Charles L Brooks Iii (Charles L Brooks)

Publication Activity (10 Years)

Years Active: 2017-2024
Publications (10 Years): 78

Top Topics

Molecular Dynamics

Top Venues

Journal of chemical theory and computation

Journal of chemical information and modeling

Proceedings of the National Academy of Sciences of the United States of America

Journal of the American Chemical Society

This page only lists publications with an associated author ORCID identifier.

Publications

Sarah E Champagne, Chang-Hwa Chiang, Philipp M Gemmel, Charles L Brooks Iii, Alison R H Narayan
Biocatalytic Stereoselective Oxidation of 2-Arylindoles. Journal of the American Chemical Society 146 (4) (2024)
Ryan L Hayes, Charlotte F Nixon, Susan Marqusee, Charles L Brooks Iii
Selection pressures on evolution of ribonuclease H explored with rigorous free-energy-based design. Proceedings of the National Academy of Sciences of the United States of America 121 (3) (2024)
Ryan L Hayes, Charlotte F Nixon, Susan Marqusee, Charles L Brooks Iii
Selection pressures on evolution of ribonuclease H explored with rigorous free-energy-based design. Proceedings of the National Academy of Sciences of the United States of America 121 (3) (2024)
Ryan L Hayes, Charlotte F Nixon, Susan Marqusee, Charles L Brooks Iii
Selection pressures on evolution of ribonuclease H explored with rigorous free-energy-based design. Proceedings of the National Academy of Sciences of the United States of America 121 (3) (2024)
Bhaskar K Chatterjee, Maroof Alam, Arghya Chakravorty, Shannon M Lacy, Jason Rech, Charles L Brooks Iii, Peter D Arvan, Matthias C Truttmann
Small molecule FICD inhibitors suppress endogenous and pathologic FICD-mediated protein AMPylation. bioRxiv : the preprint server for biology (2024)
Yujin Wu, Fangyu Liu, Isabella Glenn, Karla Fonseca-Valencia, Lu Paris, Yuyue Xiong, Steven V Jerome, Charles L Brooks Iii, Brian K Shoichet
Identifying Artifacts from Large Library Docking. Journal of medicinal chemistry (2024)
Ryan L Hayes, Luis F Cervantes, Justin Cruz Abad Santos, Amirmasoud Samadi, Jonah Z Vilseck, Charles L Brooks Iii
How to Sample Dozens of Substitutions per Site with λ Dynamics. Journal of chemical theory and computation 20 (14) (2024)
Ryan L Hayes, Luis F Cervantes, Justin Cruz Abad Santos, Amirmasoud Samadi, Jonah Z Vilseck, Charles L Brooks Iii
How to Sample Dozens of Substitutions per Site with λ Dynamics. Journal of chemical theory and computation 20 (14) (2024)
Xiaorong Liu, Charles L Brooks Iii
Enhanced Sampling of Buried Charges in Free Energy Calculations Using Replica Exchange with Charge Tempering. Journal of chemical theory and computation 20 (3) (2024)
Xiaorong Liu, Charles L Brooks Iii
Enhanced Sampling of Buried Charges in Free Energy Calculations Using Replica Exchange with Charge Tempering. Journal of chemical theory and computation 20 (3) (2024)
Sarah E Champagne, Chang-Hwa Chiang, Philipp M Gemmel, Charles L Brooks Iii, Alison R H Narayan
Biocatalytic Stereoselective Oxidation of 2-Arylindoles. Journal of the American Chemical Society (2024)
Arghya Chakravorty, Azam Hussain, Luis F Cervantes, Thanh T Lai, Charles L Brooks Iii
Exploring the Limits of the Generalized CHARMM and AMBER Force Fields through Predictions of Hydration Free Energy of Small Molecules. Journal of chemical information and modeling 64 (10) (2024)
