K. Merz

发表

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules

P. Kollman, T. Fox, I. Gould, 1995 .

Combined Quantum Mechanical/Molecular Mechanical Methodologies Applied to Biomolecular Systems

K. Merz, G. Monard, 1999 .

Insights into the structure and dynamics of the dinuclear zinc beta-lactamase site from Bacteroides fragilis.

K. Merz, D. Suárez, E. Brothers, 2002, Biochemistry.

PM3‐compatible zinc parameters optimized for metalloenzyme active sites

K. Merz, D. Deerfield, D. Suárez, 2004, J. Comput. Chem..

Molecular recognition and drug-lead identification: what can molecular simulations tell us?

Kenneth M Merz, Giorgio Colombo, Alessandro Genoni, 2010, Current medicinal chemistry.

Interaction energy decomposition in protein-protein association: a quantum mechanical study of barnase-barstar complex.

Kenneth M Merz, Valentin Gogonea, K. Merz, 2007, Biophysical chemistry.

The Genetic Algorithm and the Conformational Search of Polypeptides and Proteins

Scott M. Le Grand, K. Merz, 1994 .

Structure and dynamics of the dilauroylphosphatidylethanolamine lipid bilayer.

K V Damodaran, K M Merz, B P Gaber, 1992, Biochemistry.

A comparison of DMPC- and DLPE-based lipid bilayers.

K V Damodaran, K M Merz, K. Merz, 1994, Biophysical journal.

The Energy Computation Paradox and ab initio Protein Folding

Kenneth M. Merz, Bing Wang, John C. Faver, 2011, PloS one.

A carbohydrate force field for amber and its application to the study of saccharide to surface adsorption

Kenneth M. Merz, Timothy M. Glennon, K. Merz, 1997 .

Semiempirical molecular orbital calculations with linear system size scaling

S. L. Dixon, K. Merz, S. Dixon, 1996 .

Fast, accurate semiempirical molecular orbital calculations for macromolecules

S. L. Dixon, K. Merz, S. Dixon, 1997 .

Exploring the role of the active site cysteine in human muscle creatine kinase.

Allen J. Flynn, Jan H. Jensen, J. H. Jensen, 2006, Biochemistry.

Importance of dispersion and electron correlation in ab initio protein folding.

Kenneth M. Merz, Guanglei Cui, Xiao He, 2009, The journal of physical chemistry. B.

A Mixed QM/MM Scoring Function to Predict Protein-Ligand Binding Affinity.

Kenneth M Merz, K. Merz, R. Dunbrack, 2010, Journal of chemical theory and computation.

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.

Explicitly representing the solvation shell in continuum solvent calculations.

K. Merz, H. Svendsen, E. F. da Silva, 2009, The journal of physical chemistry. A.

Large-scale validation of a quantum mechanics based scoring function: predicting the binding affinity and the binding mode of a diverse set of protein-ligand complexes.

K. Merz, K. Raha, 2005, Journal of medicinal chemistry.

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules J. Am. Chem. Soc. 1995, 117, 5179−5197

P. Kollman, I. Gould, W. Cornell, 1996 .

The Genetic Algorithm and Protein Tertiary Structure Prediction

Scott M. Le Grand, K. Merz, 1994 .

Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods

Dhruva K. Chakravorty, D. Giedroc, K. Merz, 2013, Journal of biomolecular NMR.

A quantum mechanics-based scoring function: study of zinc ion-mediated ligand binding.

K. Merz, K. Raha, 2004, Journal of the American Chemical Society.

Refinement of protein crystal structures using energy restraints derived from linear-scaling quantum mechanics.

Kenneth M Merz, K. Merz, Ning Yu, 2005, Acta crystallographica. Section D, Biological crystallography.

Conformational Analysis of Free and Bound Retinoic Acid.

Kenneth M Merz, K. Merz, Zheng Fu, 2012, Journal of chemical theory and computation.

Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics program DivCon into the PHENIX refinement package.

Lance M. Westerhoff, Joshua A. Plumley, K. Merz, 2014, Acta crystallographica. Section D, Biological crystallography.

Formal Estimation of Errors in Computed Absolute Interaction Energies of Protein-ligand Complexes.

C David Sherrill, Kenneth M Merz, Xiao He, 2011, Journal of chemical theory and computation.

Simulation of liquid water using semiempirical Hamiltonians and the divide and conquer approach.

K. Merz, A. van der Vaart, G. Monard, 2005, The journal of physical chemistry. A.

Determination of pKas of ionizable groups in proteins: The pKa of Glu 7 and 35 in hen egg white lysozyme and Glu 106 in human carbonic anhydrase II

Kenneth M. Merz, K. Merz, 1991 .

Charge Transfer in Biologically Important Molecules: Comparison of High-Level ab initio and Semiempirical Methods

Kenneth M. Merz, Arjan van der Vaart, K. Merz, 2000 .

Prediction of aqueous solubility of a diverse set of compounds using quantitative structure-property relationships.

Kenneth M Merz, Ailan Cheng, K. Merz, 2003, Journal of medicinal chemistry.

A quantum mechanical-Poisson–Boltzmann equation approach for studying charge flow between ions and a dielectric continuum

K. Merz, V. Gogonea, 2000 .

GB/SA water model for the Merck molecular force field (MMFF).

K M Merz, K. Merz, C. Reynolds, 2000, Journal of molecular graphics & modelling.

Chapter 9 Calculating Binding Free Energy in Protein–Ligand Interaction

Kenneth M. Merz, Kaushik Raha, K. Merz, 2005 .

