C. Brooks

Most-cited papers

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field
Ju-Min Lee, Xi Cheng, Jason M. Swails, M. S. Yeom +13 more
2015Journal of Chemical Theory and Computation4,188 citations Open access
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CHARMM-GUI Ligand Reader & Modeler for CHARMM Force Field Generation of Small Molecules
Seonghoon Kim, Ju-Min Lee, Sunhwan Jo, C. Brooks +2 more
2017Journal of Computational Chemistry602 citations Open access
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Parametrization of Halogen Bonds in the CHARMM General Force Field: Improved treatment of ligand-protein interactions
Ignacio Soteras Gutiérrez, Fang-Yu Lin, K. Vanommeslaeghe, Justin A. Lemkul +3 more
2016Bioorganic & Medicinal Chemistry257 citations Open access
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Hierarchy of RNA Functional Dynamics
Anthony M. Mustoe, C. Brooks, H. Al-Hashimi
2014Annual Review of Biochemistry187 citations Open access
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Flexible CDOCKER: Development and application of a pseudo-explicit structure-based docking method within CHARMM
Jessica K. Gagnon, S. Law, C. Brooks
2014Journal of Computational Chemistry127 citations Open access
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WExplore: Hierarchical Exploration of High-Dimensional Spaces Using the Weighted Ensemble Algorithm
Alex Dickson, C. Brooks
2014Journal of Physical Chemistry B101 citations Open access
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Molecular mechanism for isoform-selective inhibition of acyl protein thioesterases 1 and 2 (APT1 and APT2)
S. J. Won, Dahvid Davda, Kristin J Labby, Sin Ye Hwang +13 more
2016ACS Chemical Biology100 citations Open access
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Molecular Interactions between Graphene and Biological Molecules.
Xingquan Zou, Shuai Wei, J. Jasensky, Minyu Xiao +3 more
2017Journal of the American Chemical Society96 citations
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Adaptive Landscape Flattening Accelerates Sampling of Alchemical Space in Multisite λ Dynamics
Ryan L. Hayes, K. Armacost, Jonah Z. Vilseck, C. Brooks
2017Journal of Physical Chemistry B75 citations Open access
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Automated, Accurate, and Scalable Relative Protein-Ligand Binding Free Energy Calculations using Lambda Dynamics
E. P. Raman, Thomas J. Paul, Ryan L. Hayes, C. Brooks
2020Journal of Chemical Theory and Computation70 citations Open access
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VIPERdb v3.0: a structure-based data analytics platform for viral capsids
Daniel Montiel-Garcia, Nelly Santoyo-Rivera, Phuong-Thao Ho, M. Carrillo-Tripp +3 more
2020Nucleic Acids Res.64 citations Open access
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Investigating the Effect of Two-Point Surface Attachment on Enzyme Stability and Activity.
Xingquan Zou, Shuai Wei, S. Badieyan, MC Schroeder +4 more
2018Journal of the American Chemical Society64 citations
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Ligand Modulates Cross-Coupling between Riboswitch Folding and Transcriptional Pausing
J. Widom, Y. Nedialkov, Victoria Rai, Ryan L. Hayes +3 more
2018bioRxiv63 citations Open access
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Prepaying the entropic cost for allosteric regulation in KIX
S. Law, Jessica K. Gagnon, A. Mapp, C. Brooks
2014Proceedings of the National Academy of Sciences of the United States of America62 citations Open access
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Mechanism of Vps4 hexamer function revealed by cryo-EM
Min Su, E. Guo, Xinqiang Ding, Yan Li +4 more
2017Science Advances60 citations Open access
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Probing Site-Specific Structural Information of Peptides at Model Membrane Interface In Situ
Bei Ding, Afra Panahi, J. Ho, J. Laaser +3 more
2015Journal of the American Chemical Society60 citations Open access
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Effects of Peptide Immobilization Sites on the Structure and Activity of Surface-Tethered Antimicrobial Peptides
Yaoxin Li, Shuai Wei, Jian-Feng Wu, J. Jasensky +7 more
201555 citations
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Coarse Grained Models Reveal Essential Contributions of Topological Constraints to the Conformational Free Energy of RNA Bulges
Anthony M. Mustoe, H. Al-Hashimi, C. Brooks
2014Journal of Physical Chemistry B55 citations Open access
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A Fast Solver for Large Scale Multistate Bennett Acceptance Ratio Equations
Xinqiang Ding, Jonah Z. Vilseck, C. Brooks
2019Journal of Chemical Theory and Computation53 citations Open access
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Accelerated CDOCKER with GPUs, parallel simulated annealing and fast Fourier transforms
Xinqiang Ding, Yujin Wu, Yanming Wang, Jonah Z. Vilseck +1 more
2020Journal of Chemical Theory and Computation51 citations Open access
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Different interfacial behaviors of peptides chemically immobilized on surfaces with different linker lengths and via different termini.
