Alexander D. MacKerell

MedicineBiochemistry, Genetics and Molecular Biology

Pilot corpus only

This score is computed over theSindex pilot corpus and does not cover the full scientific literature. Scores are relative to papers we have ingested — papers, authors, and institutions outside the pilot are not represented. Methodology.

Top 100%percentile

0Author DataRank

Indexed papers

0in pilot corpus

datarank_citation_only_1hop_v6· scope data_onlyMethodology

Papers

Driven by 68 papers. Top paper: “Structure of the cell-binding component of the Clostridium difficile binary toxin reveals a di-heptamer macromolecular assembly”.

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

Proceedings of the National Academy of Sciences(2020)10.1073/pnas.1919490117

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1.1DataRank · unranked

37 citations

Raquel Godoy‐Ruiz, Kaylin A. Adipietro, Christopher Peralta, Danya Ben-Hail, Kristen M. Varney +20 more

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

Journal of Chemical Theory and Computation(2021)10.1021/acs.jctc.0c00968

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0.568DataRank · unranked

43 citations

Hui Li, Alexander D. MacKerell, Toby W. Allen, Benoı̂t Roux, Sergei Y. Noskov +1 more

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

Molecules(2021)10.3390/molecules26020381

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0.373DataRank · unranked

11 citations

Wenbo Yu, Darex J. Vera Rodríguez, Kristen M. Varney, Alexander D. MacKerell, David J. Weber +1 more

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

ChemRxiv(2020)10.26434/chemrxiv.13480434

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0.360DataRank · unranked

10 citations

Andreas Krämer, Andrew C. Simmonett, Rick Venable, Alexander D. MacKerell, Jeffery B. Klauda +3 more

Detection of Putative Ligand Dissociation Pathways in Proteins Using Site-Identification by Ligand Competitive Saturation

Journal of Chemical Information and Modeling(2024)10.1021/acs.jcim.4c01814

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0.241DataRank · unranked

4 citations

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

Mapping the distribution and affinities of ligand interaction sites on human serum albumin

Biophysical Journal(2025)10.1016/j.bpj.2025.03.016

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0.104DataRank · unranked

1 citations

Agbo-oma Uwakweh, Xun Li, Ahmad Karanji, Stephen W. Hoag, Daniel Deredge +2 more

The mammalian SKI complex is a broad-spectrum antiviral drug target that upregulates cellular cholesterol to inhibit viral replication

Journal of Virology(2025)10.1128/jvi.01323-25

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0.104DataRank · unranked

1 citations

Lauren Baracco, Louis J. Taylor, Alison Scott, Gaurav Kumar, Paul Shapiro +3 more

Toward Biotherapeutics Formulation Composition Engineering using Site-Identification by Ligand Competitive Saturation (SILCS)

Journal of Pharmaceutical Sciences(2020)10.1016/j.xphs.2020.10.051

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0DataRank · unranked

27 citations

Sunhwan Jo, Renuka Thirumangalathu, Danika Rodrigues, Laura M. Tanenbaum, Ketan Amin +3 more

Contributions and competition of Mg 2+ and K + in folding and stabilization of the Twister ribozyme

RNA(2020)10.1261/rna.076851.120

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0DataRank · unranked

7 citations

Alexander D. MacKerell, Abhishek A. Kognole

Contributions and competition of Mg 2+ and K + in folding and stabilization of the Twister Ribozyme

bioRxiv (Cold Spring Harbor Laboratory)(2020)10.1101/2020.06.15.152744

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0DataRank · unranked

0 citations

Alexander D. MacKerell, Abhishek A. Kognole

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

ChemRxiv(2020)10.26434/chemrxiv.13480434.v1

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0DataRank · unranked

0 citations

Andreas Krämer, Andrew C. Simmonett, Rick Venable, Alexander D. MacKerell, Jeffery B. Klauda +3 more

Additive CHARMM36 Force Field for Nonstandard Amino Acids

Journal of Chemical Theory and Computation(2021)10.1021/acs.jctc.1c00254

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0DataRank · unranked

134 citations

Sang‐Jun Park, Anmol Kumar, Jumin Lee, Wonpil Im, Alexander D. MacKerell +2 more

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

Journal of Chemical Theory and Computation(2021)10.1021/acs.jctc.0c01326

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0DataRank · unranked

78 citations

Andreas Krämer, Richard M. Venable, Andrew C. Simmonett, Alexander D. MacKerell, Jeffery B. Klauda +3 more

