehydrogenase by physiological substrate.

Alexander D. MacKerell, R. Pietruszko, 1987, Biochimica et biophysica acta.

Hydrophobic residues in small ankyrin 1 participate in binding to obscurin

Alexander D. MacKerell, Ben Busby, R. Bloch, 2012, Molecular membrane biology.

Electrostatic interactions mediate binding of obscurin to small ankyrin 1: biochemical and molecular modeling studies.

Alexander D. MacKerell, Ben Busby, R. Bloch, 2011, Journal of molecular biology.

Computational evaluation of protein-small molecule binding.

Alexander D. MacKerell, Olgun Guvench, Alexander D MacKerell, 2009, Current opinion in structural biology.

Theoretical Studies of Nucleic Acids and Nucleic Acid-Protein Complexes using Charmm

Alexander D. MacKerell, L. Nilsson, 2006 .

Impact of branching on the conformational heterogeneity of the lipopolysaccharide from Klebsiella pneumoniae: Implications for vaccine design.

Alexander D. MacKerell, Asaminew H. Aytenfisu, R. Simon, 2019, Carbohydrate research.

Nitro-benzylideneoxymorphone, a bifunctional mu and delta opioid receptor ligand with high mu opioid receptor efficacy

Alexander D. MacKerell, J. Traynor, Payal Chatterjee, 2023, Frontiers in Pharmacology.

Assessing hERG1 Blockade from Bayesian Machine-Learning-Optimized Site Identification by Ligand Competitive Saturation Simulations

Alexander D. MacKerell, Alexander D MacKerell, Mahdi Mousaei, 2020, J. Chem. Inf. Model..

Optimization and Evaluation of Site-Identification by Ligand Competitive Saturation (SILCS) as a Tool for Target-Based Ligand Optimization

Alexander D. MacKerell, Wenbo Yu, Sirish Kaushik Lakkaraju, 2019, J. Chem. Inf. Model..

Vibrational spectrum of methoxy adsorbed on metal surfaces: ab initio calculations and experiments

Alexander D. MacKerell, P. Uvdal, 1997 .

Polarizable Empirical Force Field for Halogen-Containing Compounds Based on the Classical Drude Oscillator.

Alexander D. MacKerell, Fang-Yu Lin, Alexander D MacKerell, 2018, Journal of chemical theory and computation.

pKa Calculations with the Polarizable Drude Force Field and Poisson-Boltzmann Solvation Model.

Alexander D. MacKerell, B. Roux, A. Aleksandrov, 2020, Journal of chemical theory and computation.

Determination of Ionic Hydration Free Energies with Grand Canonical Monte Carlo/Molecular Dynamics Simulations in Explicit Water.

Alexander D. MacKerell, S. K. Lakkaraju, Sunhwan Jo, 2018, Journal of chemical theory and computation.

Polarizable Force Field for DNA Based on the Classical Drude Oscillator: II. Microsecond Molecular Dynamics Simulations of Duplex DNA.

Alexander D. MacKerell, Justin A. Lemkul, Alexander D MacKerell, 2017, Journal of chemical theory and computation.

A Comparative Study of Transferable Aspherical Pseudoatom Databank and Classical Force Fields for Predicting Electrostatic Interactions in Molecular Dimers

Alexander D. MacKerell, K. Vanommeslaeghe, K. Jarzembska, 2014, Journal of chemical theory and computation.

Development of the Charmm Polarizable Force Field for Polypeptides Based on Drude Oscillators

Alexander D. MacKerell, Pedro E. M. Lopes, B. Roux, 2011 .

Understanding the dielectric properties of liquid amides from a polarizable force field.

Alexander D. MacKerell, Benoît Roux, Edward Harder, 2008, The journal of physical chemistry. B.

Polarizable empirical force field for the primary and secondary alcohol series based on the classical Drude model.

Alexander D. MacKerell, Benoît Roux, Alexander D Mackerell, 2007, Journal of chemical theory and computation.

Polarizable empirical force field for aromatic compounds based on the classical drude oscillator.

Alexander D. MacKerell, Benoît Roux, Pedro E. M. Lopes, 2007, The journal of physical chemistry. B.

Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator.

Alexander D. MacKerell, Benoît Roux, Niu Huang, 2005, Journal of chemical theory and computation.

