Alexander D. MacKerell Jr.

Publication Activity (10 Years)

Years Active: 1988-2023
Publications (10 Years): 22

Top Topics

Molecular Dynamics

Protein Interaction

Top Venues

J. Comput. Chem.

J. Chem. Inf. Model.

J. Comput. Aided Mol. Des.

PLoS Comput. Biol.

Publications

Poonam Pandey, Alexander D. MacKerell Jr.
Combining SILCS and Artificial Intelligence for High-Throughput Prediction of the Passive Permeability of Drug Molecules. J. Chem. Inf. Model. 63 (18) (2023)
Faisal Ahmad, Nousheen Parvaiz, Alexander D. MacKerell Jr., Syed Sikander Azam
. J. Chem. Inf. Model. 63 (21) (2023)
Mingtian Zhao, Abhishek A. Kognole, Sunhwan Jo, Aoxiang Tao, Anthony Hazel, Alexander D. MacKerell Jr.
GPU-specific algorithms for improved solute sampling in grand canonical Monte Carlo simulations. J. Comput. Chem. 44 (20) (2023)
Asuka A. Orr, Suliman Sharif, Junmei Wang, Alexander D. MacKerell Jr.
Preserving the Integrity of Empirical Force Fields. J. Chem. Inf. Model. 62 (16) (2022)
Abhishek A. Kognole, Jumin Lee, Sang-Jun Park, Sunhwan Jo, Payal Chatterjee, Justin A. Lemkul, Jing Huang, Alexander D. MacKerell Jr., Wonpil Im
CHARMM-GUI Drude prepper for molecular dynamics simulation using the classical Drude polarizable force field. J. Comput. Chem. 43 (5) (2022)
Anderson A. Gomes, Gustavo F. da Silva, Sirish Kaushik Lakkaraju, Beatriz Gomes Guimarães, Alexander D. MacKerell Jr., Maria de Lourdes B. Magalhães
Insights into Glucose-6-phosphate Allosteric Activation of β-Glucosidase A. J. Chem. Inf. Model. 61 (4) (2021)
Asaminew H. Aytenfisu, Daniel Deredge, Erik H. Klontz, Jonathan Du, Eric J. Sundberg, Alexander D. MacKerell Jr.
Insights into substrate recognition and specificity for IgG by Endoglycosidase S2. PLoS Comput. Biol. 17 (7) (2021)
Fang-Yu Lin, Alexander D. MacKerell Jr.
Improved Modeling of Cation-π and Anion-Ring Interactions Using the Drude Polarizable Empirical Force Field for Proteins. J. Comput. Chem. 41 (5) (2020)
Mahdi Mousaei, Meruyert Kudaibergenova, Alexander D. MacKerell Jr., Sergei Yu Noskov
Assessing hERG1 Blockade from Bayesian Machine-Learning-Optimized Site Identification by Ligand Competitive Saturation Simulations. J. Chem. Inf. Model. 60 (12) (2020)
Anmol Kumar, Ozge Yoluk, Alexander D. MacKerell Jr.
FFParam: Standalone package for CHARMM additive and Drude polarizable force field parametrization of small molecules. J. Comput. Chem. 41 (9) (2020)
Fang-Yu Lin, Alexander D. MacKerell Jr.
Improved Modeling of Halogenated Ligand-Protein Interactions Using the Drude Polarizable and CHARMM Additive Empirical Force Fields. J. Chem. Inf. Model. 59 (1) (2019)
Stephanie A. Brocke, Alexandra Degen, Alexander D. MacKerell Jr., Bercem Dutagaci, Michael Feig
Prediction of Membrane Permeation of Drug Molecules by Combining an Implicit Membrane Model with Machine Learning. J. Chem. Inf. Model. 59 (3) (2019)
Vincent D. Ustach, Sirish Kaushik Lakkaraju, Sunhwan Jo, Wenbo Yu, Wenjuan Jiang, Alexander D. MacKerell Jr.
Optimization and Evaluation of Site-Identification by Ligand Competitive Saturation (SILCS) as a Tool for Target-Based Ligand Optimization. J. Chem. Inf. Model. 59 (6) (2019)
Jing Huang, Justin A. Lemkul, Peter K. Eastman, Alexander D. MacKerell Jr.
Molecular dynamics simulations using the drude polarizable force field on GPUs with OpenMM: Implementation, validation, and benchmarks. J. Comput. Chem. 39 (21) (2018)