GB/SA-Based Continuum Solvation Model for Octanol

K. Merz, C. Reynolds, S. A. Best, 1997 .

Fast semiempirical calculations for nuclear magnetic resonance chemical shifts: a divide-and-conquer approach.

K. Merz, A. van der Vaart, E. Brothers, 2004, The Journal of chemical physics.

Bringing Clarity to the Prediction of Protein–Ligand Binding Free Energies via “Blurring”

Kenneth M. Merz, John C. Faver, Melek N. Ucisik, 2014, Journal of chemical theory and computation.

Critical assessment of quantum mechanics based energy restraints in protein crystal structure refinement

Kenneth M Merz, Guanglei Cui, K. Merz, 2006, Protein science : a publication of the Protein Society.

Free energy calculations on protein stability: Thr-157 .fwdarw. Val-157 mutation of T4 lysozyme

Peter A. Kollman, Kenneth M. Merz, P. Kollman, 1989 .

Quantum Free Energy Perturbation Study within a PM3/MM Coupled Potential

K. Merz, R. Stanton, Lance R. Little, 1995 .

The Important Role of Active Site Water in the Catalytic Mechanism of Human Carbonic Anhydrase II – A Semiempirical MO Approach to the Hydration of CO2†

K. Merz, T. Clark, M. Hartmann, 1998 .

Energetics of zinc-mediated interactions in the allosteric pathways of metal sensor proteins.

Dhruva K. Chakravorty, D. Giedroc, K. Merz, 2013, Journal of the American Chemical Society.

Using Quantum Mechanical Approaches to Study Biological Systems

K. Merz, 2014, Accounts of chemical research.

Statistics-based model for basis set superposition error correction in large biomolecules.

K. Merz, J. Faver, Zheng Zheng, 2012, Physical chemistry chemical physics : PCCP.

Further analysis and comparative study of intermolecular interactions using dimers from the S22 database.

K. Merz, L. F. Molnar, Xiao He, 2009, The Journal of chemical physics.

Semiempirical Comparative Binding Energy Analysis (SE-COMBINE) of a Series of Trypsin Inhibitors.

Kenneth M Merz, K. Merz, M. B. Peters, 2006, Journal of chemical theory and computation.

An efficient and accurate molecular alignment and docking technique using ab initio quality scoring.

K. Merz, L. Füsti-Molnár, 2008, The Journal of chemical physics.

Quantum Mechanical-Molecular Mechanical Coupled Potentials

K. Merz, 1998 .

Apo and nickel-bound forms of the Pyrococcus horikoshii species of the metalloregulatory protein: NikR characterized by molecular dynamics simulations.

Daniel J. Sindhikara, K. Merz, A. Roitberg, 2009, Biochemistry.

Are Many-Body Effects Important in Protein Folding?

Charles L. Brooks, Kenneth M. Merz, Arjan van der Vaart, 2000 .

Insight into the cation-π interaction at the metal binding site of the copper metallochaperone CusF.

Dhruva K. Chakravorty, K. Merz, B. Wang, 2011, Journal of the American Chemical Society.

Structure and dynamics of the N-terminal domain of the Cu(I) binding protein CusB.

Dhruva K. Chakravorty, K. Merz, M. N. Ucisik, 2013, Biochemistry.

Linear scaling molecular orbital calculations of biological systems using the semiempirical divide and conquer method

S. L. Dixon, Valentin Gogonea, K. Merz, 2000, J. Comput. Chem..

Charge-Transfer Interactions in Macromolecular Systems: A New View of the Protein/Water Interface

Andrew S. Dixon, K. Merz, G. Nadig, 1998 .

A Combined QM/MM Poisson-Boltzmann Approach.

K. Merz, Seth A. Hayik, Ning-Lin Liao, 2008, Journal of chemical theory and computation.

Zinc Metallo-β-Lactamase from Bacteroides fragilis: A Quantum Chemical Study on Model Systems of the Active Site

Dimas Suárez, Natalia Díaz, Kenneth M. Merz, 2000 .

Catalyzed decomposition of urea. Molecular dynamics simulations of the binding of urea to urease.

Kenneth M Merz, K. Merz, G. Estiu, 2006, Biochemistry.

Ureases: quantum chemical calculations on cluster models.

K. Merz, D. Suárez, N. Díaz, 2003, Journal of the American Chemical Society.

Mechanism of the azulene to naphthalene rearrangement

K. Merz, M. Dewar, 1985 .

The C10H8 potential energy surface: the azulene-to-naphthalene rearrangement

K. Merz, M. Dewar, 1986 .

Thermal rearrangements of C10H8 species; benzvalene analogues and the automerization of naphthalene

K. Merz, M. Dewar, 1986 .

Letter from the Editors

Matthias Rarey, Alexander Tropsha, Kenneth M. Merz, 2015, J. Chem. Inf. Model..

An improved 6-31G basis set for atoms Ga through Kr

K. Merz, A. Mitin, 2007 .

The Ecstasy and Agony of Assay Interference Compounds

K. Merz, C. Bertozzi, C. Lindsley, 2017, J. Chem. Inf. Model..

The Ecstasy and Agony of Assay Interference Compounds.

K. Merz, C. Bertozzi, C. Lindsley, 2017, ACS chemical biology.

The gas-phase and solution-phase free energy surfaces for CO2 + OH- → HCO3-

K. Merz, Z. Peng, 1992 .

MNDO parameters for the prediction of 19F NMR chemical shifts in biologically relevant compounds.

Duane E. Williams, K. Merz, Bing Wang, 2008, The journal of physical chemistry. A.

