Molecular modeling and dynamics of neuropeptide Y. - Alexander D. MacKerell Jr. (J. Comput. Aided Mol. Des., 1988)

A molecular mechanics force field for NAD+ NADH, and the pyrophosphate groups of nucleotides. - Joseph J. Pavelites; Jiali Gao; Paul A. Bash; Alexander D. MacKerell Jr. (J. Comput. Chem., 1997)

Combined ab initio/empirical approach for optimization of Lennard-Jones parameters. - Daxu Yin; Alexander D. MacKerell Jr. (J. Comput. Chem., 1998)

All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data. - Nicolas Foloppe; Alexander D. MacKerell Jr. (J. Comput. Chem., 2000)

All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution. - Alexander D. MacKerell Jr.; Nilesh K. Banavali (J. Comput. Chem., 2000)

New insights into the structure of abasic DNA from molecular dynamics simulations. - Daniel Barsky; Nicolas Foloppe; Sarah Ahmadia; David M. Wilson III; Alexander D. MacKerell Jr. (Nucleic Acids Res., 2000)

Combined ab initio/empirical approach for optimization of Lennard-Jones parameters for polar-neutral compounds. - I-Jen Chen; Daxu Yin; Alexander D. MacKerell Jr. (J. Comput. Chem., 2002)

Consideration of Molecular Weight during Compound Selection in Virtual Target-Based Database Screening. - Yongping Pan; Niu Huang; Sam Cho; Alexander D. MacKerell Jr. (J. Chem. Inf. Comput. Sci., 2003)

Empirical force fields for biological macromolecules: Overview and issues. - Alexander D. MacKerell Jr. (J. Comput. Chem., 2004)

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 Jr.; Michael Feig; Charles L. Brooks III (J. Comput. Chem., 2004)

CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model. - Sandeep Patel; Alexander D. MacKerell Jr.; Charles L. Brooks III (J. Comput. Chem., 2004)

CH/ interactions involving aromatic amino acids: Refinement of the CHARMM tryptophan force field. - Alba T. Macias; Alexander D. MacKerell Jr. (J. Comput. Chem., 2005)

Lead Validation and SAR Development via Chemical Similarity Searching; Application to Compounds Targeting the pY+3 Site of the SH2 Domain of p56lck. - Alba T. Macias; Md. Younus Mia; Guanjun Xia; Jun Hayashi; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2005)

CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes. - Evelyn Mayaan; Adam Moser; Alexander D. MacKerell Jr.; Darrin M. York (J. Comput. Chem., 2007)

Binding Response: A Descriptor for Selecting Ligand Binding Site on Protein Surfaces. - Shijun Zhong; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2007)

Additive empirical force field for hexopyranose monosaccharides. - Olgun Guvench; Shannon N. Greene; Ganesh Kamath; John W. Brady; Richard M. Venable; Richard W. Pastor; Alexander D. MacKerell Jr. (J. Comput. Chem., 2008)

CHARMM: The biomolecular simulation program. - Bernard R. Brooks; Charles L. Brooks III; Alexander D. MacKerell Jr.; Lennart Nilsson; Robert J. Petrella; Benoît Roux; Y. Won; G. Archontis; Christian Bartels; Stefan Boresch; Amedeo Caflisch; Leo S. D. Caves; et al. (J. Comput. Chem., 2009)

Polarizable empirical force field for nitrogen-containing heteroaromatic compounds based on the classical Drude oscillator. - Pedro E. M. Lopes; Guillaume Lamoureux; Alexander D. MacKerell Jr. (J. Comput. Chem., 2009)

Computational Fragment-Based Binding Site Identification by Ligand Competitive Saturation. - Olgun Guvench; Alexander D. MacKerell Jr. (PLoS Comput. Biol., 2009)

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. - Kenno Vanommeslaeghe; Elizabeth Hatcher; Chayan Acharya; Sibsankar Kundu; Shijun Zhong; Jihyun Shim; Eva Darian; Olgun Guvench; Pedro E. M. Lopes; Igor Vorobyov; Alexander D. MacKerell Jr. (J. Comput. Chem., 2010)

Polarizable empirical force field for sulfur-containing compounds based on the classical Drude oscillator model. - Xiao Zhu; Alexander D. MacKerell Jr. (J. Comput. Chem., 2010)

Impact of 2′-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA. - Elizabeth J. Denning; U. Deva Priyakumar; Lennart Nilsson; Alexander D. MacKerell Jr. (J. Comput. Chem., 2011)

Glycan reader: Automated sugar identification and simulation preparation for carbohydrates and glycoproteins. - Sunhwan Jo; Kevin C. Song; Heather Desaire; Alexander D. MacKerell Jr.; Wonpil Im (J. Comput. Chem., 2011)

Automated Selection of Compounds with Physicochemical Properties To Maximize Bioavailability and Druglikeness. - Taiji Oashi; Ashley L. Ringer; E. Prabhu Raman; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2011)

