Publications by authors named "Alexander D MacKerell"

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Computer-Aided Drug Design Methods.
Wenbo Yu, Alexander D MacKerell

Methods Mol Biol· January 2018

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Arrhythmia Risk Predictions from Molecular Simulations of Cardiac Ion Channel-Drug Interactions.
Kyle C Rouen, Kush Narang, Yanxiao Han, David Wang, Ensley Jang, Alexander D MacKerell

Biophys J· December 2025

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Computational Modeling of PROTAC Ternary Complexes as Ensembles Using SILCS-xTAC.
Erik B Nordquist, Mingtian Zhao, Wenbo Yu, Alexander D MacKerell

J Chem Inf Model· December 2025

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Mapping the distribution and affinities of ligand interaction sites on human serum albumin.
Asuka A Orr, Agbo-Oma Uwakweh, Xun Li, Ahmad Kiani Karanji, Stephen W Hoag, Alexander D MacKerell

Biophys J· November 2025

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The mammalian SKI complex is a broad-spectrum antiviral drug target that upregulates cellular cholesterol to inhibit viral replication.
Stuart Weston, Lauren Baracco, Louis Taylor, Alison J Scott, Gaurav Kumar, Alexander D MacKerell

J Virol· October 2025

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Drude polarizable force field for phosphorylated polypeptides and proteins.
Laura I Gil Pineda, Candace J Miller, Alexander D MacKerell, Justin A Lemkul

Biophys J· October 2025

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Bile Acids Are Potential Negative Allosteric Modulators of M1 Muscarinic Receptors.
Wenbo Yu, Alexander D MacKerell, David J Weber, Jean-Pierre Raufman

Biomolecules· September 2025

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Prediction of TdP Arrhythmia Risk Through Molecular Simulations of Conformation-specific Drug Interactions with the hERG K, Na1.5, and Ca1.2 Channels.
Kyle C Rouen, Kush Narang, Yanxiao Han, David Wang, Ensley Jang, Alexander D MacKerell

bioRxiv· September 2025

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Harnessing computational technologies to facilitate antibody-drug conjugate development.
Anastasia Croitoru, Asuka A Orr, Alexander D MacKerell

Nat Chem Biol· August 2025

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GaSal-2: A Water-Soluble Antipseudomonal Agent Targeting the Extracellular Hemophore HasAp.
Aziza Frank, Lucia Hwang, William T Witt, Garrick Centola, Kieran Johnson, Alexander D MacKerell

ACS Infect Dis· August 2025

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High-Throughput Ligand Dissociation Kinetics Predictions Using Site Identification by Ligand Competitive Saturation.
Wenbo Yu, Shashi Kumar, Mingtian Zhao, David J Weber, Alexander D MacKerell

J Chem Theory Comput· May 2025

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Non-Covalent Molecular Interaction Rules to Define Internal Dimer Coordinates for Quantum Mechanical Potential Energy Scans.
Suliman Sharif, Anmol Kumar, Alexander D MacKerell

J Comput Chem· May 2025

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Investigating the Interaction between Excipients and Monoclonal Antibodies PGT121 and N49P9.6-FR-LS: A Comprehensive Analysis.
Xun Li, Asuka A Orr, Mohammad M Sajadi, Anthony L DeVico, Daniel J Deredge, Alexander D MacKerell

Mol Pharm· April 2025

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Potent and Selective Human Constitutive Androstane Receptor Activator DL5055 Facilitates Cyclophosphamide-Based Chemotherapies.
Dongdong Liang, Linhao Li, Yong Ai, Zhihui Li, William D Hedrich, Alexander D MacKerell

J Med Chem· April 2025

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The need to implement FAIR principles in biomolecular simulations.
Rommie E Amaro, Johan Åqvist, Ivet Bahar, Federica Battistini, Adam Bellaiche, Alexander D MacKerell

Nat Methods· April 2025

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Detection of Putative Ligand Dissociation Pathways in Proteins Using Site-Identification by Ligand Competitive Saturation.
Wenbo Yu, David J Weber, Alexander D MacKerell

J Chem Inf Model· March 2025

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Increasing the Accuracy and Robustness of the CHARMM General Force Field with an Expanded Training Set.
Anastasia Croitoru, Anmol Kumar, Jean-Christophe Lambry, Jihyeon Lee, Suliman Sharif, Alexander D MacKerell

J Chem Theory Comput· March 2025

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Computationally Efficient Polarizable MD Simulations: A Simple Water Model for the Classical Drude Oscillator Polarizable Force Field.
Xiaojing Teng, Wenbo Yu, Alexander D MacKerell

J Phys Chem Lett· January 2025

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Balancing Group 1 Monoatomic Ion-Polar Compound Interactions in the Polarizable Drude Force Field: Application in Protein and Nucleic Acid Systems.
Yiling Nan, Prabin Baral, Asuka A Orr, Haley M Michel, Justin A Lemkul, Alexander D MacKerell

J Phys Chem B· December 2024

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Isolation of phytoconstituents from an extract of with cytotoxicity and antioxidant activities and evaluation of their potential to bind to aldose reductase (AKR1B1).
Afifa Parvin Shanta, Fatema-Tuz-Zohora, Rumana Mahtarin, Alexander D MacKerell, Monira Ahsan

J Biomol Struct Dyn· December 2024

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Modeling Ligand Binding Site Water Networks with Site Identification by Ligand Competitive Saturation: Impact on Ligand Binding Orientations and Relative Binding Affinities.
Anmol Kumar, Himanshu Goel, Wenbo Yu, Mingtian Zhao, Alexander D MacKerell

J Chem Theory Comput· December 2024

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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.
Prabin Baral, Mert Y Sengul, Alexander D MacKerell

J Chem Phys· December 2024

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Revised 4-Point Water Model for the Classical Drude Oscillator Polarizable Force Field: SWM4-HLJ.
Xiaojing Teng, Wenbo Yu, Alexander D MacKerell

J Chem Theory Comput· November 2024

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First-in-class mitogen-activated protein kinase (MAPK) p38α: MAPK-activated protein kinase 2 dual signal modulator with anti-inflammatory and endothelial-stabilizing properties.
Mohan E Tulapurkar, Kari Ann Shirey, Katerina Lugkey, Wendy Luo, Ritu Lal, Alexander D MacKerell

J Pharmacol Exp Ther· November 2024

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Refinement of the Drude Polarizable Force Field for Hexose Monosaccharides: Capturing Ring Conformational Dynamics with Enhanced Accuracy.
Chythra J N, Olgun Guvench, Alexander D MacKerell, Takumi Yamaguchi, Sairam S Mallajosyula

J Chem Theory Comput· October 2024

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Exploring Druggable Binding Sites on the Class A GPCRs Using the Residue Interaction Network and Site Identification by Ligand Competitive Saturation.
Tugce Inan, Merve Yuce, Alexander D MacKerell, Ozge Kurkcuoglu

ACS Omega· September 2024

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