Justin A. Lemkul, Alexander D. MacKerell Jr.
Polarizable force field for RNA based on the classical drude oscillator. J. Comput. Chem. 39 (32) (2018)
Fang-Yu Lin, Pedro E. M. Lopes, Edward Harder, Benoît Roux, Alexander D. MacKerell Jr.
Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator. J. Chem. Inf. Model. 58 (5) (2018)
Alexey Aleksandrov, Fang-Yu Lin, Benoît Roux, Alexander D. MacKerell Jr.
Combining the polarizable Drude force field with a continuum electrostatic Poisson-Boltzmann implicit solvation model. J. Comput. Chem. 39 (22) (2018)
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, Alexander D. MacKerell Jr., Jeffrey B. Klauda, Yifei Qi, Wonpil Im
CHARMM-GUI 10 years for biomolecular modeling and simulation. J. Comput. Chem. 38 (15) (2017)
E. Prabhu Raman, Sirish Kaushik Lakkaraju, Rajiah A. Denny, Alexander D. MacKerell Jr.
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. J. Comput. Chem. 38 (15) (2017)
Meagan C. Small, Asaminew H. Aytenfisu, Fang-Yu Lin, Xibing He, Alexander D. MacKerell Jr.
Drude polarizable force field for aliphatic ketones and aldehydes, and their associated acyclic carbohydrates. J. Comput. Aided Mol. Des. 31 (4) (2017)
Sirish Kaushik Lakkaraju, Justin A. Lemkul, Jing Huang, Alexander D. MacKerell Jr.
-adrenergic GPCR. J. Comput. Chem. 37 (4) (2016)
You Xu, Kenno Vanommeslaeghe, Alexey Aleksandrov, Alexander D. MacKerell Jr., Lennart Nilsson
Additive CHARMM force field for naturally occurring modified ribonucleotides. J. Comput. Chem. 37 (10) (2016)
Kenno Vanommeslaeghe, Mingjun Yang, Alexander D. MacKerell Jr.
Robustness in the fitting of molecular mechanics parameters. J. Comput. Chem. 36 (14) (2015)
Justin A. Lemkul, Benoît Roux, David van der Spoel, Alexander D. MacKerell Jr.
Implementation of extended Lagrangian dynamics in GROMACS for polarizable simulations using the classical Drude oscillator model. J. Comput. Chem. 36 (19) (2015)
Wenbo Yu, Sirish Kaushik Lakkaraju, E. Prabhu Raman, Lei Fang, Alexander D. MacKerell Jr.
Pharmacophore Modeling Using Site-Identification by Ligand Competitive Saturation (SILCS) with Multiple Probe Molecules. J. Chem. Inf. Model. 55 (2) (2015)
Sirish Kaushik Lakkaraju, Wenbo Yu, E. Prabhu Raman, Alena V. Hershfeld, Lei Fang, Deepak Deshpande, Alexander D. MacKerell Jr.
Mapping Functional Group Free Energy Patterns at Protein Occluded Sites: Nuclear Receptors and G-Protein Coupled Receptors. J. Chem. Inf. Model. 55 (3) (2015)
Wenbo Yu, Sirish Kaushik Lakkaraju, E. Prabhu Raman, Alexander D. MacKerell Jr.
Site-Identification by Ligand Competitive Saturation (SILCS) assisted pharmacophore modeling. J. Comput. Aided Mol. Des. 28 (5) (2014)
Alexey Savelyev, Alexander D. MacKerell Jr.
All-atom polarizable force field for DNA based on the classical drude oscillator model. J. Comput. Chem. 35 (16) (2014)
E. Prabhu Raman, Wenbo Yu, Sirish Kaushik Lakkaraju, Alexander D. MacKerell Jr.
Inclusion of Multiple Fragment Types in the Site Identification by Ligand Competitive Saturation (SILCS) Approach. J. Chem. Inf. Model. 53 (12) (2013)
Shanthi Nagagarajan, Fengtian Xue, Alexander D. MacKerell Jr.
Impact of Substrate Protonation and Tautomerization States on Interactions with the Active Site of Arginase I. J. Chem. Inf. Model. 53 (2) (2013)
Sirish Kaushik Lakkaraju, Fengtian Xue, Alan I. Faden, Alexander D. MacKerell Jr.
