C. Brooks

发表

Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy

J. Frank, F. Tama, M. Valle, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Computer simulation of liquids

C. Brooks, 1989 .

Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field.

C. Brooks, Jianhan Chen, W. Im, 2006, Journal of the American Chemical Society.

Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis.

F. Tama, C. Brooks, O. Miyashita, 2004, Journal of molecular biology.

Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory.

W. Wriggers, F. Tama, C. Brooks, 2002, Journal of molecular biology.

Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM.

F. Tama, C. Brooks, O. Miyashita, 2004, Journal of structural biology.

Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics

M. Karplus, C. Brooks, R. Austin, 1988 .

Determination of viral capsid elastic properties from equilibrium thermal fluctuations.

Eric R. May, C. Brooks, 2011, Physical review letters.

Refinement of NMR structures using implicit solvent and advanced sampling techniques.

C. Brooks, Jianhan Chen, W. Im, 2004, Journal of the American Chemical Society.

CHARMM: The Energy Function and Its Parameterization

Alexander D. MacKerell, M. Karplus, B. Brooks, 2002 .

Stochastic boundary conditions for molecular dynamics simulations of ST2 water

M. Karplus, C. Brooks, A. Brunger, 1984 .

Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism

C. Brooks, Huiqing Zhou, Garrett B. Goh, 2014, Proteins.

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

C. Brooks, A. Mapp, Amanda L. Peiffer, 2022, PLoS Comput. Biol..

Prepaying the entropic cost for allosteric regulation in KIX

Jessica K. Gagnon, C. Brooks, A. Mapp, 2014, Proceedings of the National Academy of Sciences.

pH-dependent dynamics of complex RNA macromolecules.

Jennifer L. Knight, C. Brooks, Garrett B. Goh, 2013, Journal of chemical theory and computation.

Protein-Protein Interfaces in Viral Capsids Are Structurally Unique.

C. Brooks, Shanshan Cheng, 2015, Journal of molecular biology.

Binding and folding of the small bacterial chaperone HdeA.

Alex Dickson, Logan S. Ahlstrom, Charles L. Brooks, 2013, The journal of physical chemistry. B.

Price To Be Paid for Two-Metal Catalysis: Magnesium Ions That Accelerate Chemistry Unavoidably Limit Product Release from a Protein Kinase

Douglas M. Jacobsen, Charles L. Brooks, D. M. Jacobsen, 2012, Journal of the American Chemical Society.

CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field

Alexander D. MacKerell, Justin A. Lemkul, Jeffery B. Klauda, 2015, Journal of chemical theory and computation.

Deciphering the kinetic mechanism of spontaneous self-assembly of icosahedral capsids.

C. Brooks, H. Nguyen, V. Reddy, 2007, Nano letters (Print).

Native states of fast-folding proteins are kinetic traps.

C. Brooks, A. Dickson, Alex Dickson, 2013, Journal of the American Chemical Society.

Capturing a Dynamic Chaperone-Substrate Interaction Using NMR-Informed Molecular Modeling.

Logan S. Ahlstrom, Loïc Salmon, C. Brooks, 2016, Journal of the American Chemical Society.

Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism

C. Brooks, K. Arora, 2007, Proceedings of the National Academy of Sciences.

Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations.

C. Brooks, W. Im, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Protein Dynamics in Enzymatic Catalysis: Exploration of Dihydrofolate Reductase

C. Brooks, Jennifer L. Radkiewicz and, 2000 .

Antibody evolution constrains conformational heterogeneity by tailoring protein dynamics

Ian F. Thorpe, S. Boxer, C. Brooks, 2006, Proceedings of the National Academy of Sciences.

Effects of Peptide Immobilization Sites on the Structure and Activity of Surface-Tethered Antimicrobial Peptides

C. Brooks, Shuai Wei, Q. Wang, 2015 .

Energetics of quasiequivalence: computational analysis of protein-protein interactions in icosahedral viruses.

V S Reddy, C. Brooks, C. Post, 1998, Biophysical journal.

Characterizing the protonation state of cytosine in transient G·C Hoogsteen base pairs in duplex DNA.

C. Brooks, H. Al‐Hashimi, Garrett B. Goh, 2013, Journal of the American Chemical Society.

Constant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit Solvent.

Jennifer L. Knight, C. Brooks, Garrett B. Goh, 2012, Journal of chemical theory and computation.