Reproducing Crystal Binding Modes of Ligand Functional Groups Using Site-Identification by Ligand Competitive Saturation (SILCS) Simulations. - E. Prabhu Raman; Wenbo Yu 002; Olgun Guvench; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2011)

Balancing target flexibility and target denaturation in computational fragment-based inhibitor discovery. - Theresa J. Foster; Alexander D. MacKerell Jr.; Olgun Guvench (J. Comput. Chem., 2012)

Extension of the CHARMM general force field to sulfonyl-containing compounds and its utility in biomolecular simulations. - Wenbo Yu 002; Xibing He; Kenno Vanommeslaeghe; Alexander D. MacKerell Jr. (J. Comput. Chem., 2012)

Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing. - Kenno Vanommeslaeghe; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2012)

Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges. - Kenno Vanommeslaeghe; E. Prabhu Raman; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2012)

Intrinsic Energy Landscapes of Amino Acid Side-Chains. - Xiao Zhu; Pedro E. M. Lopes; Jihyun Shim; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2012)

Correction to Intrinsic Energy Landscapes of Amino Acid Side-Chains. - Xiao Zhu; Pedro E. M. Lopes; Jihyun Shim; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2012)

CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data. - Jing Huang 004; Alexander D. MacKerell Jr. (J. Comput. Chem., 2013)

(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. - Jihyun Shim; Xiao Zhu; Robert B. Best; Alexander D. MacKerell Jr. (J. Comput. Chem., 2013)

Estimation of Ligand Efficacies of Metabotropic Glutamate Receptors from Conformational Forces Obtained from Molecular Dynamics Simulations. - Sirish Kaushik Lakkaraju; Fengtian Xue; Alan I. Faden; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2013)

Conformational Determinants of the Activity of Antiproliferative Factor Glycopeptide. - Sairam S. Mallajosyula; Kristie M. Adams; Joseph J. Barchi; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2013)

Impact of Substrate Protonation and Tautomerization States on Interactions with the Active Site of Arginase I. - Shanthi Nagagarajan; Fengtian Xue; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2013)

Inclusion of Multiple Fragment Types in the Site Identification by Ligand Competitive Saturation (SILCS) Approach. - E. Prabhu Raman; Wenbo Yu 002; Sirish Kaushik Lakkaraju; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2013)

Impact of Ribosomal Modification on the Binding of the Antibiotic Telithromycin Using a Combined Grand Canonical Monte Carlo/Molecular Dynamics Simulation Approach. - Meagan C. Small; Pedro E. M. Lopes; Rodrigo B. Andrade; Alexander D. MacKerell Jr. (PLoS Comput. Biol., 2013)

Site-Identification by Ligand Competitive Saturation (SILCS) assisted pharmacophore modeling. - Wenbo Yu 002; Sirish Kaushik Lakkaraju; E. Prabhu Raman; Alexander D. MacKerell Jr. (J. Comput. Aided Mol. Des., 2014)

All-atom polarizable force field for DNA based on the classical drude oscillator model. - Alexey Savelyev; Alexander D. MacKerell Jr. (J. Comput. Chem., 2014)

Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model. - Justin A. Lemkul; Benoît Roux; David van der Spoel; Alexander D. MacKerell Jr. (J. Comput. Chem., 2015)

Robustness in the fitting of molecular mechanics parameters. - Kenno Vanommeslaeghe; Mingjun Yang; Alexander D. MacKerell Jr. (J. Comput. Chem., 2015)

Mapping Functional Group Free Energy Patterns at Protein Occluded Sites: Nuclear Receptors and G-Protein Coupled Receptors. - Sirish Kaushik Lakkaraju; Wenbo Yu 002; E. Prabhu Raman; Alena V. Hershfeld; Lei Fang; Deepak Deshpande; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2015)

Pharmacophore Modeling Using Site-Identification by Ligand Competitive Saturation (SILCS) with Multiple Probe Molecules. - Wenbo Yu 002; Sirish Kaushik Lakkaraju; E. Prabhu Raman; Lei Fang; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2015)

DIRECT-ID: An automated method to identify and quantify conformational variations - application to β2-adrenergic GPCR. - Sirish Kaushik Lakkaraju; Justin A. Lemkul; Jing Huang 004; Alexander D. MacKerell Jr. (J. Comput. Chem., 2016)

Additive CHARMM force field for naturally occurring modified ribonucleotides. - You Xu; Kenno Vanommeslaeghe; Alexey Aleksandrov; Alexander D. MacKerell Jr.; Lennart Nilsson (J. Comput. Chem., 2016)

Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates. - Meagan C. Small; Asaminew H. Aytenfisu; Fang-Yu Lin; Xibing He; Alexander D. MacKerell Jr. (J. Comput. Aided Mol. Des., 2017)