Estimation of Ligand Efficacies of Metabotropic Glutamate Receptors from Conformational Forces Obtained from Molecular Dynamics Simulations. J. Chem. Inf. Model. 53 (6) (2013)
Jing Huang, Alexander D. MacKerell Jr.
CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data. J. Comput. Chem. 34 (25) (2013)
Sairam S. Mallajosyula, Kristie M. Adams, Joseph J. Barchi, Alexander D. MacKerell Jr.
Conformational Determinants of the Activity of Antiproliferative Factor Glycopeptide. J. Chem. Inf. Model. 53 (5) (2013)
Jihyun Shim, Xiao Zhu, Robert B. Best, Alexander D. MacKerell Jr.
amino acid side-chain dihedral empirical force field parameters. J. Comput. Chem. 34 (7) (2013)
Meagan C. Small, Pedro E. M. Lopes, Rodrigo B. Andrade, Alexander D. MacKerell Jr.
Impact of Ribosomal Modification on the Binding of the Antibiotic Telithromycin Using a Combined Grand Canonical Monte Carlo/Molecular Dynamics Simulation Approach. PLoS Comput. Biol. 9 (6) (2013)
Wenbo Yu, Xibing He, Kenno Vanommeslaeghe, Alexander D. MacKerell Jr.
Extension of the CHARMM general force field to sulfonyl-containing compounds and its utility in biomolecular simulations. J. Comput. Chem. 33 (31) (2012)
Xiao Zhu, Pedro E. M. Lopes, Jihyun Shim, Alexander D. MacKerell Jr.
Intrinsic Energy Landscapes of Amino Acid Side-Chains. J. Chem. Inf. Model. 52 (6) (2012)
Theresa J. Foster, Alexander D. MacKerell Jr., Olgun Guvench
Balancing target flexibility and target denaturation in computational fragment-based inhibitor discovery. J. Comput. Chem. 33 (23) (2012)
Xiao Zhu, Pedro E. M. Lopes, Jihyun Shim, Alexander D. MacKerell Jr.
Correction to Intrinsic Energy Landscapes of Amino Acid Side-Chains. J. Chem. Inf. Model. 52 (8) (2012)
Kenno Vanommeslaeghe, E. Prabhu Raman, Alexander D. MacKerell Jr.
Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges. J. Chem. Inf. Model. 52 (12) (2012)
Kenno Vanommeslaeghe, Alexander D. MacKerell Jr.
Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing. J. Chem. Inf. Model. 52 (12) (2012)
Elizabeth J. Denning, U. Deva Priyakumar, Lennart Nilsson, Alexander D. MacKerell Jr.
Impact of 2′-hydroxyl sampling on the conformational properties of RNA: Update of the CHARMM all-atom additive force field for RNA. J. Comput. Chem. 32 (9) (2011)
Taiji Oashi, Ashley L. Ringer, E. Prabhu Raman, Alexander D. MacKerell Jr.
Automated Selection of Compounds with Physicochemical Properties To Maximize Bioavailability and Druglikeness. J. Chem. Inf. Model. 51 (1) (2011)
E. Prabhu Raman, Wenbo Yu, Olgun Guvench, Alexander D. MacKerell Jr.
Reproducing Crystal Binding Modes of Ligand Functional Groups Using Site-Identification by Ligand Competitive Saturation (SILCS) Simulations. J. Chem. Inf. Model. 51 (4) (2011)
Sunhwan Jo, Kevin C. Song, Heather Desaire, Alexander D. MacKerell Jr., Wonpil Im
Glycan reader: Automated sugar identification and simulation preparation for carbohydrates and glycoproteins. J. Comput. Chem. 32 (14) (2011)
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.
CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J. Comput. Chem. 31 (4) (2010)
Xiao Zhu, Alexander D. MacKerell Jr.
Polarizable empirical force field for sulfur-containing compounds based on the classical Drude oscillator model. J. Comput. Chem. 31 (12) (2010)
Pedro E. M. Lopes, Guillaume Lamoureux, Alexander D. MacKerell Jr.