Xiaofeng Han, Yu-Wei Liu, Fu-Lin Wu, Joshua Jansensky +7 more
2014Journal of Physical Chemistry B49 citations
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Molecular Mechanisms of Interactions between Monolayered Transition Metal Dichalcogenides and Biological Molecules.
Minyu Xiao, Shuai Wei, Junjie Chen, Jiayi Tian +3 more
2019Journal of the American Chemical Society45 citations
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BLaDE: A Basic Lambda Dynamics Engine for GPU Accelerated Molecular Dynamics Free Energy Calculations
Ryan L. Hayes, Josh Buckner, C. Brooks
2021Journal of Chemical Theory and Computation44 citations Open access
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Molecular-Level Insights into Orientation-Dependent Changes in the Thermal Stability of Enzymes Covalently Immobilized on Surfaces.
Tadeusz L. Ogorzalek, Shuai Wei, Yu-Wei Liu, Quiming Wang +3 more
2015Langmuir44 citations
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Predicting Binding Free Energies in a Large Combinatorial Chemical Space Using Multisite λ Dynamics
Jonah Z. Vilseck, K. Armacost, Ryan L. Hayes, Garrett B. Goh +1 more
2018Journal of Physical Chemistry Letters41 citations Open access
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Flipping of the ribosomal A-site adenines provides a basis for tRNA selection
Xiancheng Zeng, J. Chugh, Anette Casiano-Negroni, H. Al-Hashimi +1 more
2014Journal of Molecular Biology40 citations Open access
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Uncovering pH-Dependent Transient States of Proteins with Buried Ionizable Residues
Garrett B. Goh, E. Laricheva, C. Brooks
2014Journal of the American Chemical Society39 citations Open access
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VIPERdb: A Tool for Virus Research.
Phuong-Thao Ho, Daniel Montiel-Garcia, Jonathan Wong, M. Carrillo-Tripp +3 more
2018Annual Review of Virology37 citations
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Visualizing chaperone-assisted protein folding
S. Horowitz, Loïc Salmon, P. Koldewey, Logan S. Ahlstrom +9 more
201637 citations
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Effect of immobilization site on the orientation and activity of surface-tethered enzymes.