The MNDO potential energy surface and tunnelling dynamics of the cyclobutane radical cation

K. Merz, M. Dewar, 1985 .

Drug Design: STRUCTURAL BIOLOGY

Kenneth M. Merz, Charles H. Reynolds, Dagmar Ringe, 2010 .

Drug Design: Drug Design

Kenneth M. Merz, Dagmar Ringe, Charles H. Reynolds, 2010 .

Drug Design: Preface

Kenneth M. Merz, Charles H. Reynolds, Dagmar Ringe, 2010 .

Tunneling dynamics of cyclobutadiene

K. Merz, M. Dewar, J. Stewart, 1984 .

Assessment of the "6-31+G** + LANL2DZ" mixed basis set coupled with density functional theory methods and the effective core potential: prediction of heats of formation and ionization potentials for first-row-transition-metal complexes.

K. Merz, Yue Yang, Michael N. Weaver, 2009, The journal of physical chemistry. A.

Computer-aided drug design, quantum-mechanical methods for biological problems.

K. Merz, M. Manathunga, A. Götz, 2022, Current opinion in structural biology.

Molecular dynamics simulations of the mononuclear zinc-beta-lactamase from Bacillus cereus complexed with benzylpenicillin and a quantum chemical study of the reaction mechanism.

K. Merz, D. Suárez, N. Díaz, 2001, Journal of the American Chemical Society.

Effects of fluorine substitution on the edge-to-face interaction of the benzene dimer.

Kevin E. Riley, K. Merz, 2005, The journal of physical chemistry. B.

Tautomerism in free base porphyrins: the porphyrin potential energy surface

K. Merz, C. Reynolds, 1988 .

Confronting Racism in Chemistry Journals

Scott J. Miller, Thomas F. Hofmann, Sarah B. Tegen, 2020, ACS Central Science.

Confronting Racism in Chemistry Journals

Scott J. Miller, Thomas F. Hofmann, Sarah B. Tegen, 2020, ACS Omega.

Confronting Racism in Chemistry Journals.

Scott J. Miller, Thomas F. Hofmann, Sarah B. Tegen, 2020, ACS Applied Bio Materials.

Confronting Racism in Chemistry Journals.

Scott J. Miller, Thomas F. Hofmann, Sarah B. Tegen, 2020, The Journal of organic chemistry.

Confronting Racism in Chemistry Journals.

Scott J. Miller, Thomas F. Hofmann, Sarah B. Tegen, 2020, Journal of the American Chemical Society.

Confronting Racism in Chemistry Journals.

Scott J. Miller, Thomas F. Hofmann, Sarah B. Tegen, 2020, ACS combinatorial science.

Confronting Racism in Chemistry Journals.

Scott J. Miller, Thomas F. Hofmann, Sarah B. Tegen, 2020, Biomacromolecules.

Update to Our Reader, Reviewer, and Author Communities-April 2020.

Scott J. Miller, Thomas F. Hofmann, Bryan W. Brooks, 2020, Journal of proteome research.

Molecular Recognition of K+ and Na+ by Valinomycin in Methanol

K. Merz, T. Marrone, 1995 .

Role of solvation in the energy stabilization inside the hydrophobic core of the protein rubredoxin.

Kevin E. Riley, K. Merz, 2006, The journal of physical chemistry. B.

Molecular recognition of potassium ion by the naturally occurring antibiotic ionophore nonactin

K. Merz, T. Marrone, 1992 .

Head group-water interactions in lipid bilayers: a comparison between DMPC- and DLPE-based lipid bilayers

K. Merz, K. Damodaran, 1993 .

Theoretical study of the electron density distributions of glycyl-L-threonine dihydrate

K. Merz, Ning Yu, 2004 .

Competitive hydrolytic and elimination mechanisms in the urease catalyzed decomposition of urea.

K. Merz, G. Estiu, 2007, The journal of physical chemistry. B.

Enzymatic catalysis of urea decomposition: elimination or hydrolysis?

K. Merz, G. Estiu, 2004, Journal of the American Chemical Society.

The hydrolysis of urea and the proficiency of urease.

K. Merz, G. Estiu, 2004, Journal of the American Chemical Society.

Interaction of the Fusion Inhibiting Peptide Carbobenzoxy-D-Phe-L-Phe-Gly with N-Methyldioleoylphosphatidylethanolamine Lipid Bilayers

K. Merz, K. Damodaran, 1995 .

JCIM Special Issue on Generative Models for Molecular Design

Gianni De Fabritiis, Kenneth M. Merz, Guowei Wei, 2020, Journal of Chemical Information and Modeling.

Aspects of organomercury chemistry

K. Merz, M. Dewar, 1985 .

The hydrolysis of amides and the proficiency of amidohydrolases. The burden borne by kw.

K. Merz, G. Estiu, 2007, The journal of physical chemistry. B.

Through-Bond Interactions in the Solid State

K. Merz, R. Hoffmann, Alexandru T. Balabant, 1987 .

Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods

Dhruva K. Chakravorty, D. Giedroc, K. Merz, 2013, Journal of biomolecular NMR.

Protein NMR chemical shift calculations based on the automated fragmentation QM/MM approach.

K. Merz, B. Wang, Xiao He, 2009, The journal of physical chemistry. B.

The reformatsky reaction

K. Merz, M. Dewar, 1987 .

d10-d10 Interactions: multinuclear copper(I) complexes

K. Merz, R. Hoffmann, 1988 .

Quantum mechanical and molecular dynamics simulations of ureases and Zn β‐lactamases

Dimas Suárez, Kenneth M. Merz, Guillermina Estiu, 2006, Journal of computational chemistry.

Thiosemicarbazones as Aedes aegypti larvicidal.