Polarizable empirical force field for nitrogen-containing heteroaromatic compounds based on the classical Drude oscillator. J. Comput. Chem. 30 (12) (2009)
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, Qiang Cui, Aaron R. Dinner, Michael Feig, S. Fischer, Jiali Gao, Milan Hodoscek, Wonpil Im, Krzysztof Kuczera, Themis Lazaridis, J. Ma, V. Ovchinnikov, Emanuele Paci, Richard W. Pastor, C. B. Post, J. Z. Pu, Michael Schaefer, Bruce Tidor, Richard M. Venable, H. Lee Woodcock III, X. Wu, W. Yang, Darrin M. York, Martin Karplus
CHARMM: The biomolecular simulation program. J. Comput. Chem. 30 (10) (2009)
Olgun Guvench, Alexander D. MacKerell Jr.
Computational Fragment-Based Binding Site Identification by Ligand Competitive Saturation. PLoS Comput. Biol. 5 (7) (2009)
Olgun Guvench, Shannon N. Greene, Ganesh Kamath, John W. Brady, Richard M. Venable, Richard W. Pastor, Alexander D. MacKerell Jr.
Additive empirical force field for hexopyranose monosaccharides. J. Comput. Chem. 29 (15) (2008)
Evelyn Mayaan, Adam Moser, Alexander D. MacKerell Jr., Darrin M. York
CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes. J. Comput. Chem. 28 (2) (2007)
Shijun Zhong, Alexander D. MacKerell Jr.
Binding Response: A Descriptor for Selecting Ligand Binding Site on Protein Surfaces. J. Chem. Inf. Model. 47 (6) (2007)
Alba T. Macias, Alexander D. MacKerell Jr.
CH/ interactions involving aromatic amino acids: Refinement of the CHARMM tryptophan force field. J. Comput. Chem. 26 (14) (2005)
Alba T. Macias, Md. Younus Mia, Guanjun Xia, Jun Hayashi, Alexander D. MacKerell Jr.
. J. Chem. Inf. Model. 45 (6) (2005)
Alexander D. MacKerell Jr.
Empirical force fields for biological macromolecules: Overview and issues. J. Comput. Chem. 25 (13) (2004)
Sandeep Patel, Alexander D. MacKerell Jr., Charles L. Brooks III
CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model. J. Comput. Chem. 25 (12) (2004)
Alexander D. MacKerell Jr., Michael Feig, Charles L. Brooks III
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. J. Comput. Chem. 25 (11) (2004)
Yongping Pan, Niu Huang, Sam Cho, Alexander D. MacKerell Jr.
Consideration of Molecular Weight during Compound Selection in Virtual Target-Based Database Screening. J. Chem. Inf. Comput. Sci. 43 (1) (2003)
I-Jen Chen, Daxu Yin, Alexander D. MacKerell Jr.
Combined ab initio/empirical approach for optimization of Lennard-Jones parameters for polar-neutral compounds. J. Comput. Chem. 23 (2) (2002)
Daniel Barsky, Nicolas Foloppe, Sarah Ahmadia, David M. Wilson III, Alexander D. MacKerell Jr.
New insights into the structure of abasic DNA from molecular dynamics simulations. Nucleic Acids Res. 28 (13) (2000)
Alexander D. MacKerell Jr., Nilesh K. Banavali
All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution. J. Comput. Chem. 21 (2) (2000)
Nicolas Foloppe, Alexander D. MacKerell Jr.
All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data. J. Comput. Chem. 21 (2) (2000)
Daxu Yin, Alexander D. MacKerell Jr.
Combined ab initio/empirical approach for optimization of Lennard-Jones parameters. J. Comput. Chem. 19 (3) (1998)
Joseph J. Pavelites, Jiali Gao, Paul A. Bash, Alexander D. MacKerell Jr.
A molecular mechanics force field for NAD+ NADH, and the pyrophosphate groups of nucleotides. J. Comput. Chem. 18 (2) (1997)
Alexander D. MacKerell Jr.
Molecular modeling and dynamics of neuropeptide Y. J. Comput. Aided Mol. Des. 2 (1) (1988)