Search Results - "Brooks, Charles L"

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

“…Protein sequences contain rich information about protein evolution, fitness landscapes, and stability. Here we investigate how latent space models trained…”
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Molecular Mechanisms of Prolactin and Its Receptor by Brooks, Charles L

“…Prolactin and the prolactin receptors are members of a family of hormone/receptor pairs which include GH, erythropoietin, and other ligand/receptor pairs. The…”
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Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism by Arora, Karunesh, Brooks, Charles L. III

“…Large-scale conformational changes in proteins are often associated with the binding of a substrate. Because conformational changes may be related to the…”
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Enhanced Sampling of Buried Charges in Free Energy Calculations Using Replica Exchange with Charge Tempering by Liu, Xiaorong, Brooks III, Charles L.

“…Buried ionizable groups in proteins often play important structural and functional roles. However, it is generally challenging to study the detailed molecular…”
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FASTDock: A Pipeline for Allosteric Drug Discovery by Ahmed, Furyal, Brooks, 3rd, Charles L

“…Allostery is involved in innumerable biological processes and plays a fundamental role in human disease. Thus, the exploration of allosteric modulation is…”
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Accuracy and Reproducibility of Lipari-Szabo Order Parameters From Molecular Dynamics by Lai, Thanh T.

“…The Lipari-Szabo generalized order parameter probes the picosecond to nanosecond time scale motions of a protein and is useful for rationalizing a multitude of…”
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CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field by 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

“…Proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (MD) simulations, especially in studies of lipid bilayers. The…”
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WExplore: Hierarchical Exploration of High-Dimensional Spaces Using the Weighted Ensemble Algorithm by Dickson, Alex, Brooks, Charles L

“…As most relevant motions in biomolecular systems are inaccessible to conventional molecular dynamics simulations, algorithms that enhance sampling of rare…”
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Parametrization of halogen bonds in the CHARMM general force field: Improved treatment of ligand–protein interactions by Soteras Gutiérrez, Ignacio, Lin, Fang-Yu, Vanommeslaeghe, Kenno, Lemkul, Justin A., Armacost, Kira A., Brooks, Charles L., MacKerell, Alexander D.

“…[Display omitted] A halogen bond is a highly directional, non-covalent interaction between a halogen atom and another electronegative atom. It arises due to…”
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Flexible CDOCKER: Development and application of a pseudo-explicit structure-based docking method within CHARMM by Gagnon, Jessica K., Law, Sean M., Brooks III, Charles L.

“…Protein‐ligand docking is a commonly used method for lead identification and refinement. While traditional structure‐based docking methods represent the…”
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CHARMM‐GUI ligand reader and modeler for CHARMM force field generation of small molecules by Kim, Seonghoon, Lee, Jumin, Jo, Sunhwan, Brooks, Charles L., Lee, Hui Sun, Im, Wonpil

“…Reading ligand structures into any simulation program is often nontrivial and time consuming, especially when the force field parameters and/or structure files…”
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Fast Solver for Large Scale Multistate Bennett Acceptance Ratio Equations by Ding, Xinqiang, Vilseck, Jonah Z, Brooks, Charles L

“…The multistate Bennett acceptance ratio method (MBAR) and unbinned weighted histogram analysis method (UWHAM) are widely employed approaches to calculate…”
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VIPERdb v3.0: a structure-based data analytics platform for viral capsids by Montiel-Garcia, Daniel, Santoyo-Rivera, Nelly, Ho, Phuong, Carrillo-Tripp, Mauricio, III, Charles L Brooks, Johnson, John E, Reddy, Vijay S

“…Abstract VIrus Particle ExploreR data base (VIPERdb) (http://viperdb.scripps.edu) is a curated repository of virus capsid structures and a database of…”
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Selection pressures on evolution of ribonuclease H explored with rigorous free-energy-based design by Hayes, Ryan L, Nixon, Charlotte F, Marqusee, Susan, Brooks, 3rd, Charles L

“…Understanding natural protein evolution and designing novel proteins are motivating interest in development of high-throughput methods to explore large…”
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Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism by Goh, Garrett B., Hulbert, Benjamin S., Zhou, Huiqing, Brooks III, Charles L.

“…ABSTRACT pH is a ubiquitous regulator of biological activity, including protein‐folding, protein‐protein interactions, and enzymatic activity. Existing…”
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Crowding Induced Collective Hydration of Biological Macromolecules over Extended Distances by King, John T, Arthur, Evan J, Brooks, Charles L, Kubarych, Kevin J

“…Ultrafast two-dimensional infrared (2D-IR) spectroscopy reveals picosecond protein and hydration dynamics of crowded hen egg white lysozyme (HEWL) labeled with…”
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λ-Dynamics free energy simulation methods by Knight, Jennifer L, Brooks, Charles L. III

“…Free energy calculations are fundamental to obtaining accurate theoretical estimates of many important biological phenomena including hydration energies,…”
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Free Gangliosides Can Alter Amyloid‑β Aggregation by Chakravorty, Arghya, McCalpin, Samuel D., Sahoo, Bikash R., Ramamoorthy, Ayyalusamy

“…A recently proposed lipid-chaperone hypothesis suggests that free lipid molecules, not bound to membranes, affect the aggregation of amyloidogenic peptides…”
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Recent advances in implicit solvent-based methods for biomolecular simulations by Chen, Jianhan, Brooks, Charles L, Khandogin, Jana

“…Implicit solvent-based methods play an increasingly important role in molecular modeling of biomolecular structure and dynamics. Recent methodological…”
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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 by Mackerell, Alexander D., Feig, Michael, Brooks, Charles L.

“…Computational studies of proteins based on empirical force fields represent a powerful tool to obtain structure–function relationships at an atomic level, and…”
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