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

C. Brooks, H. Torabifard, Afra Panahi, 2020, Proceedings of the National Academy of Sciences.

Tilable nature of virus capsids and the role of topological constraints in natural capsid design.

Ranjan V. Mannige, C. Brooks, Charles L Brooks, 2008, Physical review. E, Statistical, nonlinear, and soft matter physics.

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

Jonah Z. Vilseck, C. Brooks, R. L. Hayes, 2017, Journal of chemical theory and computation.

3D maps of RNA interhelical junctions

C. Brooks, H. Al‐Hashimi, M. H. Bailor, 2011, Nature Protocols.

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

Jonah Z. Vilseck, Kira A Armacost, Ryan L Hayes, 2017, The journal of physical chemistry. B.

Exploring Protein-Nanoparticle Interactions with Coarse-Grained Protein Folding Models.

Logan S. Ahlstrom, C. Brooks, Shuai Wei, 2017, Small.

Developing improved MD codes for understanding processive cellulases

E. Uberbacher, M. Himmel, C. Brooks, 2008 .

Collective Variable Approaches for Single Molecule Flexible Fitting and Enhanced Sampling

C. Brooks, G. Skiniotis, H. Vashisth, 2014, Chemical reviews.

A Simple and Fast Approach for Predicting 1H and 13C Chemical Shifts: Toward Chemical Shift-Guided Simulations of RNA

C. Brooks, A. Frank, S. Law, 2014, The journal of physical chemistry. B.

Wenqin Wang Bacteria Chromosome Organization by a Nucleoid-Associated Protein in Live

Cherisse R. Loucks, C. Brooks, B. Strunk, 2011 .

Secondary structure encodes a cooperative tertiary folding funnel in the Azoarcus ribozyme

C. Brooks, H. Al‐Hashimi, A. M. Mustoe, 2015, Nucleic acids research.

Steric and thermodynamic limits of design for the incorporation of large unnatural amino acids in aminoacyl‐tRNA synthetase enzymes

C. Brooks, R. Armen, S. Schiller, 2010, Proteins.

A Synthetic Loop Replacement Peptide That Blocks Canonical NF-κB Signaling.

C. Brooks, A. Mapp, A. Morriss-Andrews, 2016, Angewandte Chemie.

Hexameric helicase deconstructed: interplay of conformational changes and substrate coupling.

Kenji Yoshimoto, Karunesh Arora, C. Brooks, 2010, Biophysical journal.

Ordering a dynamic protein via a small-molecule stabilizer.

Jessica K. Gagnon, Chinmay Y. Majmudar, C. Brooks, 2013, Journal of the American Chemical Society.

pH‐sensitive residues in the p19 RNA silencing suppressor protein from carnation Italian ringspot virus affect siRNA binding stability

C. Brooks, S. Law, Bin Zhang, 2013, Protein science : a publication of the Protein Society.

Mechanism of Vps 4 hexamer function revealed by cryo -

C. Brooks, G. Skiniotis, Zhaohui Xu, 2017 .

Multiscale modeling of a conditionally disordered pH-sensing chaperone.

Alex Dickson, Logan S. Ahlstrom, Logan S Ahlstrom, 2015, Journal of molecular biology.

Hamiltonian Mapping Revisited: Calibrating Minimalist Models to Capture Molecular Recognition by Intrinsically Disordered Proteins

Logan S. Ahlstrom, C. Brooks, S. Law, 2014, The journal of physical chemistry letters.

Frequent side chain methyl carbon‐oxygen hydrogen bonding in proteins revealed by computational and stereochemical analysis of neutron structures

C. Brooks, R. Trievel, S. Horowitz, 2015, Proteins.

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

C. Brooks, S. Badieyan, Shuai Wei, 2018, Journal of the American Chemical Society.

Regulation of calreticulin–major histocompatibility complex (MHC) class I interactions by ATP

Jessica K. Gagnon, Sanjeeva J. Wijeyesakere, C. Brooks, 2015, Proceedings of the National Academy of Sciences.

Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch

C. Brooks, H. Al‐Hashimi, N. Walter, 2011, Nucleic acids research.

Generalized structural polymorphism in self-assembled viral particles.

C. Brooks, H. Nguyen, 2008, Nano letters.

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

Jonah Z. Vilseck, C. Brooks, R. L. Hayes, 2018, The journal of physical chemistry letters.