K. Merz, Q. Lan, D. Moreira, 2015, European journal of medicinal chemistry.

Hybrid QM/MM and DFT investigations of the catalytic mechanism and inhibition of the dinuclear zinc metallo-beta-lactamase CcrA from Bacteroides fragilis.

Hwangseo Park, Kenneth M Merz, Edward N Brothers, 2005, Journal of the American Chemical Society.

Novel acyclic diaminocarbene ligands with increased steric demand and their application in gold catalysis.

K. Merz, K. Abboud, H. Seo, 2010, Organic letters.

Trapping intermediates in metal transfer reactions of the CusCBAF export pump of Escherichia coli

K. Merz, M. N. Ucisik, K. Chacón, 2018, Communications Biology.

Mechanism of the human carbonic anhydrase II-catalyzed hydration of carbon dioxide

Kenneth M. Merz, K. Merz, Ya-Jun Zheng, 1992 .

Computer modeling of the interactions of complex molecules

Peter A. Kollman, Kenneth M. Merz, P. Kollman, 1990 .

Binding of cyanide, cyanate, and thiocyanate to human carbonic anhydrase II

K. Merz, L. Banci, Z. Peng, 1993, Proteins.

Assessment of density functional theory methods for the computation of heats of formation and ionization potentials of systems containing third row transition metals.

Kevin E. Riley, Kenneth M Merz, Kevin E Riley, 2007, The journal of physical chemistry. A.

Force Field Design for Metalloproteins

Kenneth M. Merz, K. Merz, Stephen C. Hoops, 1991 .

d10-d10 Interactions: Multinuclear Copper(I) Complexes.

K. Merz, R. Hoffmann, 1988 .

Accurate assessment of the strain energy in a protein‐bound drug using QM/MM X‐ray refinement and converged quantum chemistry

Xue Li, Zheng Fu, Kenneth M. Merz, 2011, J. Comput. Chem..

Conformational variability of benzamidinium-based inhibitors.

Xiao He, K. Merz, B. Wang, 2009, Journal of the American Chemical Society.

Atomic charges derived from semiempirical methods

P. Kollman, K. Merz, Kenneth M. Merz, 1990 .

The Amber biomolecular simulation programs

Holger Gohlke, Ray Luo, Bing Wang, 2005, J. Comput. Chem..

Mechanistic insights into Mg2+-independent prenylation by CloQ from classical molecular mechanics and hybrid quantum mechanics/molecular mechanics molecular dynamics simulations.

K. Merz, C. A. Bayse, 2014, Biochemistry.

On the question of heavy atom tunneling in the 2-norbornyl cation

K. Merz, M. Dewar, 1986 .

X-ray diffraction "fingerprinting" of DNA structure in solution for quantitative evaluation of molecular dynamics simulation.

Kenneth M Merz, Guanglei Cui, Xiaobing Zuo, 2006, Proceedings of the National Academy of Sciences of the United States of America.

Models for the Metal Transfer Complex of the N-Terminal Region of CusB and CusF.

Dhruva K. Chakravorty, K. Merz, M. N. Ucisik, 2015, Biochemistry.

Study of hydrogen bonding interactions relevant to biomolecular structure and function

Kenneth M. Merz, K. Merz, Ya-Jun Zheng, 1992 .

Computational studies of the farnesyltransferase ternary complex part I: substrate binding.

K. Merz, Guanglei Cui, B. Wang, 2005, Biochemistry.

Finding a needle in the haystack: computational modeling of Mg2+ binding in the active site of protein farnesyltransferase.

Kenneth M Merz, Dhruva K. Chakravorty, Yue Yang, 2010, Biochemistry.

Insights into the mechanistic dichotomy of the protein farnesyltransferase peptide substrates CVIM and CVLS.

K. Merz, C. Fierke, B. Wang, 2012, Journal of the American Chemical Society.

Computational studies of the farnesyltransferase ternary complex part II: the conformational activation of farnesyldiphosphate.

K. Merz, Guanglei Cui, 2007, Biochemistry.

Limits of Free Energy Computation for Protein-Ligand Interactions.

Kenneth M Merz, K. Merz, 2010, Journal of chemical theory and computation.

QM/MM X-ray refinement of zinc metalloenzymes.

Kenneth M Merz, K. Merz, Seth A. Hayik, 2010, Journal of inorganic biochemistry.

Mechanism of Formation of the Nonstandard Product in the Prenyltransferase Reaction of the G115T Mutant of FtmPT1: A Case of Reaction Dynamics Calling the Shots?

K. Merz, L. Song, Yue Yang, 2017, Biochemistry.

Synthesis and crystallography of the wurtzite form of silicon carbide

K. Merz, R. Adamsky, 1959 .

SYNTHESIS OF THE WURTZITE FORM OF SILICON CARBIDE

K. Merz, R. Adamsky, 1959 .

Ice-binding mechanism of winter flounder antifreeze proteins.

K. Merz, A. Cheng, Ailan Cheng, 1997, Biophysical journal.

Evaluation of the catalytic mechanism of AICAR transformylase by pH-dependent kinetics, mutagenesis, and quantum chemical calculations.

J. H. Shim, K. Merz, S. Benkovic, 2001, Journal of the American Chemical Society.

Binding preferences of hydroxamate inhibitors of the matrix metalloproteinase human fibroblast collagenase.

K V Damodaran, S Toba, K M Merz, 1999, Journal of medicinal chemistry.

Conformational preferences for hydroxyl groups in substituted tetrahydropyrans

K. Merz, S. Le Grand, Ya-Jun Zheng, 1992 .

Theoretical examination of the mechanism of aldose-ketose isomerization.