Parveen Gartan, Fahimeh Khorsand, Pushpak Mizar, Juha Ilmari Vahokovski, Luis F Cervantes, Bengt Erik Haug, Ruth Brenk, Charles L Brooks Iii, Nathalie Reuter
Investigating Polypharmacology through Targeting Known Human Neutrophil Elastase Inhibitors to Proteinase 3. Journal of chemical information and modeling (2024)
Parveen Gartan, Fahimeh Khorsand, Pushpak Mizar, Juha Ilmari Vahokovski, Luis F Cervantes, Bengt Erik Haug, Ruth Brenk, Charles L Brooks Iii, Nathalie Reuter
Investigating Polypharmacology through Targeting Known Human Neutrophil Elastase Inhibitors to Proteinase 3. Journal of chemical information and modeling 64 (3) (2024)
Sarah E Champagne, Chang-Hwa Chiang, Philipp M Gemmel, Charles L Brooks Iii, Alison R H Narayan
Biocatalytic Stereoselective Oxidation of 2-Arylindoles. Journal of the American Chemical Society 146 (4) (2024)
Sarah E Champagne, Chang-Hwa Chiang, Philipp M Gemmel, Charles L Brooks Iii, Alison R H Narayan
Biocatalytic Stereoselective Oxidation of 2-Arylindoles. Journal of the American Chemical Society 146 (4) (2024)
Ryan L Hayes, Charlotte F Nixon, Susan Marqusee, Charles L Brooks Iii
Selection pressures on evolution of ribonuclease H explored with rigorous free-energy-based design. Proceedings of the National Academy of Sciences of the United States of America 121 (3) (2024)
Ryan L Hayes, Luis F Cervantes, Justin Cruz Abad Santos, Amirmasoud Samadi, Jonah Z Vilseck, Charles L Brooks Iii
How to Sample Dozens of Substitutions per Site with λ Dynamics. Journal of chemical theory and computation (2024)
Ryan L Hayes, Charlotte F Nixon, Susan Marqusee, Charles L Brooks Iii
Selection pressures on evolution of ribonuclease H explored with rigorous free-energy-based design. Proceedings of the National Academy of Sciences of the United States of America 121 (3) (2024)
Parveen Gartan, Fahimeh Khorsand, Pushpak Mizar, Juha Ilmari Vahokovski, Luis F Cervantes, Bengt Erik Haug, Ruth Brenk, Charles L Brooks Iii, Nathalie Reuter
Investigating Polypharmacology through Targeting Known Human Neutrophil Elastase Inhibitors to Proteinase 3. Journal of chemical information and modeling 64 (3) (2024)
Parveen Gartan, Fahimeh Khorsand, Pushpak Mizar, Juha Ilmari Vahokovski, Luis F Cervantes, Bengt Erik Haug, Ruth Brenk, Charles L Brooks Iii, Nathalie Reuter
Investigating Polypharmacology through Targeting Known Human Neutrophil Elastase Inhibitors to Proteinase 3. Journal of chemical information and modeling 64 (3) (2024)
Ryan L Hayes, Luis F Cervantes, Justin Cruz Abad Santos, Amirmasoud Samadi, Jonah Z Vilseck, Charles L Brooks Iii
How to Sample Dozens of Substitutions per Site with λ Dynamics. Journal of chemical theory and computation 20 (14) (2024)
Parveen Gartan, Fahimeh Khorsand, Pushpak Mizar, Juha Ilmari Vahokovski, Luis F Cervantes, Bengt Erik Haug, Ruth Brenk, Charles L Brooks Iii, Nathalie Reuter
Investigating Polypharmacology through Targeting Known Human Neutrophil Elastase Inhibitors to Proteinase 3. Journal of chemical information and modeling 64 (3) (2024)
Bhaskar K Chatterjee, Maroof Alam, Arghya Chakravorty, Shannon M Lacy, Jason Rech, Charles L Brooks Iii, Peter D Arvan, Matthias C Truttmann
Small molecule FICD inhibitors suppress endogenous and pathologic FICD-mediated protein AMPylation. bioRxiv : the preprint server for biology (2024)
Sarah E Champagne, Chang-Hwa Chiang, Philipp M Gemmel, Charles L Brooks Iii, Alison R H Narayan