HICOMB-01 Three-dimensional reconstruction of viruses: challenges and strategies (Invited Paper)

Charles L. Brooks, Alex Pothen, Michela Taufer, 2004 .

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

Thomas J. Paul, C. Brooks, R. L. Hayes, 2020, Journal of chemical theory and computation.

Stability and orientation of cecropin P1 on maleimide self-assembled monolayer (SAM) surfaces and suggested functional mutations

C. Brooks, Shuai Wei, 2015 .

Enhanced Sampling Applied to Modeling Allosteric Regulation in Transcription.

C. Brooks, Yanming Wang, 2019, The journal of physical chemistry letters.

Effect of immobilization site on the orientation and activity of surface-tethered enzymes.

C. Brooks, Shuai Wei, Zhan Chen, 2018, Physical chemistry chemical physics : PCCP.

Predicting Protein Backbone Chemical Shifts From Cα Coordinates: Extracting High Resolution Experimental Observables from Low Resolution Models

Logan S. Ahlstrom, C. Brooks, A. Frank, 2014, Journal of chemical theory and computation.

Sekikaic acid and lobaric acid target a dynamic interface of the coactivator CBP/p300.

Jessica K. Gagnon, Chinmay Y. Majmudar, C. Brooks, 2012, Angewandte Chemie.

Structural basis for selectivity in flavin-dependent monooxygenase-catalyzed oxidative dearomatization.

Attabey Rodríguez Benítez, Alison R. H. Narayan, C. Brooks, 2018, ACS catalysis.

The highly inducible member of the 70 kDa family of heat shock proteins increases canine distemper virus polymerase activity.

C. Brooks, Z. Liu, H. Kenney, 1996, The Journal of general virology.

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

Jonah Z. Vilseck, C. Brooks, R. L. Hayes, 2021, Journal of chemical theory and computation.

Community-wide assessment of GPCR structure modeling and docking understanding

R. Stevens, J. S. Dixon, J. Moult, 2009 .

New insights into the fundamental role of topological constraints as a determinant of two-way junction conformation

C. Brooks, H. Al‐Hashimi, M. H. Bailor, 2011, Nucleic acids research.

Unveiling Molecular Mechanisms of Biological Functions in Large Macromolecular Assemblies Using Elastic Network Normal Mode Analysis

F. Tama, C. Brooks, 2005 .

Biomolecular Hydration Dynamics Probed with 2D-IR Spectroscopy: From Dilute Solution to a Macromolecular Crowd

E. J. Arthur, C. Brooks, Derek G. Osborne, 2015 .

Hydrophobic hydration of globular proteins studied with 2D-IR spectroscopy

E. J. Arthur, C. Brooks, K. Kubarych, 2013 .

Covalent docking in CDOCKER

C. Brooks, Yujin Wu, 2022, Journal of Computer-Aided Molecular Design.

A molecular dynamics simulation study of segment B1 of protein G

C. Brooks, F. Sheinerman, 1997, Proteins.

Environmental effect on surface immobilized biological molecules.

C. Brooks, Zunliang Wang, N. He, 2014, The journal of physical chemistry. B.

Molecular structures of C- and N-terminus cysteine modified cecropin P1 chemically immobilized onto maleimide-terminated self-assembled monolayers investigated by molecular dynamics simulation.

C. Brooks, Zunliang Wang, N. He, 2014, The journal of physical chemistry. B.

On the mechanism of crystalline polymorph selection by polymer heteronuclei.

Jennifer L. Knight, A. Matzger, C. Brooks, 2011, Langmuir : the ACS journal of surfaces and colloids.

pH-dependent transient conformational states control optical properties in cyan fluorescent protein.

Alex Dickson, Charles L. Brooks, C. Brooks, 2015, Journal of the American Chemical Society.

Predicting extreme pKa shifts in staphylococcal nuclease mutants with constant pH molecular dynamics

E. J. Arthur, Evan J Arthur, C. Brooks, 2011, Proteins.

Coarse Grained Models Reveal Essential Contributions of Topological Constraints to the Conformational Free Energy of RNA Bulges

Hashim M. Al-Hashimi, Charles L. Brooks, C. Brooks, 2014, The journal of physical chemistry. B.

CHARMM: The biomolecular simulation program

Jianpeng Ma, Charles L. Brooks, Themis Lazaridis, 2009, J. Comput. Chem..