Alexander D. MacKerell, P. Wilder, J. Yap, 2013, Molecular Cancer.

Novel protein-inhibitor interactions in site 3 of Ca(2+)-bound S100B as discovered by X-ray crystallography.

Alexander D. MacKerell, David J Weber, M. Cavalier, 2016, Acta crystallographica. Section D, Structural biology.

Expedient access to pre-organized α-helix mimetics based on an isocinchomeronic acid core

Alexander D. MacKerell, S. Fletcher, B. Drennen, 2015 .

Site-Specific Fragment Identification Guided by Single-Step Free Energy Perturbation Calculations.

Alexander D. MacKerell, E. P. Raman, K. Vanommeslaeghe, 2012, Journal of Chemical Theory and Computation.

Integrated Covalent Drug Design Workflow Using Site Identification by Ligand Competitive Saturation.

Alexander D. MacKerell, Wenbo Yu, David J. Weber, 2023, Journal of chemical theory and computation.

Site Identification by Ligand Competitive Saturation-Biologics Approach for Structure-Based Protein Charge Prediction.

Alexander D. MacKerell, Asuka A. Orr, Olgun Guvench, 2023, Molecular pharmaceutics.

Development of CHARMM polarizable force field for nucleic acid bases based on the classical Drude oscillator model.

Alexander D. MacKerell, Alexander D MacKerell, Christopher M Baker, 2011, The journal of physical chemistry. B.

Atomic detail investigation of the structure and dynamics of DNA.RNA hybrids: a molecular dynamics study.

Alexander D. MacKerell, U Deva Priyakumar, Alexander D Mackerell, 2008, The journal of physical chemistry. B.

Combined ab initio/empirical approach for optimization of Lennard‐Jones parameters for polar‐neutral compounds

Alexander D. MacKerell, I JEN CHEN, DAXU YIN, 2002, J. Comput. Chem..

Small molecule antivirulents targeting the iron-regulated heme oxygenase (HemO) of P. aeruginosa.

Alexander D. MacKerell, Pedro E. M. Lopes, A. Wilks, 2013, Journal of medicinal chemistry.

Transmembrane Domain II of the Human Bile Acid Transporter SLC10A2 Coordinates Sodium Translocation*

Alexander D. MacKerell, Sairam S. Mallajosyula, P. Swaan, 2013, The Journal of Biological Chemistry.

Rearrangement of 5-trimethylsilylthebaine on treatment with L-selectride: an efficient synthesis of (+)-bractazonine.

Alexander D. MacKerell, J. Deschamps, J. Flippen-Anderson, 2003, The Journal of organic chemistry.

Conformational Dynamics of Two Natively Unfolded Fragment Peptides: Comparison of the AMBER and CHARMM Force Fields.

Alexander D. MacKerell, Jana K. Shen, Chuanyin Shi, 2015, The journal of physical chemistry. B.

Proper balance of solvent-solute and solute-solute interactions in the treatment of the diffusion of glucose using the Drude polarizable force field.

Alexander D. MacKerell, Alexander D MacKerell, Mingjun Yang, 2018, Carbohydrate research.

Deep Neural Network Model to Predict the Electrostatic Parameters in the Polarizable Classical Drude Oscillator Force Field.

Alexander D. MacKerell, Payal Chatterjee, Poonam Pandey, 2022, Journal of chemical theory and computation.

Global Optimization of the Lennard-Jones Parameters for the Drude Polarizable Force Field.

Alexander D. MacKerell, B. Roux, Chetan Rupakheti, 2021, Journal of chemical theory and computation.

Towards Development of Small Molecule Lipid II Inhibitors as Novel Antibiotics

Alexander D. MacKerell, Jing Huang, S. Fletcher, 2016, PloS one.

Atomistic simulation study of linear alkylbenzene sulfonates at the water/air interface.

Alexander D. MacKerell, Olgun Guvench, Michael L Klein, 2010, The journal of physical chemistry. B.

Tyr66 acts as a conformational switch in the closed-to-open transition of the SHP-2 N-SH2-domain phosphotyrosine-peptide binding cleft

Alexander D. MacKerell, Olgun Guvench, C. Qu, 2007 .

Spatial analysis and quantification of the thermodynamic driving forces in protein-ligand binding: binding site variability.