Biocatalytic Stereoselective Oxidation of 2-Arylindoles. Journal of the American Chemical Society 146 (4) (2024)
Sarah E Champagne, Chang-Hwa Chiang, Philipp M Gemmel, Charles L Brooks Iii, Alison R H Narayan
Biocatalytic Stereoselective Oxidation of 2-Arylindoles. Journal of the American Chemical Society 146 (4) (2024)
Sarah E Champagne, Chang-Hwa Chiang, Philipp M Gemmel, Charles L Brooks Iii, Alison R H Narayan
Biocatalytic Stereoselective Oxidation of 2-Arylindoles. Journal of the American Chemical Society 146 (4) (2024)
Ryan L Hayes, Luis F Cervantes, Justin Cruz Abad Santos, Amirmasoud Samadi, Jonah Z Vilseck, Charles L Brooks Iii
How to Sample Dozens of Substitutions per Site with λ Dynamics. Journal of chemical theory and computation 20 (14) (2024)
Arghya Chakravorty, Azam Hussain, Luis F Cervantes, Thanh T Lai, Charles L Brooks Iii
Exploring the Limits of the Generalized CHARMM and AMBER Force Fields through Predictions of Hydration Free Energy of Small Molecules. Journal of chemical information and modeling 64 (10) (2024)
Xiaorong Liu, Charles L Brooks Iii
Enhanced Sampling of Buried Charges in Free Energy Calculations Using Replica Exchange with Charge Tempering. Journal of chemical theory and computation (2024)
Ryan L Hayes, Charlotte F Nixon, Susan Marqusee, Charles L Brooks Iii
Selection pressures on evolution of ribonuclease H explored with rigorous free-energy-based design. Proceedings of the National Academy of Sciences of the United States of America 121 (3) (2024)
Arghya Chakravorty, Azam Hussain, Luis F Cervantes, Thanh T Lai, Charles L Brooks Iii
Exploring the Limits of the Generalized CHARMM and AMBER Force Fields through Predictions of Hydration Free Energy of Small Molecules. Journal of chemical information and modeling (2024)
Wonmuk Hwang, Steven L Austin, Arnaud Blondel, Eric D Boittier, Stefan Boresch, Matthias Buck, Joshua Buckner, Amedeo Caflisch, Hao-Ting Chang, Xi Cheng, Yeol Kyo Choi, Jhih-Wei Chu, Michael F Crowley, Qiang Cui, Ana Damjanovic, Yuqing Deng, Michael Devereux, Xinqiang Ding, Michael F Feig, Jiali Gao, David R Glowacki, James E Gonzales, Mehdi Bagerhi Hamaneh, Edward D Harder, Ryan L Hayes, Jing Huang, Yandong Huang, Phillip S Hudson, Wonpil Im, Shahidul M Islam, Wei Jiang, Michael R Jones, Silvan Käser, Fiona L Kearns, Nathan R Kern, Jeffery B Klauda, Themis Lazaridis, Jinhyuk Lee, Justin A Lemkul, Xiaorong Liu, Yun Lyna Luo, Alexander D MacKerell, Dan Thomas Major, Markus Meuwly, Kwangho Nam, Lennart Nilsson, Victor Ovchinnikov, Emanuele Paci, Soohyung Park, Richard W Pastor, Amanda R Pittman, Carol Beth Post, Samarjeet Prasad, Jingzhi Pu, John Z H Zhang, Thenmalarchelvi Rathinavelan, Daniel R Roe, Benoı T Roux, Christopher N Rowley, Jana Shen, Andrew C Simmonett, Alexander J Sodt, Kai Töpfer, Meenu Upadhyay, Arjan van der Vaart, Luis Itza Vazquez-Salazar, Richard M Venable, Luke C Warrensford, H Lee Woodcock, Yujin Wu, Charles L Brooks Iii, Bernard R Brooks, Martin Karplus
CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed. The journal of physical chemistry. B (2024)
Xiaorong Liu, Charles L Brooks Iii
Enhanced Sampling of Buried Charges in Free Energy Calculations Using Replica Exchange with Charge Tempering. Journal of chemical theory and computation 20 (3) (2024)
Parveen Gartan, Fahimeh Khorsand, Pushpak Mizar, Juha Ilmari Vahokovski, Luis F Cervantes, Bengt Erik Haug, Ruth Brenk, Charles L Brooks Iii, Nathalie Reuter