CHARMM‐GUI ligand reader and modeler for CHARMM force field generation of small molecules

Charles L. Brooks, Sunhwan Jo, Jumin Lee, 2017, J. Comput. Chem..

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

Alison R. H. Narayan, P. Zimmerman, C. Brooks, 2019, The journal of physical chemistry. B.

Interactions of the complete cellobiohydrolase I from Trichodera reesei with microcrystalline cellulose Iβ

M. Himmel, C. Brooks, J. Brady, 2008 .

Two-dimensional polyacrylamide gel electrophoresis of bovine semen after cryopreservation in half-milliliter straws.

C. Brooks, G. Frazer, D. Bucci, 1996, Theriogenology.

Towards Accurate Prediction of Protonation Equilibrium of Nucleic Acids.

Jennifer L. Knight, C. Brooks, Garrett B. Goh, 2013, The journal of physical chemistry letters.

Flipping of the ribosomal A-site adenines provides a basis for tRNA selection.

C. Brooks, H. Al‐Hashimi, Anette Casiano-Negroni, 2014, Journal of molecular biology.

Structure of the E. coli protein-conducting channel bound to a translating ribosome

Florence Tama, Joachim Frank, Christiane Schaffitzel, 2005, Nature.

Multi-Site λ-dynamics for simulated Structure-Activity Relationship studies.

Jennifer L. Knight, C. Brooks, Charles L Brooks, 2011, Journal of chemical theory and computation.

A Universal Trend among Proteomes Indicates an Oily Last Common Ancestor

Charles L. Brooks, Eugene I. Shakhnovich, Ranjan V. Mannige, 2012, PLoS Comput. Biol..

Efficient in silico exploration of RNA interhelical conformations using Euler angles and WExplore

Loïc Salmon, C. Brooks, A. Dickson, 2014, Nucleic acids research.

TMPRSS2 inhibitor discovery facilitated through an in silico and biochemical screening platform

C. Brooks, A. Mapp, Amanda L. Peiffer, 2021, bioRxiv.

Ribosome Assembly Factors Prevent Premature Translation Initiation by 40S Assembly Intermediates

Cherisse R. Loucks, C. Brooks, G. Skiniotis, 2011, Science.

Crowding induced collective hydration of biological macromolecules over extended distances.

E. J. Arthur, C. Brooks, K. Kubarych, 2014, Journal of the American Chemical Society.

VIPERdb2: an enhanced and web API enabled relational database for structural virology

Mauricio Carrillo-Tripp, Craig M. Shepherd, Ian A. Borelli, 2008, Nucleic Acids Res..

Viral Capsid Proteins Are Segregated in Structural Fold Space

Charles L. Brooks, Shanshan Cheng, C. Brooks, 2013, PLoS Comput. Biol..

Mechanism of Vps4 hexamer function revealed by cryo-EM

Yan Li, Xinqiang Ding, Georgios Skiniotis, 2017, Science Advances.

A Mechanism for Evolving Novel Plant Sesquiterpene Synthase Function

Troy Wymore, Hugh B Nicholas, Alexander J Ropelewski, 2011, Molecular informatics.

Structure of the E. coli protein-conducting channel bound to a translating ribosome

J. Frank, F. Tama, C. Brooks, 2006, Nature.

VIPERdb v3.0: a structure-based data analytics platform for viral capsids

Mauricio Carrillo-Tripp, John E. Johnson, Charles L. Brooks, 2020, Nucleic Acids Res..

A Synthetic Loop Replacement Peptide That Blocks Canonical NF-κB Signaling.

C. Brooks, A. Mapp, A. Morriss-Andrews, 2016, Angewandte Chemie.

Ligand Modulates Cross-Coupling between Riboswitch Folding and Transcriptional Pausing

C. Brooks, R. L. Hayes, N. Walter, 2018, bioRxiv.

Ligand Modulates Cross-Coupling between Riboswitch Folding and Transcriptional Pausing

C. Brooks, R. L. Hayes, N. Walter, 2018, bioRxiv.

Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure

J. Wedekind, C. Brooks, H. Al‐Hashimi, 2013, Nucleic acids research.

Cooperative and directional folding of the preQ1 riboswitch aptamer domain.

Jun Feng, Nils G Walter, C. Brooks, 2011, Journal of the American Chemical Society.