Yaoxin Li, Tadeusz L. Ogorzalek, Shuai Wei, Xiao-Xian Zhang +5 more
2018Physical Chemistry, Chemical Physics - PCCP35 citations Open access
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Gibbs Sampler Based λ-Dynamics and Rao-Blackwell Estimator for Alchemical Free Energy Calculation
Xinqiang Ding, Jonah Z. Vilseck, Ryan L. Hayes, C. Brooks
2017Journal of Chemical Theory and Computation35 citations Open access
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Residue-level resolution of alphavirus envelope protein interactions in pH-dependent fusion
Xian-Cheng Zeng, S. Mukhopadhyay, C. Brooks
2015Proceedings of the National Academy of Sciences of the United States of America32 citations Open access
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A Simple and Fast Approach for Predicting 1H and 13C Chemical Shifts: Toward Chemical Shift-Guided Simulations of RNA
A. Frank, S. Law, C. Brooks
2014Journal of Physical Chemistry B29 citations Open access
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Covalent Docking in CDOCKER
Yujin Wu, C. Brooks
2022Journal of Computer-Aided Molecular Design28 citations Open access
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Multiscale Modeling of a Conditionally Disordered pH-Sensing Chaperone
Logan S. Ahlstrom, S. Law, Alex Dickson, C. Brooks
2015Journal of Molecular Biology28 citations Open access
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Flexible CDOCKER: Hybrid Searching Algorithm and Scoring Function with Side Chain Conformational Entropy
Yu-jie Wu, C. Brooks
2021Journal of Chemical Information and Modeling27 citations Open access
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Overcoming Challenging Substituent Perturbations with Multisite λ-Dynamics: A Case Study Targeting β-Secretase 1
Jonah Z. Vilseck, Noor Sohail, Ryan L. Hayes, C. Brooks
2019Journal of Physical Chemistry Letters26 citations Open access
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Conservation of coactivator engagement mechanism enables small-molecule allosteric modulators
Andrew R. Henderson, Matthew J. Henley, N. J. Foster, Amanda L. Peiffer +10 more
2018Proceedings of the National Academy of Sciences of the United States of America26 citations Open access
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Exploring protein-nanoparticle interactions with coarse-grained protein folding models
Shuai Wei, Logan S. Ahlstrom, C. Brooks
2017Small26 citations Open access
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Capturing a Dynamic Chaperone–Substrate Interaction Using NMR-Informed Molecular Modeling
Loïc Salmon, Logan S. Ahlstrom, S. Horowitz, Alex Dickson +2 more
2016Journal of the American Chemical Society26 citations Open access
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Coupled folding and binding with 2D Window-Exchange Umbrella Sampling
Alex Dickson, Logan S. Ahlstrom, C. Brooks
2015Journal of Computational Chemistry26 citations Open access
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Deciphering the evolution of flavin-dependent monooxygenase stereoselectivity using ancestral sequence reconstruction
Chang-Hwa Chiang, T. Wymore, Attabey Rodríguez Benítez, Azam Hussain +3 more
2023Proceedings of the National Academy of Sciences of the United States of America25 citations Open access
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A rapid solvent accessible surface area estimator for coarse grained molecular simulations
Shuai Wei, C. Brooks, A. Frank
2017Journal of Computational Chemistry24 citations Open access
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Modulation of frustration in folding by sequence permutation
R. P. Nobrega, K. Arora, Sagar V. Kathuria, R. Graceffa +7 more
2014Proceedings of the National Academy of Sciences of the United States of America24 citations Open access
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PCASSO: A Fast and Efficient Cα-based Method for Accurately Assigning Protein Secondary Structure Elements
S. Law, A. Frank, C. Brooks
2014Journal of Computational Chemistry24 citations Open access
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A Strategy for Proline and Glycine Mutations to Proteins with Alchemical Free Energy Calculations
Ryan L. Hayes, C. Brooks
2021Journal of Computational Chemistry23 citations Open access
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Topological constraints are major determinants of tRNA tertiary structure and dynamics and provide basis for tertiary folding cooperativity
Anthony M. Mustoe, C. Brooks, H. Al-Hashimi
2014Nucleic Acids Research23 citations Open access
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Frustration and folding of a TIM barrel protein
Kevin T. Halloran, Yanming Wang, K. Arora, S. Chakravarthy +4 more
2019Proceedings of the National Academy of Sciences of the United States of America22 citations Open access
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Interfacial Behaviors of Antimicrobial Peptide Cecropin P1 Immobilized on Different Self-Assembled Monolayers
Qiu-Ming Wang, Shuai Wei, Jian-Feng Wu, Xingquan Zou +5 more
201522 citations
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Efficient in silico exploration of RNA interhelical conformations using Euler angles and WExplore
Alex Dickson, Anthony M. Mustoe, Loïc Salmon, C. Brooks
2014Nucleic Acids Research22 citations Open access
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