Alexander D. MacKerell, E. P. Raman, 2015, Journal of the American Chemical Society.

Polarizable empirical force field for alkanes based on the classical Drude oscillator model.

Alexander D. MacKerell, Alexander D MacKerell, Victor M Anisimov, 2005, The journal of physical chemistry. B.

Improved Modeling of Halogenated Ligand-Protein Interactions Using the Drude Polarizable and CHARMM Additive Empirical Force Fields

Alexander D. MacKerell, Fang-Yu Lin, Alexander D MacKerell, 2018, J. Chem. Inf. Model..

Rapid and accurate estimation of protein–ligand relative binding affinities using site-identification by ligand competitive saturation†

Alexander D. MacKerell, Sunhwan Jo, Himanshu Goel, 2021, Chemical science.

Impact of arsenic/phosphorus substitution on the intrinsic conformational properties of the phosphodiester backbone of DNA investigated using ab initio quantum mechanical calculations.

Alexander D. MacKerell, Elizabeth J. Denning, Alexander D Mackerell, 2011, Journal of the American Chemical Society.

Development of CHARMM Additive Potential Energy Parameters for α-Methyl Amino Acids.

Alexander D. MacKerell, Asaminew H. Aytenfisu, R. Pastor, 2021, The journal of physical chemistry. B.

Estimating glycosaminoglycan-protein interaction affinity: water dominates the specific antithrombin-heparin interaction.

Alexander D. MacKerell, U. Desai, P. Mosier, 2016, Glycobiology.

Identification of small molecular weight inhibitors of Src homology 2 domain-containing tyrosine phosphatase 2 (SHP-2) via in silico database screening combined with experimental assay.

Alexander D. MacKerell, Olgun Guvench, C. Qu, 2008, Journal of medicinal chemistry.

Estimating glycosaminoglycan-protein interaction affinity: water dominates the specific antithrombin-heparin interaction.

Alexander D. MacKerell, U. Desai, P. Mosier, 2016, Glycobiology.

Induction of peptide bond dipoles drives cooperative helix formation in the (AAQAA)3 peptide.

Alexander D. MacKerell, Jing Huang, 2014, Biophysical journal.

CHARMM additive all-atom force field for glycosidic linkages in carbohydrates involving furanoses.

Alexander D. MacKerell, Olgun Guvench, E. P. Raman, 2010, The journal of physical chemistry. B.

Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing

Alexander D. MacKerell, K. Vanommeslaeghe, 2012, J. Chem. Inf. Model..

Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model

Alexander D. MacKerell, Justin A. Lemkul, D. Spoel, 2015, J. Comput. Chem..

Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges

Alexander D. MacKerell, E. P. Raman, K. Vanommeslaeghe, 2012, J. Chem. Inf. Model..

DIRECT‐ID: An automated method to identify and quantify conformational variations—application to β2‐adrenergic GPCR

Alexander D. MacKerell, Justin A. Lemkul, S. K. Lakkaraju, 2016, J. Comput. Chem..

Protonation of trimethylamine N-oxide (TMAO) is required for stabilization of RNA tertiary structure.

Alexander D. MacKerell, Elizabeth J. Denning, D. Thirumalai, 2013, Biophysical chemistry.

Targeting zymogen activation to control the matriptase-prostasin proteolytic cascade.

Alexander D. MacKerell, P. Wilder, Michael D. Johnson, 2011, Journal of medicinal chemistry.

Structure–activity exploration of a small-molecule Lipid II inhibitor

Alexander D. MacKerell, Jing Huang, S. Fletcher, 2015, Drug design, development and therapy.

Molecular dynamics studies of polyethylene oxide and polyethylene glycol: hydrodynamic radius and shape anisotropy.

Alexander D. MacKerell, R. Pastor, R. Venable, 2008, Biophysical journal.

Six-site polarizable model of water based on the classical Drude oscillator.

Alexander D. MacKerell, Pedro E. M. Lopes, B. Roux, 2013, The Journal of chemical physics.

Ribonuclease T1: Interaction with 2’GMP and 3’GMP as Studied by Time-Resolved Fluorescence Spectroscopy

Alexander D. MacKerell, U. Hahn, W. Saenger, 1987 .

Small molecules bound to unique sites in the target protein binding cleft of calcium-bound S100B as characterized by nuclear magnetic resonance and X-ray crystallography.