Invariant polymorphism in virus capsid assembly.

Vijay S Reddy, C. Brooks, H. Nguyen, 2009, Journal of the American Chemical Society.

VIPERdb: a relational database for structural virology

Chandrajit L. Bajaj, Craig M. Shepherd, Ian A. Borelli, 2005, Nucleic Acids Res..

Hierarchy of RNA functional dynamics.

C. Brooks, H. Al‐Hashimi, Charles L Brooks, 2014, Annual review of biochemistry.

Visualizing chaperone-assisted protein folding

Logan S. Ahlstrom, H. V. D. Bedem, Loïc Salmon, 2016 .

From Molecular Phylogenetics to Quantum Chemistry: Discovering Enzyme Design Principles through Computation

Charles L. Brooks, Troy Wymore, C. Brooks, 2012, Computational and Structural Biotechnology Journal.

Molecular evolution of affinity and flexibility in the immune system

Ian F. Thorpe, C. Brooks, I. Thorpe, 2007, Proceedings of the National Academy of Sciences.

Parametrization of halogen bonds in the CHARMM general force field: Improved treatment of ligand-protein interactions.

Justin A. Lemkul, Fang-Yu Lin, Kenno Vanommeslaeghe, 2016, Bioorganic & medicinal chemistry.

Chromosome Organization by a Nucleoid-Associated Protein in Live Bacteria

Harish Vashisth, Cherisse R. Loucks, Min Su, 2013 .

An essential sensor histidine kinase controlled by transmembrane helix interactions with its auxiliary proteins

H. Szurmant, J. Hoch, C. Brooks, 2008, Proceedings of the National Academy of Sciences.

Topological constraints are major determinants of tRNA tertiary structure and dynamics and provide basis for tertiary folding cooperativity

Hashim M. Al-Hashimi, Charles L. Brooks, C. Brooks, 2014, Nucleic acids research.

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

Eric R. May, C. Brooks, R. Callender, 2019, The journal of physical chemistry. B.

Multiple intermediates, diverse conformations, and cooperative conformational changes underlie the catalytic hydride transfer reaction of dihydrofolate reductase.

C. Brooks, K. Arora, 2013, Topics in current chemistry.

Conformational dynamics in human purine nucleoside phosphorylase with reactants and transition-state analogues.

Karunesh Arora, V. Schramm, C. Brooks, 2010, The journal of physical chemistry. B.

Chaperone activation by unfolding

C. Brooks, J. Bardwell, Linda Foit, 2013, Proceedings of the National Academy of Sciences.

Norstictic acid is a selective allosteric transcriptional regulator

S. Merajver, C. Brooks, A. Mapp, 2021, bioRxiv.

Molecular Mechanism for Isoform-Selective Inhibition of Acyl Protein Thioesterases 1 and 2 (APT1 and APT2).

Brent R. Martin, C. Brooks, J. Stuckey, 2016, ACS chemical biology.

Probing pH-dependent dissociation of HdeA dimers.

Lucia Brunetti, C. Brooks, Charles L Brooks, 2011, Journal of the American Chemical Society.

Growth-incompetent monomers of human calcitonin lead to a noncanonical direct relationship between peptide concentration and aggregation lag time

C. Brooks, A. Naito, A. Ramamoorthy, 2017, The Journal of Biological Chemistry.

Frustration and folding of a TIM barrel protein

C. Brooks, T. Irving, C. Matthews, 2019, Proceedings of the National Academy of Sciences.

Flexible CDOCKER: Development and application of a pseudo‐explicit structure‐based docking method within CHARMM

Charles L. Brooks, Sean M. Law, Jessica K. Gagnon, 2014, J. Comput. Chem..

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

C. Brooks, P. Langan, A. Kovalevsky, 2021, ACS catalysis.

Barriers to Hydride Transfer in Wild Type and Mutant Dihydrofolate Reductase from E. coli

C. Brooks, I. Thorpe, 2003 .

Quantifying Chaperone-Mediated Transitions in the Proteostasis Network of E. coli

Charles L. Brooks, Alex Dickson, C. Brooks, 2013, PLoS Comput. Biol..

Multiscale Modeling of Virus Structure, Assembly, and Dynamics

Ranjan V. Mannige, Eric R. May, C. Brooks, 2012 .

Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids

Joanna Trylska, Nathan A. Baker, Florence Tama, 2006, Biopolymers.