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

Journal of Computational Chemistry(2021)10.1002/jcc.26795

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0DataRank · unranked

57 citations

Jumin Lee, Sang‐Jun Park, Sunhwan Jo, Payal Chatterjee, Justin A. Lemkul +4 more

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

Chemical Science(2021)10.1039/d1sc01781k

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0DataRank · unranked

51 citations

Anthony Hazel, Vincent D. Ustach, Sunhwan Jo, Wenbo Yu, Alexander D. MacKerell +1 more

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

Journal of Chemical Theory and Computation(2021)10.1021/acs.jctc.1c00664

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0DataRank · unranked

26 citations

Alexander D. MacKerell, Benoı̂t Roux, Chetan Rupakheti

Application of site-identification by ligand competitive saturation in computer-aided drug design

New Journal of Chemistry(2021)10.1039/d1nj04028f

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0DataRank · unranked

26 citations

Anthony Hazel, Wenbo Yu, Sunhwan Jo, Alexander D. MacKerell, Himanshu Goel

Accurate Modeling of RNA Hairpins Through the Explicit Treatment of Electronic Polarizability with the Classical Drude Oscillator Force Field

Journal of Computational Biophysics and Chemistry(2021)10.1142/s2737416521420060

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0DataRank · unranked

15 citations

Alexander D. MacKerell, Mert Y. Sengul

Functional Group Distributions, Partition Coefficients, and Resistance Factors in Lipid Bilayers Using Site Identification by Ligand Competitive Saturation

Journal of Chemical Theory and Computation(2021)10.1021/acs.jctc.1c00089

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0DataRank · unranked

10 citations

Poonam Pandey, Richard W. Pastor, Alexander D. MacKerell, Christoffer Lind

Insights into substrate recognition and specificity for IgG by Endoglycosidase S2

PLoS Computational Biology(2021)10.1371/journal.pcbi.1009103

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0DataRank · unranked

7 citations

Daniel Deredge, Erik H. Klontz, Jonathan J. Du, Eric J. Sundberg, Alexander D. MacKerell +1 more

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

The Journal of Physical Chemistry B(2021)10.1021/acs.jpcb.1c07202

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0DataRank · unranked

1 citations

Wenbo Yu, Asaminew H. Aytenfisu, Jude Tunyi, Richard M. Venable, Alexander D. MacKerell +2 more

Computer-Aided Drug Design: An Update

Methods in molecular biology(2022)10.1007/978-1-0716-2855-3_7

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0DataRank · unranked

18 citations

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

Glycosidic α-linked mannopyranose disaccharides: an NMR spectroscopy and molecular dynamics simulation study employing additive and Drude polarizable force fields

Physical Chemistry Chemical Physics(2022)10.1039/d2cp05203b

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0DataRank · unranked

18 citations

Asaminew H. Aytenfisu, Thibault Angles d’Ortoli, Alexander D. MacKerell, Göran Widmalm, Alessandro Ruda

Scaffold hopping from indoles to indazoles yields dual MCL-1/BCL-2 inhibitors from MCL-1 selective leads

RSC Medicinal Chemistry(2022)10.1039/d2md00095d

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0DataRank · unranked

16 citations

Christopher C. Goodis, Nathan G. Bowen, Wenbo Yu, Gregory E.A. Vickers, Paul T. Wilder +3 more

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

Chemistry(2022)10.3390/chemistry4030045

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0DataRank · unranked

13 citations

Wenbo Yu, Alexander D. MacKerell, Himanshu Goel

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

Preprints.org(2022)10.20944/preprints202205.0255.v1

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0DataRank · unranked

4 citations

Wenbo Yu, Alexander D. MacKerell, Himanshu Goel

Drude Polarizable Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids

Journal of Chemical Theory and Computation(2023)10.1021/acs.jctc.3c00203

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0DataRank · unranked

38 citations

Richard M. Venable, Jonathan Thirman, Payal Chatterjee, Anmol Kumar, Richard W. Pastor +4 more

Biomolecular dynamics in the 21st century

Biochimica et Biophysica Acta (BBA) - General Subjects(2023)10.1016/j.bbagen.2023.130534

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0DataRank · unranked

25 citations

Alexander D. MacKerell, Carol Beth Post, Lennart Nilsson, Charles L. Brooks

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

Journal of Medicinal Chemistry(2023)10.1021/acs.jmedchem.2c01750

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0DataRank · unranked

24 citations

Evelyn J. Franco, Ana C. Rojas, Kaley C. Hanrahan, A. V. Kolesnikov, Wenbo Yu +7 more