K. Merz, G. Farber, Y. Zheng, 1993, Protein engineering.

New developments in applying quantum mechanics to proteins.

K M Merz, K. Merz, A. van der Vaart, 2001, Current opinion in structural biology.

Analysis of a large data base of electrostatic potential derived atomic charges

K. Merz, Kenneth M. Merz, 1992 .

The Ecstasy and Agony of Assay Interference Compounds.

Kenneth M Merz, Gunda I Georg, Carolyn Bertozzi, 2017, Journal of medicinal chemistry.

Development of the Knowledge-Based and Empirical Combined Scoring Algorithm (KECSA) To Score Protein-Ligand Interactions

Zheng Zheng, Kenneth M. Merz, K. Merz, 2013, J. Chem. Inf. Model..

The Movable Type Method Applied to Protein-Ligand Binding.

Kenneth M Merz, K. Merz, Zheng Zheng, 2013, Journal of chemical theory and computation.

Adenine formation without HCN.

K. Merz, E. C. Aguiar, J. B. da Silva, 2014, The journal of physical chemistry. A.

Density functional transition states of organic and organometallic reactions

Kenneth M. Merz, Robert V. Stanton, K. Merz, 1994 .

Hydration of zinc ions: theoretical study of [Zn(H2O)4](H2O)82+ and [Zn(H2O)6](H2O)62+

K. Merz, D. Suárez, N. Díaz, 2000 .

Density functional study of symmetric proton transfers

K. Merz, R. Stanton, 1994 .

Drug Design : Structure-and Ligand-Based Approaches

Kenneth M. Merz, Charles H. Reynolds, Dagmar Ringe, 2017 .

Charge transfer in small hydrogen bonded clusters

K. Merz, A. V. D. Vaart, 2002 .

Structural Survey of Zinc Containing Proteins and the Development of the Zinc AMBER Force Field (ZAFF).

Kenneth M Merz, Yue Yang, K. Merz, 2010, Journal of chemical theory and computation.

An ab initio investigation of the double proton shift in azophenine

K. Merz, M. Holloway, C. Reynolds, 1989 .

Molecular dynamics study of ethanolamine as a pure liquid and in aqueous solution.

K. Merz, B. Kvamme, E. F. da Silva, 2007, The journal of physical chemistry. B.

Catalytic mechanism of aromatic prenylation by NphB.

K. Merz, Guanglei Cui, B. Wang, 2012, Biochemistry.

Interpreting The Observed Substrate Selectivity And The Product Regioselectivity In Orf2-Catalyzed Prenylation From X-Ray Structures

K. Merz, Guanglei Cui, Ning Yu, 2009 .

Computational prediction of the three-dimensional structures for the Caenorhabditis elegans tubulin family.

K. Merz, V. Gogonea, C. Gogonea, 1999, Journal of molecular graphics & modelling.

Rapid approximation to molecular surface area via the use of Boolean logic and look‐up tables

Kenneth M. Merz, Scott M. Le Grand, K. Merz, 1993, J. Comput. Chem..

Ligand Identification Scoring Algorithm (LISA)

Zheng Zheng, Kenneth M. Merz, K. Merz, 2011, J. Chem. Inf. Model..

Solvent Dynamics and Mechanism of Proton Transfer in Human Carbonic Anhydrase II

Kenneth M. Merz, Giorgio Colombo, Samuel Toba, 1999 .

Mode of action of carbonic anhydrase

Kenneth M. Merz, Roald Hoffmann, Michael J. S. Dewar, 1989 .

Application of the Nosé−Hoover Chain Algorithm to the Study of Protein Dynamics

Kenneth M. Merz, Ailan Cheng, K. Merz, 1996 .

The Ecstasy and Agony of Assay Interference Compounds.

K. Merz, C. Bertozzi, C. Lindsley, 2017, ACS infectious diseases.

The Ecstasy and Agony of Assay Interference Compounds.

Kenneth M Merz, Gunda I Georg, Carolyn Bertozzi, 2017, ACS medicinal chemistry letters.

The Ecstasy and Agony of Assay Interference Compounds.

Shaomeng Wang, Kenneth M. Merz, Carolyn Bertozzi, 2017, Journal of chemical information and modeling.

Importance of loop dynamics in the neocarzinostatin chromophore binding and release mechanisms.

K. Merz, B. Wang, 2010, Physical chemistry chemical physics : PCCP.

Disruption of the active site solvent network in carbonic anhydrase II decreases the efficiency of proton transfer

K. Merz, C. Fierke, J. Jackman, 1996 .

Assigning the protonation states of the key aspartates in β-Secretase using QM/MM X-ray structure refinement.

Kenneth M Merz, Charles H Reynolds, K. Merz, 2006, Journal of chemical theory and computation.

The application of the genetic algorithm to the minimization of potential energy functions

Kenneth M. Merz, Scott M. Le Grand, K. Merz, 1993, J. Glob. Optim..

Computation of the physio‐chemical properties and data mining of large molecular collections

Kenneth M. Merz, Steven L. Dixon, Ailan Cheng, 2002, J. Comput. Chem..

Assessment of Semiempirical Quantum Mechanical Methods for the Evaluation of Protein Structures.

Kenneth M Merz, Andrew M Wollacott, K. Merz, 2007, Journal of chemical theory and computation.

Conformational analysis and parallel QM/MM X-ray refinement of protein bound anti-Alzheimer drug donepezil.

Xue Li, Kenneth M Merz, Zheng Fu, 2013, Journal of chemical theory and computation.