Exploring icosahedral virus structures with VIPER

John E. Johnson, C. Brooks, G. Lander, 2005, Nature Reviews Microbiology.

Flexible CDOCKER: Hybrid Searching Algorithm and Scoring Function with Side Chain Conformational Entropy

C. Brooks, Yu-jie Wu, 2021, J. Chem. Inf. Model..

Modeling pH-Dependent NMR Chemical Shift Perturbations in Peptides.

C. Brooks, E. Artikis, 2019, Biophysical journal.

Conformational dynamics of a regulator of G-protein signaling protein reveals a mechanism of allosteric inhibition by a small molecule.

R. Neubig, C. Brooks, H. Vashisth, 2013, ACS chemical biology.

Different interfacial behaviors of peptides chemically immobilized on surfaces with different linker lengths and via different termini.

C. Brooks, Zunliang Wang, Fulin Wu, 2014, The journal of physical chemistry. B.

Probing Site-Specific Structural Information of Peptides at Model Membrane Interface In Situ.

Jennifer E. Laaser, C. Brooks, M. Zanni, 2015, Journal of the American Chemical Society.

Removal of Divalent Cations Induces Structural Transitions in Red Clover Necrotic Mosaic Virus, Revealing a Potential Mechanism for RNA Release

F. Tama, C. Brooks, E. Orlova, 2006, Journal of Virology.

Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008

Charles L. Brooks, Adrian W. R. Serohijos, John Moult, 2009, Nature Reviews Drug Discovery.

Parallelization and improvements of the generalized born model with a simple sWitching function for modern graphics processors

Charles L. Brooks, Evan J. Arthur, E. J. Arthur, 2016, J. Comput. Chem..

Surveying implicit solvent models for estimating small molecule absolute hydration free energies

Charles L. Brooks, Jennifer L. Knight, C. Brooks, 2011, J. Comput. Chem..

Developing improved MD codes for understanding processive cellulases

E. Uberbacher, M. Himmel, C. Brooks, 2008 .

Optimizing Multisite λ-Dynamics Throughput with Charge Renormalization

Jonah Z. Vilseck, C. Brooks, R. L. Hayes, 2022, J. Chem. Inf. Model..

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

C. Brooks, R. L. Hayes, Josh Buckner, 2021, Journal of chemical theory and computation.

Accelerated CDOCKER with GPUs, parallel simulated annealing and fast Fourier transforms.

Jonah Z. Vilseck, C. Brooks, Xinqiang Ding, 2020, Journal of chemical theory and computation.

Fast Solver for Large Scale Multistate Bennett Acceptance Ratio Equations.

Jonah Z. Vilseck, C. Brooks, Xinqiang Ding, 2019, Journal of chemical theory and computation.

WExplore: hierarchical exploration of high-dimensional spaces using the weighted ensemble algorithm.

Alex Dickson, Charles L Brooks, C. Brooks, 2014, The journal of physical chemistry. B.

Harmonic Fourier beads method for studying rare events on rugged energy surfaces.

Karunesh Arora, C. Brooks, K. Arora, 2006, The Journal of chemical physics.

PCalign: a method to quantify physicochemical similarity of protein-protein interfaces

Yang Zhang, Charles L. Brooks, Shanshan Cheng, 2015, BMC Bioinformatics.

Coupled folding and binding with 2D Window‐Exchange Umbrella Sampling

Charles L. Brooks, Alex Dickson, Logan S. Ahlstrom, 2016, J. Comput. Chem..

QSAR via multisite λ‐dynamics in the orphaned TSSK1B kinase

C. Brooks, Xiaorong Liu, M. Soellner, 2023, Protein science : a publication of the Protein Society.

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

Jonah Z. Vilseck, C. Brooks, R. L. Hayes, 2019, The journal of physical chemistry letters.

λ‐Dynamics free energy simulation methods

Charles L. Brooks, Jennifer L. Knight, C. Brooks, 2009, J. Comput. Chem..

Periodic Table of Virus Capsids: Implications for Natural Selection and Design

Ranjan V. Mannige, Charles L. Brooks, C. Brooks, 2010, PloS one.

Mechanics of bacteriophage maturation

John E. Johnson, Gijs J. L. Wuite, Eric R. May, 2012, Proceedings of the National Academy of Sciences.