Investigating Polypharmacology through Targeting Known Human Neutrophil Elastase Inhibitors to Proteinase 3. Journal of chemical information and modeling 64 (3) (2024)
Ryan L Hayes, Charlotte F Nixon, Susan Marqusee, Charles L Brooks Iii
Selection pressures on evolution of ribonuclease H explored with rigorous free-energy-based design. Proceedings of the National Academy of Sciences of the United States of America 121 (3) (2024)
Parveen Gartan, Fahimeh Khorsand, Pushpak Mizar, Juha Ilmari Vahokovski, Luis F Cervantes, Bengt Erik Haug, Ruth Brenk, Charles L Brooks Iii, Nathalie Reuter
Investigating Polypharmacology through Targeting Known Human Neutrophil Elastase Inhibitors to Proteinase 3. Journal of chemical information and modeling 64 (3) (2024)
Xiaorong Liu, Charles L Brooks Iii
Enhanced Sampling of Buried Charges in Free Energy Calculations Using Replica Exchange with Charge Tempering. Journal of chemical theory and computation 20 (3) (2024)
Chang-Hwa Chiang, Troy Wymore, Attabey Rodríguez Benítez, Azam Hussain, Janet L Smith, Charles L Brooks Iii, Alison R H Narayan
Deciphering the evolution of flavin-dependent monooxygenase stereoselectivity using ancestral sequence reconstruction. Proceedings of the National Academy of Sciences of the United States of America 120 (15) (2023)
Furyal Ahmed, Charles L Brooks Iii
FASTDock: A Pipeline for Allosteric Drug Discovery. Journal of chemical information and modeling (2023)
Xiaorong Liu, Pui Ki Tsang, Matthew B Soellner, Charles L Brooks Iii
QSAR via Multisite λ-Dynamics in the Orphaned TSSK1B Kinase. Protein science : a publication of the Protein Society (2023)
Amanda L Peiffer, Julie M Garlick, Yujin Wu, Jesse W Wotring, Sahil Arora, Alexander S Harmata, Daniel A Bochar, Corey R J Stephenson, Matthew B Soellner, Jonathan Z Sexton, Charles L Brooks Iii, Anna K Mapp
TMPRSS2 Inhibitor Discovery Facilitated through an In Silico and Biochemical Screening Platform. ACS medicinal chemistry letters 14 (6) (2023)
Joshua Buckner, Xiaorong Liu, Arghya Chakravorty, Yujin Wu, Luis F Cervantes, Thanh T Lai, Charles L Brooks Iii
pyCHARMM: Embedding CHARMM Functionality in a Python Framework. Journal of chemical theory and computation (2023)
Xiaorong Liu, Pui Ki Tsang, Matthew B Soellner, Charles L Brooks Iii
QSAR via Multisite λ-Dynamics in the Orphaned TSSK1B Kinase. Protein science : a publication of the Protein Society (2023)
Ellen E Guest, Luis F Cervantes, Stephen D Pickett, Charles L Brooks Iii, Jonathan D Hirst
Alchemical Free Energy Methods Applied to Complexes of the First Bromodomain of BRD4. Journal of chemical information and modeling 62 (6) (2022)
Arghya Chakravorty, Samuel D McCalpin, Bikash R Sahoo, Ayyalusamy Ramamoorthy, Charles L Brooks Iii
Free Gangliosides Can Alter Amyloid-β Aggregation. The journal of physical chemistry letters 13 (40) (2022)
Amanda L Peiffer, Julie M Garlick, Stephen T Joy, Anna K Mapp, Charles L Brooks Iii
Allostery in the dynamic coactivator domain KIX occurs through minor conformational micro-states. PLoS computational biology 18 (4) (2022)
Duncan W S MacKenzie, Anna Schaefer, Julia Steckner, Christopher A Leo, Dalia Naser, Efrosini Artikis, Aron Broom, Travis Ko, Purnank Shah, Mikaela Q Ney, Elisa Tran, Martin T J Smith, Brian Fuglestad, A Joshua Wand, Charles L Brooks Iii, Elizabeth M Meiering
A fine balance of hydrophobic-electrostatic communication pathways in a pH-switching protein. Proceedings of the National Academy of Sciences of the United States of America 119 (26) (2022)
