Alex MacKerell - Dissemin

All papers authored by Alex MacKerell

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2024 Anmol Kumar

, Alexander D. MacKerell

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

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This paper is made freely available by the publisher.

2023 Mert Y. Sengul

, Alexander D. MacKerell

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

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Yalun Yu

, Richard M. Venable, Jonathan Thirman, Payal Chatterjee, Anmol Kumar

, Richard W. Pastor

, Benoît Roux

, Alexander D. MacKerell

, Jeffery B. Klauda

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

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Asuka A. Orr

, Aoxiang Tao

, Olgun Guvench

, Alexander D. MacKerell

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

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2022 Asuka A. Orr

, Suliman Sharif, Junmei Wang

, Alexander D. MacKerell

Preserving the Integrity of Empirical Force Fields

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Abhishek A. Kognole

, Anthony Hazel

, Alexander D. MacKerell

SILCS-RNA: Toward a Structure-Based Drug Design Approach for Targeting RNAs with Small Molecules

Download from pubs.acs.org

Payal Chatterjee

, Mert Y. Sengul

, Anmol Kumar

, Alexander D. MacKerell

Harnessing Deep Learning for Optimization of Lennard-Jones Parameters for the Polarizable Classical Drude Oscillator Force Field

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Anmol Kumar

, Poonam Pandey, Payal Chatterjee, Alexander D. MacKerell

Deep Neural Network Model to Predict the Electrostatic Parameters in the Polarizable Classical Drude Oscillator Force Field

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Himanshu Goel

, Anthony Hazel

, Wenbo Yu

, Sunhwan Jo

, Alexander D. MacKerell

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

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2021 Anastasia Croitoru, Sang-Jun Park

, Anmol Kumar

, Jumin Lee

, Wonpil Im

, Alexander D. MacKerell

, Alexey Aleksandrov

Additive CHARMM36 Force Field for Nonstandard Amino Acids

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This paper was not found in any repository; the policy of its publisher is unknown or unclear.

Van Ngo, Hui Li, Alexander D. MacKerell

, Toby W. Allen

, Benoît Roux

, Sergei Noskov

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

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Himanshu Goel

, Anthony Hazel

, Vincent D. Ustach

, Sunhwan Jo

, Wenbo Yu, Alexander D. MacKerell

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

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2020 Benjamin Diethelm-Varela, Anmol Kumar

, Caitlin Lynch

, Gregory H. Imler, Jeffrey R. Deschamps

, Yue Li

, Menghang Xia, Alexander D. MacKerell

, Fengtian Xue

Stereoisomerization of human constitutive androstane receptor agonist CITCO

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Mahdi Mousaei, Meruyert Kudaibergenova, Alexander D. MacKerell

, Sergei Noskov

Assessing hERG1 Blockade from Bayesian Machine-Learning-Optimized Site Identification by Ligand Competitive Saturation Simulations

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Mattia Turchi, Abhishek A. Kognole, Anmol Kumar

, Qiong Cai

, Guoping Lian, Alexander D. MacKerell

Predicting Partition Coefficients of Neutral and Charged Solutes in the Mixed SLES–Fatty Acid Micellar System

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2019 Anmol Kumar

, Ozge Yoluk, Alexander D. MacKerell

FFParam: Standalone package for CHARMM additive and Drude polarizable force field parametrization of small molecules

Download from api.wiley.com

2018 Hanif M. Khan

, Alexander D. MacKerell

, Nathalie Reuter

Cation-π Interactions between Methylated Ammonium Groups and Tryptophan in the CHARMM36 Additive Force Field

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Gerhard König

, Frank Pickard, Jing Huang, Walter Thiel, Alexander MacKerell

, Bernard Brooks, Darrin York

A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes

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2017 Jing Huang, Ye Mei

, Gerhard König

, Andrew C. Simmonett, Frank C. Pickard

, Qin Wu

, Lee-Ping Wang

, Alexander D. MacKerell

, Bernard R. Brooks, Yihan Shao

An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches

Download from europepmc.org

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All papers authored by Alex MacKerell