Protein dynamics and solvation in aqueous and nonaqueous environments

D. Hartsough, K. Merz, 1993 .

Protein flexibility in aqueous and nonaqueous solutions

D. Hartsough, K. Merz, 1992 .

Validation of the binding site structure of the cellular retinol-binding protein (CRBP) by ligand NMR chemical shift perturbations.

K. Merz, B. Wang, 2005, Journal of the American Chemical Society.

Pose scoring by NMR.

Kenneth M Merz, Kaushik Raha, K. Merz, 2004, Journal of the American Chemical Society.

Molecular dynamics simulations of the dinuclear zinc‐β‐lactamase from Bacteroides fragilis complexed with imipenem

Dimas Suárez, Natalia Díaz, Kenneth M. Merz, 2002, J. Comput. Chem..

Molecular dynamics simulations of the mononuclear zinc-beta-lactamase from Bacillus cereus.

K M Merz, K. Merz, D. Suárez, 2001, Journal of the American Chemical Society.

Accurate Atomic and Molecular Calculations without Gradient Corrections: Scaled SVWNV Density Functional.

Kevin E. Riley, Kenneth M Merz, Edward N Brothers, 2005, Journal of chemical theory and computation.

Update to Our Reader, Reviewer, and Author Communities-April 2020.

Scott J. Miller, Thomas F. Hofmann, Bryan W. Brooks, 2020, ACS applied materials & interfaces.

Aspects of organotin chemistry

K. Merz, M. Dewar, G. L. Grady, 1984 .

MNDO calculations for compounds containing mercury

K. Merz, M. Dewar, J. Stewart, 1985 .

GROUND STATES OF MOLECULES. 69. ASPECTS OF ORGANOTIN CHEMISTRY

K. Merz, M. Dewar, G. L. Grady, 1985 .

Computer Simulation of Lipid Systems

K. Merz, K. Damodaran, 2007 .

Molecular dynamics simulations of lipid bilayers.

K. Merz, 1997, Current opinion in structural biology.

The intrinsic dynamics and function of nickel-binding regulatory protein: insights from elastic network analysis.

K. Merz, Guanglei Cui, 2008, Biophysical journal.

Simulations of allosteric motions in the zinc sensor CzrA.

Bing Wang, Kenneth M. Merz, Dhruva K. Chakravorty, 2012, Journal of the American Chemical Society.

QM/MM refinement and analysis of protein bound retinoic acid

Xue Li, Zheng Fu, Kenneth M. Merz, 2012, J. Comput. Chem..

CO2 binding to human carbonic anhydrase II

Kenneth M. Merz, K. Merz, 1991 .

AM1 parameters for zinc

K. Merz, M. Dewar, 1988 .

A critical assessment of the performance of protein-ligand scoring functions based on NMR chemical shift perturbations.

Lance M. Westerhoff, Kenneth M Merz, Lance M Westerhoff, 2007, Journal of medicinal chemistry.

Electronic structure, chemical bonding, and oxidation numbers of first‐row transition metals in [MePIm2] complexes and their cations

K. Merz, A. Mitin, J. Kubicki, 2011 .

The Ecstasy and Agony of Assay Interference Compounds.

K. Merz, C. Bertozzi, C. Lindsley, 2017, Biochemistry.

Free energy perturbation simulations of the inhibition of thermolysin: prediction of the free energy of binding of a new inhibitor

Peter A. Kollman, Kenneth M. Merz, P. Kollman, 1989 .

A force field for monosaccharides and (1 → 4) linked polysaccharides

Kenneth M. Merz, Scott M. Le Grand, Timothy M. Glennon, 1994, J. Comput. Chem..

An examination of a density functional/molecular mechanical coupled potential

Kenneth M. Merz, Robert V. Stanton, David S. Hartsough, 1995, J. Comput. Chem..

Confronting Racism in Chemistry Journals.

Scott J. Miller, Thomas F. Hofmann, Sarah B. Tegen, 2020, ACS applied materials & interfaces.

A Fast QM/MM (Quantum Mechanical/Molecular Mechanical) Approach to Calculate Nuclear Magnetic Resonance Chemical Shifts for Macromolecules.

Kenneth M Merz, Bing Wang, B. Wang, 2006, Journal of chemical theory and computation.

The Protein Folding Problem and Tertiary Structure Prediction

Kenneth M. Merz, Scott M. Le Grand, K. Merz, 2012 .

Editorial: Method and Data Sharing and Reproducibility of Scientific Results

Rommie E. Amaro, A. Tropsha, M. Rarey, 2020, J. Chem. Inf. Model..

On the double proton shift in azophenine

K. Merz, M. Dewar, 1985 .

AM1 parameters for the prediction of 1H and 13C NMR chemical shifts in proteins.

Duane E. Williams, K. Merz, A. Roitberg, 2009, The journal of physical chemistry. A.

Relative configuration of natural products using NMR chemical shifts.

A. T. Dossey, K. Merz, S. Walse, 2009, Journal of natural products.

Stability and Activity of Mesophilic Subtilisin E and Its Thermophilic Homolog: Insights from Molecular Dynamics Simulations

Kenneth M. Merz, Giorgio Colombo, K. Merz, 1999 .

Critical Assessment of the Performance of Density Functional Methods for Several Atomic and Molecular Properties.

Kevin E. Riley, Kenneth M Merz, Kevin E Riley, 2007, Journal of chemical theory and computation.

An Improved 6-31G* Basis Set for Third-Row Atoms

K. Merz, A. Mitin, 2007 .

Insights into Cu(I) exchange in HAH1 using quantum mechanical and molecular simulations.

Kenneth M Merz, K. Merz, Bryan T Op't Holt, 2007, Biochemistry.