Heterogeneous Preferential Solvation of Water and Trifluoroethanol in Homologous Lysozymes

E. J. Arthur, C. Brooks, K. Kubarych, 2014, The journal of physical chemistry. B.

Site-specific hydration dynamics of globular proteins and the role of constrained water in solvent exchange with amphiphilic cosolvents.

E. J. Arthur, C. Brooks, K. Kubarych, 2012, The journal of physical chemistry. B.

Using enhanced sampling and structural restraints to refine atomic structures into low-resolution electron microscopy maps.

Georgios Skiniotis, Harish Vashisth, C. Brooks, 2012, Structure.

Applying efficient implicit nongeometric constraints in alchemical free energy simulations

Charles L. Brooks, Jennifer L. Knight, C. Brooks, 2011, J. Comput. Chem..

Computational simulations of the Trichoderma reesei cellobiohydrolase I acting on microcrystalline cellulose Ibeta: the enzyme-substrate complex.

Ross C Walker, Michael E Himmel, Michael F Crowley, 2009, Carbohydrate research.

Interfacial Behaviors of Antimicrobial Peptide Cecropin P1 Immobilized on Different Self-Assembled Monolayers

C. Brooks, Qiuming Wang, Shuai Wei, 2015 .

Enhanced sampling and overfitting analyses in structural refinement of nucleic acids into electron microscopy maps.

Georgios Skiniotis, Harish Vashisth, C. Brooks, 2013, The journal of physical chemistry. B.

Geometric considerations in virus capsid size specificity, auxiliary requirements, and buckling

Ranjan V. Mannige, C. Brooks, Charles L Brooks, 2009, Proceedings of the National Academy of Sciences.

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

Ryan L. Hayes, Charles L. Brooks, C. Brooks, 2021, J. Comput. Chem..

PCASSO: A fast and efficient Cα‐based method for accurately assigning protein secondary structure elements

Charles L. Brooks, Aaron T. Frank, Sean M. Law, 2014, J. Comput. Chem..

Quantifying hub-like behavior in protein folding networks.

Alex Dickson, Charles L Brooks, C. Brooks, 2012, Journal of chemical theory and computation.

Topological constraints: using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation.

C. Brooks, H. Al‐Hashimi, M. H. Bailor, 2011, Current opinion in structural biology.

Efficient implementation of constant pH molecular dynamics on modern graphics processors

Charles L. Brooks, Evan J. Arthur, E. J. Arthur, 2016, J. Comput. Chem..

Assessing the quality of absolute hydration free energies among CHARMM‐compatible ligand parameterization schemes

Charles L. Brooks, Jennifer L. Knight, Joseph D. Yesselman, 2013, J. Comput. Chem..

Accurate modeling of ionic surfactants at high concentration.

David M. Eike, C. Brooks, Garrett B. Goh, 2015, The journal of physical chemistry. B.

Selective complexation of K+ and Na+ in simple polarizable ion-ligating systems.

C. Brooks, C. Brooks, D. Bostick, 2010, Journal of the American Chemical Society.

On the morphology of viral capsids: elastic properties and buckling transitions.

Eric R. May, C. Brooks, Charles L Brooks, 2012, The journal of physical chemistry. B.

Viral capsid equilibrium dynamics reveals nonuniform elastic properties.

Ankush Aggarwal, William S Klug, Eric R. May, 2011, Biophysical journal.

Orientation Determination of a Hybrid Peptide Immobilized on CVD-Based Reactive Polymer Surfaces

J. Lahann, C. Brooks, Qiuming Wang, 2016 .

Developing improved MD and QMMM codes for modeling enzymes essential to biomass liquid fuel production

C. Brooks, E. Knoll, M. Crowley, 2011 .

K+/Na+ selectivity in toy cation binding site models is determined by the 'host'.

C. Brooks, K. Arora, D. Bostick, 2009, Biophysical journal.

Noncanonical secondary structure stabilizes mitochondrial tRNA(Ser(UCN)) by reducing the entropic cost of tertiary folding.

C. Brooks, H. Al‐Hashimi, C. Fierke, 2015, Journal of the American Chemical Society.

Application of solid-state NMR restraint potentials in membrane protein modeling.

Wonpil Im, Jianhan Chen, Jinhyuk Lee, 2008, Journal of magnetic resonance.

