Deciphering protein evolution and fitness landscapes with latent space models von Ding, Xinqiang, Zou, Zhengting, Brooks III, Charles L.

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CHARMM‐GUI ligand reader and modeler for CHARMM force field generation of small molecules von Kim, Seonghoon, Lee, Jumin, Jo, Sunhwan, Brooks, Charles L., Lee, Hui Sun, Im, Wonpil

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Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism von Arora, Karunesh, Brooks, Charles L. III

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FASTDock: A Pipeline for Allosteric Drug Discovery von Ahmed, Furyal, Brooks, 3rd, Charles L

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Molecular Mechanisms of Prolactin and Its Receptor von Brooks, Charles L

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Enhanced Sampling of Buried Charges in Free Energy Calculations Using Replica Exchange with Charge Tempering von Liu, Xiaorong, Brooks III, Charles L.

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Accuracy and Reproducibility of Lipari-Szabo Order Parameters From Molecular Dynamics von Lai, Thanh T.

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CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field von Lee, Jumin, Cheng, Xi, Swails, Jason M, Yeom, Min Sun, Eastman, Peter K, Lemkul, Justin A, Wei, Shuai, Buckner, Joshua, Jeong, Jong Cheol, Qi, Yifei, Jo, Sunhwan, Pande, Vijay S, Case, David A, Brooks, Charles L, MacKerell, Alexander D, Klauda, Jeffery B, Im, Wonpil

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Flexible CDOCKER: Development and application of a pseudo-explicit structure-based docking method within CHARMM von Gagnon, Jessica K., Law, Sean M., Brooks III, Charles L.

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WExplore: Hierarchical Exploration of High-Dimensional Spaces Using the Weighted Ensemble Algorithm von Dickson, Alex, Brooks, Charles L

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Linking folding with aggregation in Alzheimer's β-amyloid peptides von Khandogin, Jana, Brooks, Charles L. III

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Parametrization of halogen bonds in the CHARMM general force field: Improved treatment of ligand–protein interactions von Soteras Gutiérrez, Ignacio, Lin, Fang-Yu, Vanommeslaeghe, Kenno, Lemkul, Justin A., Armacost, Kira A., Brooks, Charles L., MacKerell, Alexander D.

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Classical molecular dynamics von Brooks, Charles L., Case, David A., Plimpton, Steve, Roux, Benoît, van der Spoel, David, Tajkhorshid, Emad

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Selection pressures on evolution of ribonuclease H explored with rigorous free-energy-based design von Hayes, Ryan L, Nixon, Charlotte F, Marqusee, Susan, Brooks, 3rd, Charles L

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λ-Dynamics free energy simulation methods von Knight, Jennifer L, Brooks, Charles L. III

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Flexible CDOCKER: Hybrid Searching Algorithm and Scoring Function with Side Chain Conformational Entropy von Wu, Yujin

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Viral capsid proteins are segregated in structural fold space von Cheng, Shanshan, Brooks, 3rd, Charles L

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Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism von Goh, Garrett B., Hulbert, Benjamin S., Zhou, Huiqing, Brooks III, Charles L.

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M2 amphipathic helices facilitate pH-dependent conformational transition in influenza A virus von Torabifard, Hedieh, Panahi, Afra, Brooks, Charles L.

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Fast Solver for Large Scale Multistate Bennett Acceptance Ratio Equations von Ding, Xinqiang, Vilseck, Jonah Z, Brooks, Charles L

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