Kenneth M Merz

发表

Using AMBER18 for Relative Free Energy Calculations

Lin Frank Song, Tai-Sung Lee, Chun Zhu, 2019, J. Chem. Inf. Model..

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.

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.

Investing in the Future

Kenneth M Merz, 2018, J. Chem. Inf. Model..

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

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

Computer-aided Drug Design: Using Numbers to your Advantage.

Wei Yang, Kenneth M Merz, John C Faver, 2013, ACS medicinal chemistry letters.

Confronting Racism in Chemistry Journals

Sharon Hammes-Schiffer, Sébastien Lecommandoux, Joan-Emma Shea, 2020, J. Chem. Inf. Model..

MRP.py: A Parametrizer of Post-Translationally Modified Residues

Kenneth M Merz, Patrick G Sahrmann, Patrick H Donnan, 2020, J. Chem. Inf. Model..

Converging Interests: Chemoinformatics, History, and Bibliometrics

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

Validation of Free Energy Methods in AMBER

Tai-Sung Lee, Darrin M York, Kenneth M Merz, 2020, J. Chem. Inf. Model..

Quantum mechanics in structure-based drug design.

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

Evolution of Alchemical Free Energy Methods in Drug Discovery

Lin Frank Song, Kenneth M Merz, K. Merz, 2020, J. Chem. Inf. Model..

Random Forest Refinement of Pairwise Potentials for Protein-Ligand Decoy Detection

Jun Pei, Zheng Zheng, Lin Frank Song, 2019, J. Chem. Inf. Model..

Parallel Implementation of Density Functional Theory Methods in the Quantum Interaction Computational Kernel Program.

Kenneth M Merz, Dawei Mu, Yipu Miao, 2020, Journal of chemical theory and computation.

Pair Potentials as Machine Learning Features.

Jun Pei, Lin Frank Song, Kenneth M Merz, 2020, 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.

Acceleration of Electron Repulsion Integral Evaluation on Graphics Processing Units via Use of Recurrence Relations.

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

Limits of Free Energy Computation for Protein-Ligand Interactions.

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

Refinement of pairwise potentials via logistic regression to score protein‐protein interactions

Jun Pei, Kenneth M Merz, Kiyoto A Tanemura, 2020, Proteins.

Haptic applications for molecular structure manipulation.

Kenneth M Merz, Andrew M Wollacott, 2007, Journal of molecular graphics & modelling.

Impact of the Journal of Chemical Information and Modeling Special Issue on Women in Computational Chemistry

Zoe Cournia, Rommie E Amaro, Kenneth M Merz, 2020, J. Chem. Inf. Model..

Random Forest Refinement of the KECSA2 Knowledge-Based Scoring Function for Protein Decoy Detection

Jun Pei, Zheng Zheng, Kenneth M Merz, 2019, J. Chem. Inf. Model..

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.

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.

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.

Understanding the substrate selectivity and the product regioselectivity of Orf2-catalyzed aromatic prenylations.

Kenneth M Merz, Guanglei Cui, Xue Li, 2007, Biochemistry.

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.

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.

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.

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.

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.

The Ecstasy and Agony of Assay Interference Compounds.

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

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.

Kenneth M Merz, Gunda I Georg, Carolyn Bertozzi, 2017, ACS chemical neuroscience.

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.

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.

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.

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.

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.

Conformational Analysis of Free and Bound Retinoic Acid.

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

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.

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.

Pose scoring by NMR.

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

QM/MM X-ray refinement of zinc metalloenzymes.

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

Insights into the acylation mechanism of class A beta-lactamases from molecular dynamics simulations of the TEM-1 enzyme complexed with benzylpenicillin.

Dimas Suárez, Natalia Díaz, Kenneth M Merz, 2003, Journal of the American Chemical Society.

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

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

The Movable Type Method Applied to Protein-Ligand Binding.

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

Molecular dynamics simulations of the TEM-1 beta-lactamase complexed with cephalothin.

Dimas Suárez, Natalia Díaz, Kenneth M Merz, 2005, Journal of medicinal chemistry.

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

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

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.