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List of works by Charles L Brooks

A strategy for proline and glycine mutations to proteins with alchemical free energy calculations

scientific article published on 12 April 2021

Adaptive Landscape Flattening Accelerates Sampling of Alchemical Space in Multisite λ Dynamics.

scientific article published on 23 January 2017

Addressing Intersite Coupling Unlocks Large Combinatorial Chemical Spaces for Alchemical Free Energy Methods

scientific article published on 07 March 2022

Allostery in the dynamic coactivator domain KIX occurs through minor conformational micro-states

scientific article published on 22 April 2022

Automated, Accurate, and Scalable Relative Protein-Ligand Binding Free-Energy Calculations Using Lambda Dynamics

scientific article published on 17 November 2020

BLaDE: A Basic Lambda Dynamics Engine for GPU-Accelerated Molecular Dynamics Free Energy Calculations

scientific article published on 28 October 2021

CDOCKER and λ-dynamics for prospective prediction in D₃R Grand Challenge 2.

scientific article published on 7 September 2017

Capturing the Catalytic Proton of Dihydrofolate Reductase: Implications for General Acid-Base Catalysis

scientific article published on 28 April 2021

Computational Studies of Catalytic Loop Dynamics in Yersinia Protein Tyrosine Phosphatase Using Pathway Optimization Methods

scientific article published on 04 September 2019

Deciphering protein evolution and fitness landscapes with latent space models

scientific article published on 10 December 2019

Electrostatic Forces Control the Negative Allosteric Regulation in a Disordered Protein Switch

scientific article published on 22 January 2020

Enhanced Sampling Applied to Modeling Allosteric Regulation in Transcription

scientific article published on 23 September 2019

Fast Solver for Large Scale Multistate Bennett Acceptance Ratio Equations

scientific article published on 04 February 2019

Frustration and folding of a TIM barrel protein

scientific article published on 25 July 2019

Generalizing the Discrete Gibbs Sampler-Based λ-Dynamics Approach for Multisite Sampling of Many Ligands

scientific article published on 08 June 2021

Gibbs Sampler-Based λ-Dynamics and Rao-Blackwell Estimator for Alchemical Free Energy Calculation

scientific article

Hydroxyl Radical-Coupled Electron-Transfer Mechanism of Flavin-Dependent Hydroxylases

scientific article published on 18 September 2019

Investigating the Effect of Two-point Surface Attachment on Enzyme Stability and Activity

scientific article published on 19 November 2018

M2 amphipathic helices facilitate pH-dependent conformational transition in influenza A virus

scientific article published on 03 February 2020

Mechanism of Vps4 hexamer function revealed by cryo-EM

scientific article

Molecular Interactions between Graphene and Biological Molecules.

scientific article published on 16 January 2017

Molecular Mechanisms of Interactions between Monolayered Transition Metal Dichalcogenides and Biological Molecules

scientific article published on 14 June 2019

Molecular interactions between single layered MoS2 and biological molecules.

scientific article

Overcoming Challenging Substituent Perturbations with Multisite λ-Dynamics: A Case Study Targeting β-Secretase 1

scientific article published on 13 August 2019

Predicting Binding Free Energies in a Large Combinatorial Chemical Space Using Multisite λ Dynamics

scientific article published on 06 June 2018

pyCHARMM: Embedding CHARMM Functionality in a Python Framework

scientific article published in 2023

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