CHARMM-GUI 10 years for biomolecular modeling and simulation. - Sunhwan Jo; Xi Cheng; Jumin Lee; Seonghoon Kim; Sang-Jun Park; Dhilon S. Patel; Andrew H. Beaven; Kyu Il Lee; Huan Rui; Soohyung Park; Hui Sun Lee; Benoît Roux; et al. (J. Comput. Chem., 2017)

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. - E. Prabhu Raman; Sirish Kaushik Lakkaraju; Rajiah Aldrin Denny; Alexander D. MacKerell Jr. (J. Comput. Chem., 2017)

Combining the polarizable Drude force field with a continuum electrostatic Poisson-Boltzmann implicit solvation model. - Alexey Aleksandrov; Fang-Yu Lin; Benoît Roux; Alexander D. MacKerell Jr. (J. Comput. Chem., 2018)

Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks. - Jing Huang 004; Justin A. Lemkul; Peter K. Eastman; Alexander D. MacKerell Jr. (J. Comput. Chem., 2018)

Polarizable force field for RNA based on the classical drude oscillator. - Justin A. Lemkul; Alexander D. MacKerell Jr. (J. Comput. Chem., 2018)

Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator. - Fang-Yu Lin; Pedro E. M. Lopes; Edward Harder; Benoît Roux; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2018)

Prediction of Membrane Permeation of Drug Molecules by Combining an Implicit Membrane Model with Machine Learning. - Stephanie A. Brocke; Alexandra Degen; Alexander D. MacKerell Jr.; Bercem Dutagaci; Michael Feig (J. Chem. Inf. Model., 2019)

Improved Modeling of Halogenated Ligand-Protein Interactions Using the Drude Polarizable and CHARMM Additive Empirical Force Fields. - Fang-Yu Lin; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2019)

Optimization and Evaluation of Site-Identification by Ligand Competitive Saturation (SILCS) as a Tool for Target-Based Ligand Optimization. - Vincent D. Ustach; Sirish Kaushik Lakkaraju; Sunhwan Jo; Wenbo Yu 002; Wenjuan Jiang; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2019)

FFParam: Standalone package for CHARMM additive and Drude polarizable force field parametrization of small molecules. - Anmol Kumar; Ozge Yoluk; Alexander D. MacKerell Jr. (J. Comput. Chem., 2020)

Improved Modeling of Cation-π and Anion-Ring Interactions Using the Drude Polarizable Empirical Force Field for Proteins. - Fang-Yu Lin; Alexander D. MacKerell Jr. (J. Comput. Chem., 2020)

Assessing hERG1 Blockade from Bayesian Machine-Learning-Optimized Site Identification by Ligand Competitive Saturation Simulations. - Mahdi Mousaei; Meruyert Kudaibergenova; Alexander D. MacKerell Jr.; Sergei Yu Noskov (J. Chem. Inf. Model., 2020)

Insights into Glucose-6-phosphate Allosteric Activation of β-Glucosidase A. - Anderson A. Gomes; Gustavo F. da Silva; Sirish Kaushik Lakkaraju; Beatriz Gomes Guimarães; Alexander D. MacKerell Jr.; Maria de Lourdes B. Magalhães (J. Chem. Inf. Model., 2021)

Insights into substrate recognition and specificity for IgG by Endoglycosidase S2. - Asaminew H. Aytenfisu; Daniel Deredge; Erik H. Klontz; Jonathan Du; Eric J. Sundberg; Alexander D. MacKerell Jr. (PLoS Comput. Biol., 2021)

CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field. - Abhishek A. Kognole; Jumin Lee; Sang-Jun Park; Sunhwan Jo; Payal Chatterjee; Justin A. Lemkul; Jing Huang 004; Alexander D. MacKerell Jr.; Wonpil Im (J. Comput. Chem., 2022)

Preserving the Integrity of Empirical Force Fields. - Asuka A. Orr; Suliman Sharif; Junmei Wang; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2022)

GPU-specific algorithms for improved solute sampling in grand canonical Monte Carlo simulations. - Mingtian Zhao; Abhishek A. Kognole; Sunhwan Jo; Aoxiang Tao; Anthony Hazel; Alexander D. MacKerell Jr. (J. Comput. Chem., 2023)

Combining SILCS and Artificial Intelligence for High-Throughput Prediction of the Passive Permeability of Drug Molecules. - Poonam Pandey; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2023)

Non-β Lactam Inhibitors of the Serine β-Lactamase blaCTX-M15 in Drug-Resistant Salmonella typhi. - Faisal Ahmad; Nousheen Parvaiz; Alexander D. MacKerell Jr.; Syed Sikander Azam (J. Chem. Inf. Model., 2023)

Combined Physics- and Machine-Learning-Based Method to Identify Druggable Binding Sites Using SILCS-Hotspots. - Erik B. Nordquist; Mingtian Zhao; Anmol Kumar; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2024)

Detection of Putative Ligand Dissociation Pathways in Proteins Using Site-Identification by Ligand Competitive Saturation. - Wenbo Yu 002; David J. Weber; Alexander D. MacKerell Jr. (J. Chem. Inf. Model., 2025)