Combining SILCS and Artificial Intelligence for High-Throughput Prediction of the Passive Permeability of Drug Molecules

Journal of Chemical Information and Modeling(2023)10.1021/acs.jcim.3c00514

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0DataRank · unranked

13 citations

Alexander D. MacKerell, Poonam Pandey

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

Journal of Chemical Theory and Computation(2023)10.1021/acs.jctc.3c00232

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0DataRank · unranked

12 citations

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

GPU‐specific algorithms for improved solute sampling in grand canonical Monte Carlo simulations

Journal of Computational Chemistry(2023)10.1002/jcc.27121

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0DataRank · unranked

10 citations

Abhishek A. Kognole, Sunhwan Jo, Aoxiang Tao, Anthony Hazel, Alexander D. MacKerell +1 more

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

Molecular Pharmaceutics(2023)10.1021/acs.molpharmaceut.3c00064

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0DataRank · unranked

6 citations

Aoxiang Tao, Olgun Guvench, Alexander D. MacKerell, Asuka A. Orr

Non-β Lactam Inhibitors of the Serine β-Lactamase blaCTX-M15 in Drug-Resistant Salmonella typhi

Journal of Chemical Information and Modeling(2023)10.1021/acs.jcim.3c00780

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0DataRank · unranked

2 citations

Nousheen Parvaiz, Alexander D. MacKerell, Syed Sikander Azam, Faisal Ahmad

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

Frontiers in Pharmacology(2023)10.3389/fphar.2023.1230053

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0DataRank · unranked

3 citations

Andrea L. Devereaux, Payal Chatterjee, Savanah L. Saldaña-Shumaker, Amanda M. Shafer, A. A. Plotkin +5 more

Balancing Group I Monoatomic Ion-Polar Compound Interactions for Condensed Phase Simulation in the Polarizable Drude Force Field

ChemRxiv(2023)10.26434/chemrxiv-2023-gft5p

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0DataRank · unranked

1 citations

Alexander D. MacKerell, Yiling Nan

Influence of Mg2+ Distribution on the Stability of Folded States of the Twister Ribozyme Revealed using Grand Canonical Monte Carlo and Generative Deep Learning Enhanced Sampling

ChemRxiv(2023)10.26434/chemrxiv-2023-wkfrk

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0DataRank · unranked

0 citations

Alexander D. MacKerell, Mert Y. Sengul

Influence of Mg2+ Distribution on the Stability of Folded States of the Twister Ribozyme Revealed using Grand Canonical Monte Carlo and Generative Deep Learning Enhanced Sampling

ChemRxiv(2023)10.26434/chemrxiv-2023-wkfrk-v2

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0DataRank · unranked

0 citations

Alexander D. MacKerell, Mert Y. Sengul

An Integrated Covalent Drug Design Workflow using Site-Identification by Ligand Competitive Saturation

ChemRxiv(2023)10.26434/chemrxiv-2023-sc37c

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0DataRank · unranked

0 citations

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

Combining SILCS and Artificial Intelligence for High-Throughput Prediction of Drug Molecule Passive Permeability

ChemRxiv(2023)10.26434/chemrxiv-2023-rjv6c

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0DataRank · unranked

0 citations

Poonam Pandey, Alexander D. MacKerell

CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed

The Journal of Physical Chemistry B(2024)10.1021/acs.jpcb.4c04100

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0DataRank · unranked

116 citations

Steven L. Austin, Arnaud Blondel, Eric D. Boittier, Stefan Boresch, Matthias Buck +68 more

Revised 4-Point Water Model for the Classical Drude Oscillator Polarizable Force Field: SWM4-HLJ

Journal of Chemical Theory and Computation(2024)10.1021/acs.jctc.4c00966

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0DataRank · unranked

13 citations

Wenbo Yu, Alexander D. MacKerell, Xiaojing Teng

Balancing Group I Monatomic Ion–Polar Compound Interactions for Condensed Phase Simulation in the Polarizable Drude Force Field

Journal of Chemical Theory and Computation(2024)10.1021/acs.jctc.3c01380

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0DataRank · unranked

12 citations

Alexander D. MacKerell, Yiling Nan

FFParam-v2.0: A Comprehensive Tool for CHARMM Additive and Drude Polarizable Force-Field Parameter Optimization and Validation