Free Energy Perturbation Study of Octanol/Water Partition Coefficients: Comparison with Continuum GB/SA Calculations

Kenneth M. Merz, Charles H. Reynolds, K. Merz, 1999 .

N‐Terminal Domain of the Cu(I)‐Binding Protein CusB

K. Merz, M. N. Ucisik, 2015 .

Divide and Conquer for Semiempirical MO Methods

S. L. Dixon, K. Merz, S. Dixon, 2002 .

High throughput docking for library design and library prioritization

D J Diller, K M Merz, K. Merz, 2001, Proteins.

3,4-connected carbon nets: through-space and through-bond interactions in the solid state

Kenneth M. Merz, Alexandru T. Balaban, Roald Hoffmann, 1987 .

Acylation of Class A β-lactamases by Penicillins: A Theoretical Examination of the Role of Serine 130 and the β-lactam Carboxylate Group

Dimas Suárez, Natalia Díaz, Kenneth M. Merz, 2001 .

An Efficient Method to Evaluate Intermolecular Interaction Energies in Large Systems Using Overlapping Multicenter ONIOM and the Fragment Molecular Orbital Method.

Kenneth M Merz, Kazuo Kitaura, Dmitri G Fedorov, 2012, The journal of physical chemistry letters.

Binding of Bicarbonate to Human Carbonic Anhydrase II: A Continuum of Binding States

Kenneth M. Merz, Lucia Banci, K. Merz, 1997 .

An Examination of a Hartree-Fock/Molecular Mechanical Coupled Potential

Kenneth M. Merz, Robert V. Stanton, K. Merz, 1995 .

Dynamic Force Field Models: Molecular Dynamics Simulations of Human Carbonic Anhydrase II Using a Quantum Mechanical/Molecular Mechanical Coupled Potential

Kenneth M. Merz, David S. Hartsough, D. Hartsough, 1995 .

Flexibility of serine protease in nonaqueous solvent

D. Hartsough, K. Merz, S. Toba, 1997 .

Rationalization of the enantioselectivity of subtilisin in DMF

Kenneth M. Merz, Giorgio Colombo, Samuel Toba, 1999 .

Theoretical investigation of the CO2 + OH- → HCO3- reaction in the gas and aqueous phases

Kenneth M. Merz, K. Merz, Z. Peng, 1993 .

Wide-open flaps are key to urease activity.

Bill R. Miller, K. Merz, A. Roitberg, 2012, Journal of the American Chemical Society.

Binding of Azide to Human Carbonic Anhydrase II: The Role Electrostatic Complementarity Plays in Selecting the Preferred Resonance Structure of Azide

K. Merz, L. Banci, 1996 .

Solution structure of Mycobacterium tuberculosis NmtR in the apo state: insights into Ni(II)-mediated allostery.

Yuzhen Ye, Kenneth M Merz, Dhruva K. Chakravorty, 2012, Biochemistry.

Reply to comment on "transferability of ion models"

K. Merz, T. Marrone, 1994 .

Transferability of ion models

K. Merz, T. Marrone, 1993 .

Determination of Conformationally Dependent Point Charges for Potential of Mean Force Simulations

D. Hartsough, K. Merz, T. Marrone, 1994 .

Pairwise additivity of energy components in protein-ligand binding: the HIV II protease-Indinavir case.

Kenneth M Merz, John C Faver, Danial S. Dashti, 2011, The Journal of chemical physics.

The Utility of the HSAB Principle via the Fukui Function in Biological Systems.

Kenneth M Merz, K. Merz, J. Faver, 2010, Journal of chemical theory and computation.

The role of quantum mechanics in structure-based drug design.

Bing Wang, Lance M. Westerhoff, Kenneth M Merz, 2007, Drug discovery today.

Pairwise decomposition of residue interaction energies using semiempirical quantum mechanical methods in studies of protein-ligand interaction.

Kevin E. Riley, Lance M. Westerhoff, Kenneth M Merz, 2005, Journal of the American Chemical Society.

Critical assessment of the performance of the semiempirical divide and conquer method for single point calculations and geometry optimizations of large chemical systems

Dimas Suárez, Kenneth M. Merz, Arjan van der Vaart, 2000 .

Fragment-based error estimation in biomolecular modeling.

K. Merz, J. Faver, 2014, Drug discovery today.

Quantum mechanical description of the interactions between DNA and water.

Lance M. Westerhoff, K. Merz, 2006, Journal of molecular graphics & modelling.

Simulating the Chelate Effect.

K. Merz, Arkajyoti Sengupta, A. Seitz, 2018, Journal of the American Chemical Society.

Insights into the strength and origin of halogen bonding: the halobenzene-formaldehyde dimer.

Kevin E. Riley, Kenneth M Merz, Kevin E Riley, 2007, The journal of physical chemistry. A.

Quantum mechanics in structure-based drug design.

Kenneth M Merz, Martin B Peters, Kaushik Raha, 2006, Current opinion in drug discovery & development.

Charge Flow between Ions and a Dielectric Continuum. 2. Variational Method for Distributing Charge into the Dielectric

K. Merz, V. Gogonea, 2000 .

The Role of Polarization and Charge Transfer in the Solvation of Biomolecules

Kenneth M. Merz, K. Merz, Arjan van der Vaart and, 1999 .

Fully Quantum Mechanical Description of Proteins in Solution. Combining Linear Scaling Quantum Mechanical Methodologies with the Poisson−Boltzmann Equation

Kenneth M. Merz, Valentin Gogonea, K. Merz, 1999 .

Prediction of trypsin/molecular fragment binding affinities by free energy decomposition and empirical scores

Zheng Zheng, Kenneth M. Merz, John C. Faver, 2012, Journal of Computer-Aided Molecular Design.