Alexander D. MacKerell, David J Weber, P. Wilder, 2009, Biochemistry.

A polarizable force field of dipalmitoylphosphatidylcholine based on the classical Drude model for molecular dynamics simulations of lipids.

Alexander D. MacKerell, Pedro E. M. Lopes, Edward D Harder, 2013, The journal of physical chemistry. B.

Atomistic Models and Force Fields

Alexander D. MacKerell, Alexander MacKerell, 2001 .

Toward Prediction of Electrostatic Parameters for Force Fields That Explicitly Treat Electronic Polarization.

Alexander D. MacKerell, Payal Chatterjee, C. Schröder, 2019, Journal of chemical theory and computation.

PROTON AND HYDRIDE TRANSFERS IN SOLUTION : HYBRID QM/MM FREE ENERGY PERTURBATION STUDY

Alexander D. MacKerell, P. Bash, L. Ho, 1996 .

Structure-based inhibitor design targeting HIV-1 integrase.

Alexander D. MacKerell, Alexander D MacKerell, Nouri Neamati, 2002, Current drug targets. Infectious disorders.

Improving the Force Field Description of Tyrosine-Choline Cation-π Interactions: QM Investigation of Phenol-N(Me)4+ Interactions.

Alexander D. MacKerell, N. Reuter, Cédric Grauffel, 2016, Journal of Chemical Theory and Computation.

Molecular simulations of dodecyl-β-maltoside micelles in water: influence of the headgroup conformation and force field parameters.

Alexander D. MacKerell, M. Marchi, E. P. Raman, 2011, The journal of physical chemistry. B.

Delineating the conformational flexibility of trisaccharides from NMR spectroscopy experiments and computer simulations.

Alexander D. MacKerell, G. Widmalm, Madhurima Jana, 2016, Physical chemistry chemical physics : PCCP.

All‐atom polarizable force field for DNA based on the classical drude oscillator model

Alexander D. MacKerell, A. Savelyev, 2014, J. Comput. Chem..

Impact of 2′‐hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all‐atom additive force field for RNA

Alexander D. MacKerell, Elizabeth J. Denning, L. Nilsson, 2011, J. Comput. Chem..

Role of the adenine ligand on the stabilization of the secondary and tertiary interactions in the adenine riboswitch.

Alexander D. MacKerell, U. Priyakumar, 2010, Journal of Molecular Biology.

Conformational determinants of tandem GU mismatches in RNA: insights from molecular dynamics simulations and quantum mechanical calculations.

Alexander D. MacKerell, U Deva Priyakumar, Alexander D MacKerell, 2005, Biochemistry.

Mapping the Drude polarizable force field onto a multipole and induced dipole model.

Alexander D. MacKerell, Andrew C. Simmonett, Frank C. Pickard, 2017, Journal of Chemical Physics.

Optimized Lennard-Jones Parameters for Druglike Small Molecules.

Alexander D. MacKerell, B. Roux, E. Boulanger, 2018, Journal of Chemical Theory and Computation.

CHARMM additive all-atom force field for aldopentofuranoses, methyl-aldopentofuranosides, and fructofuranose.

Alexander D. MacKerell, Olgun Guvench, Elizabeth Hatcher, 2009, The journal of physical chemistry. B.

CHARMM Additive All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates and Inositol.

Alexander D. MacKerell, Olgun Guvench, Elizabeth Hatcher, 2009, Journal of chemical theory and computation.

Enhanced Conformational Sampling Using Replica Exchange with Concurrent Solute Scaling and Hamiltonian Biasing Realized in One Dimension

Alexander D. MacKerell, Jing Huang, Mingjun Yang, 2015, Journal of chemical theory and computation.

Atomistic view of base flipping in DNA

Alexander D. MacKerell, Niu Huang, 2004, Philosophical Transactions of the Royal Society of London. Series A: Mathematical, Physical and Engineering Sciences.

Observations on the A versus B Equilibrium in Molecular Dynamics Simulations of Duplex DNA and RNA

Alexander D. MacKerell, 1997 .

Characterization of Conformational Ensembles of Protonated N-glycans in the Gas-Phase

Alexander D. MacKerell, Y. Sugita, E. Muneyuki, 2018, Scientific Reports.