The Journal of Physical Chemistry B(2024)10.1021/acs.jpcb.4c01314

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0DataRank · unranked

10 citations

Alexander D. MacKerell, Anmol Kumar

Combined Physics- and Machine-Learning-Based Method to Identify Druggable Binding Sites Using SILCS-Hotspots

Journal of Chemical Information and Modeling(2024)10.1021/acs.jcim.4c01189

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0DataRank · unranked

10 citations

Mingtian Zhao, Anmol Kumar, Alexander D. MacKerell, Erik B. Nordquist

Grand canonical Monte Carlo and deep learning assisted enhanced sampling to characterize the distribution of Mg2+ and influence of the Drude polarizable force field on the stability of folded states of the twister ribozyme

The Journal of Chemical Physics(2024)10.1063/5.0241246

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0DataRank · unranked

8 citations

Mert Y. Sengul, Alexander D. MacKerell, Prabin Baral

Identifying and Assessing Putative Allosteric Sites and Modulators for CXCR4 Predicted through Network Modeling and Site Identification by Ligand Competitive Saturation

The Journal of Physical Chemistry B(2024)10.1021/acs.jpcb.4c00925

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0DataRank · unranked

6 citations

Robin Flinko, George K. Lewis, Alexander D. MacKerell, Özge Kürkçüoğlu, Tuğçe İnan

First-in-class mitogen-activated protein kinase (MAPK) p38α: MAPK-activated protein kinase 2 dual signal modulator with anti-inflammatory and endothelial-stabilizing properties

Journal of Pharmacology and Experimental Therapeutics(2024)10.1124/jpet.124.002281

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0DataRank · unranked

5 citations

Kari Ann Shirey, Katerina N. Lugkey, Wendy Luo, Ritu Lal, Adam Galan +12 more

Balancing Group 1 Monoatomic Ion–Polar Compound Interactions in the Polarizable Drude Force Field: Application in Protein and Nucleic Acid Systems

The Journal of Physical Chemistry B(2024)10.1021/acs.jpcb.4c06354

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0DataRank · unranked

5 citations

Prabin Baral, Asuka A. Orr, Haley M. Michel, Justin A. Lemkul, Alexander D. MacKerell +1 more

Site‐Identificationby Ligand Competitive Saturation as a Paradigm of Co‐solventMDMethods

(2024)10.1002/9783527840748.ch5

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0DataRank · unranked

2 citations

Alexander D. MacKerell, Asuka A. Orr

FFParam-v2.0: A Comprehensive Tool for CHARMM Additive and Drude Polarizable Force-Field Parameter Optimization and Validation

ChemRxiv(2024)10.26434/chemrxiv-2024-8cmgq

N/A

0DataRank · unranked

1 citations

Alexander D. MacKerell, Anmol Kumar

Combined physics- and machine-learning-based method to identify druggable binding sites using SILCS-Hotspots

ChemRxiv(2024)10.26434/chemrxiv-2024-hrqq9

N/A

0DataRank · unranked

1 citations

Mingtian Zhao, Anmol Kumar, Alexander D. MacKerell, Erik B. Nordquist

Grand Canonical Monte Carlo and Deep Learning Assisted Enhanced Sampling to Characterize the Distribution of Mg2+ and Influence of the Drude Polarizable Force Field on the Stability of Folded States of the Twister Ribozyme

ChemRxiv(2024)10.26434/chemrxiv-2024-395q6

N/A

0DataRank · unranked

0 citations

Mert Y. Sengul, Alexander D. MacKerell, Prabin Baral

First-in-Class Potent, Dual HDAC6/Proteasome Inhibitors Lacking a Hydroxamic Acid Motif: Discovery of Novel Anti-Multiple Myeloma Agents

ACS Medicinal Chemistry Letters(2025)10.1021/acsmedchemlett.5c00500

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0DataRank · unranked

3 citations

Brandon D. Lowe, Andrea L. Cottingham, Daniel Van Eker, Asaminew H. Aytenfisu, Jace W. Jones +4 more

Bile Acids Are Potential Negative Allosteric Modulators of M1 Muscarinic Receptors