Jonah Z Vilseck, Luis F Cervantes, Ryan L Hayes, Charles L Brooks Iii
Optimizing Multisite λ-Dynamics Throughput with Charge Renormalization. Journal of chemical information and modeling 62 (6) (2022)
Ryan L Hayes, Jonah Z Vilseck, Charles L Brooks Iii
Addressing Intersite Coupling Unlocks Large Combinatorial Chemical Spaces for Alchemical Free Energy Methods. Journal of chemical theory and computation 18 (4) (2022)
Jonah Z Vilseck, Xinqiang Ding, Ryan L Hayes, Charles L Brooks Iii
Generalizing the Discrete Gibbs Sampler-Based λ-Dynamics Approach for Multisite Sampling of Many Ligands. Journal of chemical theory and computation 17 (7) (2021)
Yujin Wu, Charles L Brooks Iii
Flexible CDOCKER: Hybrid Searching Algorithm and Scoring Function with Side Chain Conformational Entropy. Journal of chemical information and modeling 61 (11) (2021)
Ryan L Hayes, Charles L Brooks Iii
A strategy for proline and glycine mutations to proteins with alchemical free energy calculations. Journal of computational chemistry 42 (15) (2021)
Qun Wan, Brad C Bennett, Troy Wymore, Zhihong Li, Mark A Wilson, Charles L Brooks Iii, Paul Langan, Andrey Y Kovalevsky, Chris G Dealwis
Capturing the Catalytic Proton of Dihydrofolate Reductase: Implications for General Acid-Base Catalysis. ACS catalysis 11 (9) (2021)
Julie M Garlick, Steven M Sturlis, Paul A Bruno, Joel A Yates, Amanda L Peiffer, Yejun Liu, Laura Goo, LiWei Bao, Samantha N De Salle, Giselle Tamayo-Castillo, Charles L Brooks Iii, Sofia D Merajver, Anna K Mapp
Norstictic Acid Is a Selective Allosteric Transcriptional Regulator. Journal of the American Chemical Society 143 (25) (2021)
Ryan L Hayes, Joshua Buckner, Charles L Brooks Iii
BLaDE: A Basic Lambda Dynamics Engine for GPU-Accelerated Molecular Dynamics Free Energy Calculations. Journal of chemical theory and computation 17 (11) (2021)
Charles L Brooks Iii, David A Case, Steve Plimpton, Benoı T Roux, David van der Spoel, Emad Tajkhorshid
Classical molecular dynamics. The Journal of chemical physics 154 (10) (2021)
Thomas J Paul, Jonah Z Vilseck, Ryan L Hayes, Charles L Brooks Iii
Exploring pH Dependent Host/Guest Binding Affinities. The journal of physical chemistry. B 124 (30) (2020)
Hedieh Torabifard, Afra Panahi, Charles L Brooks Iii
M2 amphipathic helices facilitate pH-dependent conformational transition in influenza A virus. Proceedings of the National Academy of Sciences of the United States of America 117 (7) (2020)
E Prabhu Raman, Thomas J Paul, Ryan L Hayes, Charles L Brooks Iii
Automated, Accurate, and Scalable Relative Protein-Ligand Binding Free-Energy Calculations Using Lambda Dynamics. Journal of chemical theory and computation 16 (12) (2020)
Xinqiang Ding, Yujin Wu, Yanming Wang, Jonah Z Vilseck, Charles L Brooks Iii
Accelerated CDOCKER with GPUs, Parallel Simulated Annealing, and Fast Fourier Transforms. Journal of chemical theory and computation 16 (6) (2020)
Yanming Wang, Charles L Brooks Iii
Electrostatic Forces Control the Negative Allosteric Regulation in a Disordered Protein Switch. The journal of physical chemistry letters 11 (3) (2020)
Minyu Xiao, Shuai Wei, Junjie Chen, Jiayi Tian, Charles L Brooks Iii, E Neil G Marsh, Zhan Chen
Molecular Mechanisms of Interactions between Monolayered Transition Metal Dichalcogenides and Biological Molecules. Journal of the American Chemical Society 141 (25) (2019)