Inhibition of carbonic anhydrase

Mark A. Murcko, Peter A. Kollman, Kenneth M. Merz, 1991 .

Quantum mechanical/quantum mechanical methods. I. A divide and conquer strategy for solving the Schrödinger equation for large molecular systems using a composite density functional–semiempirical Hamiltonian

Kenneth M. Merz, Lance M. Westerhoff, Valentin Gogonea, 2000 .

Combined Quantum Mechanical/Molecular Mechanical Methodologies Applied to Biomolecular Systems

Kenneth M. Merz, K. Merz, G. Monard, 1999 .

Model for the fast estimation of basis set superposition error in biomolecular systems.

K. Merz, J. Faver, Zheng Zheng, 2011, The Journal of chemical physics.

The Concept of Solvent Compatibility and Its Impact on Protein Stability and Activity Enhancement in Nonaqueous Solvents

K. Merz, S. Toba, 1997 .

Gas-phase and solution-phase potential energy surfaces for CO2 + nH2O (n = 1,2)

Kenneth M. Merz, K. Merz, 1990 .

Insights into the function of the zinc hydroxide-Thr199-Glu106 hydrogen bonding network in carbonic anhydrases.

K M Merz, K. Merz, 1990, Journal of molecular biology.

Origin of Product Selectivity in a Prenyl Transfer Reaction from the Same Intermediate: Exploration of Multiple FtmPT1-Catalyzed Prenyl Transfer Pathways

K. Merz, Yue Yang, L. Pan, 2014, Biochemistry.

Converging Interests: Chemoinformatics, History, and Bibliometrics

Dmitriy Korobskiy, Kenneth M Merz, Wenxi Zhao, 2020, J. Chem. Inf. Model..

Potential of mean force calculations on the SN1 fragmentation of tert-butyl chloride

D. Hartsough, K. Merz, 1995 .

Sodium parameters for AM1 and PM3 optimized using a modified genetic algorithm

Kenneth M. Merz, K. Merz, 2002 .

Prediction of drug absorption using multivariate statistics.

J J Baldwin, K. Merz, W. Egan, 2000, Journal of medicinal chemistry.

OSiRIS: A Distributed Storage and Networking Project Update

Ezra Kissel, Kenneth M. Merz, Shawn McKee, 2020, EPJ Web of Conferences.

Generative Models for Molecular Design

G. Wei, K. Merz, G. D. Fabritiis, 2020, J. Chem. Inf. Model..

Divide and Conquer Interaction Energy Decomposition

Kenneth M. Merz, K. Merz, A. V. D. Vaart, 1999 .

Intermolecular interaction of thiosemicarbazone derivatives to solvents and a potential Aedes aegypti target

K. Merz, D. Moreira, J. B. P. D. Silva, 2015 .

Update to Our Reader, Reviewer, and Author Communities - April 2020

Sébastien Lecommandoux, Harry A. Atwater, Kenneth M. Merz, 2020, Journal of Chemical Information and Modeling.

Development of a Parametrized Force Field To Reproduce Semiempirical Geometries.

K. Merz, A. Wollacott, 2006, Journal of chemical theory and computation.

The Effects of Computational Modeling Errors on the Estimation of Statistical Mechanical Variables.

Wei Yang, Kenneth M Merz, John C Faver, 2012, Journal of chemical theory and computation.

A Combined QM/MM Poisson-Boltzmann Approach.

K. Merz, Seth A. Hayik, Ning-Lin Liao, 2008, Journal of chemical theory and computation.

The role of quantum mechanics in structure-based drug design.

Lance M. Westerhoff, K. Merz, A. Wollacott, 2007, Drug discovery today.

Accurate macromolecular crystallographic refinement: incorporation of the linear scaling, semiempirical quantum-mechanics program DivCon into the PHENIX refinement package.

Lance M. Westerhoff, Joshua A. Plumley, K. Merz, 2014, Acta crystallographica. Section D, Biological crystallography.

Incorporation of the quantum chemical package DivCon into the PHENIX suite

Lance M. Westerhoff, K. Merz, O. Borbulevych, 2011 .

QMQSAR: Utilization of a semiempirical probe potential in a field‐based QSAR method

Kenneth M. Merz, Steven L. Dixon, S. L. Dixon, 2005, J. Comput. Chem..

Drug Design: STRUCTURAL BIOLOGY

D. Ringe, K. Merz, C. Reynolds, 2010 .

Free Energy Perturbation Calculations within Quantum Mechanical Methodologies

S. L. Dixon, K. Merz, R. Stanton, 2002 .

A second generation force field for the simulation of proteins

P. Kollman, T. Fox, I. Gould, 1995 .

Divide-and-Conquer Hartree-Fock Calculations on Proteins.

Kenneth M Merz, Xiao He, K. Merz, 2010, Journal of chemical theory and computation.

Simulating the Chelate Effect.

K. Merz, Arkajyoti Sengupta, A. Seitz, 2018, Journal of the American Chemical Society.

Bilayer-Peptide Interactions

K. Merz, K. Damodaran, 1996 .

Solution NMR refinement of a metal ion bound protein using metal ion inclusive restrained molecular dynamics methods

Dhruva K. Chakravorty, D. Giedroc, K. Merz, 2013, Journal of Biomolecular NMR.

Implementation and Testing of a Frozen Density Matrix−Divide and Conquer Algorithm

K. Merz, M. Ermolaeva, A. Vaart, 1999 .

Disruption of the active site solvent network in carbonic anhydrase II decreases the efficiency of proton transfer.

K. Merz, C. Fierke, J. Jackman, 1996, Biochemistry.