Biomolecules(2025)10.3390/biom15091326

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0DataRank · unranked

1 citations

Alexander D. MacKerell, David J. Weber, Jean‐Pierre Raufman, Wenbo Yu

Drude polarizable force field for phosphorylated polypeptides and proteins

Biophysical Journal(2025)10.1016/j.bpj.2025.10.026

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0DataRank · unranked

1 citations

Candace Miller, Alexander D. MacKerell, Justin A. Lemkul, Laura I. Gil Pineda

Increasing the Accuracy and Robustness of the CHARMM General Force Field with an Expanded Training Set

ChemRxiv(2025)10.26434/chemrxiv-2025-zkg2q

N/A

0DataRank · unranked

1 citations

Anmol Kumar, Jean‐Christophe Lambry, Jihyeon Lee, Suliman Sharif, Wenbo Yu +3 more

Prediction of TdP Arrhythmia Risk Through Molecular Simulations of Conformation-specific Drug Interactions with the hERG K + , Na V 1.5, and Ca V 1.2 Channels

bioRxiv (Cold Spring Harbor Laboratory)(2025)10.1101/2025.09.25.678690

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0DataRank · unranked

1 citations

Kush Narang, Yanxiao Han, David Wang, Ensley Jang, Sophia Brunkow +4 more

Non-Covalent Molecular Interaction Rules to Define Internal Dimer Coordinates for Quantum Mechanical Potential Energy Scans

ChemRxiv(2025)10.26434/chemrxiv-2025-b7qp7

N/A

0DataRank · unranked

0 citations

Anmol Kumar, Alexander D. MacKerell, Suliman Sharif

High Throughput Ligand Dissociation Kinetics Predictions using Site-Identification by Ligand Competitive Saturation

ChemRxiv(2025)10.26434/chemrxiv-2025-5bc2t

N/A

0DataRank · unranked

0 citations

Shashi Kumar, Mingtian Zhao, David J. Weber, Alexander D. MacKerell, Wenbo Yu

Identification and characterization of fragment binding sites for allosteric ligand design using the site identification by ligand competitive saturation hotspots approach (SILCS-Hotspots)

Biochimica et Biophysica Acta (BBA) - General Subjects(2020)10.1016/j.bbagen.2020.129519

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0DataRank · unranked

69 citations

Sunhwan Jo, Sirish Kaushik Lakkaraju, Christoffer Lind, Wenbo Yu, Alexander D. MacKerell

High Throughput Ligand Dissociation Kinetics Predictions using Site-Identification by Ligand Competitive Saturation

ChemRxiv(2025)10.26434/chemrxiv-2025-5bc2t-v2

N/A

0DataRank · unranked

0 citations

Shashi Kumar, Mingtian Zhao, David J. Weber, Alexander D. MacKerell, Wenbo Yu

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

The Journal of Chemical Physics(2020)10.1063/5.0019987

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0DataRank · unranked

68 citations

Guillaume Lamoureux, Alexander D. MacKerell, Benoı̂t Roux, Chetan Rupakheti

Small molecules inhibitors of the heterogeneous ribonuclear protein A18 (hnRNP A18): a regulator of protein translation and an immune checkpoint

Nucleic Acids Research(2020)10.1093/nar/gkaa1254

N/A

0DataRank · unranked

17 citations

Katherine M. Coburn, Wenbo Yu, Gerald M. Wilson, Elmar Nurmemmedov, Santosh Kesari +5 more

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

Biophysical Journal(2020)10.1016/j.bpj.2020.01.021

N/A

0DataRank · unranked

14 citations

Alexander D. MacKerell, Abhishek A. Kognole

Rationally Designed Polypharmacology: α‐Helix Mimetics as Dual Inhibitors of the Oncoproteins Mcl‐1 and HDM2

ChemMedChem(2020)10.1002/cmdc.202000278

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0DataRank · unranked

14 citations

Brandon Drennen, Maryanna E. Lanning, Samuel Hughes, Rebecca Rothhaas, Paul T. Wilder +3 more

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

Proceedings of the National Academy of Sciences(2020)10.1073/pnas.2012939117

N/A

0DataRank · unranked

36 citations

Lauren Baracco, Chloe Keller, Krystal Matthews, Marisa E. McGrath, James Logue +9 more

Balanced polarizable Drude force field parameters for molecular anions: phosphates, sulfates, sulfamates, and oxides

Journal of Molecular Modeling(2020)10.1007/s00894-020-04399-0

N/A

0DataRank · unranked

30 citations

Asaminew H. Aytenfisu, Alexander D. MacKerell, Abhishek A. Kognole