Kevin T Halloran, Yanming Wang, Karunesh Arora, Srinivas Chakravarthy, Thomas C Irving, Osman Bilsel, Charles L Brooks Iii, C Robert Matthews
Frustration and folding of a TIM barrel protein. Proceedings of the National Academy of Sciences of the United States of America 116 (33) (2019)
Sara E Tweedy, Attabey Rodríguez Benítez, Alison R H Narayan, Paul M Zimmerman, Charles L Brooks Iii, Troy Wymore
Hydroxyl Radical-Coupled Electron-Transfer Mechanism of Flavin-Dependent Hydroxylases. The journal of physical chemistry. B 123 (38) (2019)
Xinqiang Ding, Zhengting Zou, Charles L Brooks Iii
Deciphering protein evolution and fitness landscapes with latent space models. Nature communications 10 (1) (2019)
Jonah Z Vilseck, Noor Sohail, Ryan L Hayes, Charles L Brooks Iii
Overcoming Challenging Substituent Perturbations with Multisite λ-Dynamics: A Case Study Targeting β-Secretase 1. The journal of physical chemistry letters 10 (17) (2019)
Hua Deng, Shan Ke, Robert Callender, Gurusamy Balakrishnan, Thomas G Spiro, Eric R May, Charles L Brooks Iii
Computational Studies of Catalytic Loop Dynamics in Yersinia Protein Tyrosine Phosphatase Using Pathway Optimization Methods. The journal of physical chemistry. B 123 (37) (2019)
Xinqiang Ding, Jonah Z Vilseck, Charles L Brooks Iii
Fast Solver for Large Scale Multistate Bennett Acceptance Ratio Equations. Journal of chemical theory and computation 15 (2) (2019)
Yanming Wang, Charles L Brooks Iii
Enhanced Sampling Applied to Modeling Allosteric Regulation in Transcription. The journal of physical chemistry letters 10 (19) (2019)
Jonah Z Vilseck, Kira A Armacost, Ryan L Hayes, Garrett B Goh, Charles L Brooks Iii
Predicting Binding Free Energies in a Large Combinatorial Chemical Space Using Multisite λ Dynamics. The journal of physical chemistry letters 9 (12) (2018)
Xingquan Zou, Shuai Wei, Somayesadat Badieyan, McKenna Schroeder, Joshua Jasensky, Charles L Brooks Iii, E Neil G Marsh, Zhan Chen
Investigating the Effect of Two-Point Surface Attachment on Enzyme Stability and Activity. Journal of the American Chemical Society 140 (48) (2018)
Xingquan Zou, Shuai Wei, Joshua Jasensky, Minyu Xiao, Qiuming Wang, Charles L Brooks Iii, Zhan Chen
Molecular Interactions between Graphene and Biological Molecules. Journal of the American Chemical Society 139 (5) (2017)
Min Su, Emily Z Guo, Xinqiang Ding, Yan Li, Jeffrey T Tarrasch, Charles L Brooks Iii, Zhaohui Xu, Georgios Skiniotis
Mechanism of Vps4 hexamer function revealed by cryo-EM. Science advances 3 (4) (2017)
Ryan L Hayes, Kira A Armacost, Jonah Z Vilseck, Charles L Brooks Iii
Adaptive Landscape Flattening Accelerates Sampling of Alchemical Space in Multisite λ Dynamics. The journal of physical chemistry. B 121 (15) (2017)
Minyu Xiao, Shuai Wei, Yaoxin Li, Joshua Jasensky, Junjie Chen, Charles L Brooks Iii, Zhan Chen
Molecular interactions between single layered MoS2 and biological molecules. Chemical science 9 (7) (2017)
Xinqiang Ding, Ryan L Hayes, Jonah Z Vilseck, Murchtricia K Charles, Charles L Brooks Iii
CDOCKER and λ-dynamics for prospective prediction in D₃R Grand Challenge 2. Journal of computer-aided molecular design 32 (1) (2017)
Xinqiang Ding, Jonah Z Vilseck, Ryan L Hayes, Charles L Brooks Iii
Gibbs Sampler-Based λ-Dynamics and Rao-Blackwell Estimator for Alchemical Free Energy Calculation. Journal of chemical theory and computation 13 (6) (2017)