Uncovering pH-Dependent Transient States of Proteins with Buried Ionizable Residues

C. Brooks, Garrett B. Goh, E. Laricheva, 2014, Journal of the American Chemical Society.

Molecular description of flexibility in an antibody combining site.

Floyd E Romesberg, C. Brooks, I. Thorpe, 2010, The journal of physical chemistry. B.

The 13 angstroms structure of a chaperonin GroEL-protein substrate complex by cryo-electron microscopy.

Florence Tama, F. Tama, C. Brooks, 2005, Journal of molecular biology.

Alchemical Free Energy Methods Applied to Complexes of the First Bromodomain of BRD4

C. Brooks, S. Pickett, J. Hirst, 2022, J. Chem. Inf. Model..

Positioning-Group-Enabled Biocatalytic Oxidative Dearomatization

Alison R. H. Narayan, C. Brooks, T. Wymore, 2019, ACS central science.

Conformational Sampling of Maltose-transporter Components in Cartesian Collective Variables is Governed by the Low-frequency Normal Modes.

C. Brooks, H. Vashisth, C L Brooks, 2012, The journal of physical chemistry letters.

Conservation of coactivator engagement mechanism enables small-molecule allosteric modulators

C. Brooks, C. Fierke, T. Cierpicki, 2018, Proceedings of the National Academy of Sciences.

Nonuniform elastic properties of macromolecules and effect of prestrain on their continuum nature.

Eric R. May, C. Brooks, A. Aggarwal, 2016, Physical review. E.

Guiding Discovery of Protein Sequence-Structure-Function Modeling

C. Brooks, Azam Hussain, 2023, bioRxiv.

VIPERdb: A Tool for Virus Research.

John E. Johnson, C. Brooks, V. Reddy, 2018, Annual Review of Virology.

Deciphering the evolution of flavin-dependent monooxygenase stereoselectivity using ancestral sequence reconstruction.

Alison R. H. Narayan, C. Brooks, Janet L. Smith, 2023, Proceedings of the National Academy of Sciences of the United States of America.

Molecular-Level Insights into Orientation-Dependent Changes in the Thermal Stability of Enzymes Covalently Immobilized on Surfaces.

C. Brooks, Shuai Wei, Tadeusz L. Ogorzalek, 2015, Langmuir : the ACS journal of surfaces and colloids.

CDOCKER and $$\lambda$$λ-dynamics for prospective prediction in D3R Grand Challenge 2

Charles L. Brooks, Xinqiang Ding, Ryan L. Hayes, 2018, J. Comput. Aided Mol. Des..

Modulation of frustration in folding by sequence permutation

C. Brooks, T. Irving, C. Matthews, 2014, Proceedings of the National Academy of Sciences.

Exploring pH Dependent Host/Guest Binding Affinities.

Jonah Z. Vilseck, Thomas J. Paul, C. Brooks, 2020, The journal of physical chemistry. B.

Enhanced Sampling Assisted Flexible Fitting of Atomic Structures into Electron Microscopy Maps

C. Brooks, Harish Vashisth, 2013 .

Chromosome Organization by a Nucleoid-Associated Protein in Live Bacteria

Cherisse R. Loucks, Gene-Wei Li, Xiaowei Zhuang, 2011, Science.

Coupled folding and binding with 2D Window‐Exchange Umbrella Sampling

Logan S. Ahlstrom, C. Brooks, A. Dickson, 2016, J. Comput. Chem..

Statistical clustering techniques for the analysis of long molecular dynamics trajectories: analysis of 2.2-ns trajectories of YPGDV.

C. Brooks, C. Brooks, M. E. Karpen, 1993, Biochemistry.

Flexible CDOCKER: Development and application of a pseudo‐explicit structure‐based docking method within CHARMM

Jessica K. Gagnon, C. Brooks, S. Law, 2014, J. Comput. Chem..

pH-Induced Stability Switching of the Bacteriophage HK97 Maturation Pathway

Eric R. May, C. Brooks, K. Arora, 2014, Journal of the American Chemical Society.

Exploring the symmetry and mechanism of virus capsid maturation via an ensemble of pathways.

Jun Feng, Eric R. May, C. Brooks, 2012, Biophysical journal.

λ‐Dynamics free energy simulation methods

Jennifer L. Knight, C. Brooks, 2009, J. Comput. Chem..

Deconstructing activation events in rhodopsin.

Jennifer L. Knight, C. Brooks, K. Arora, 2013, Journal of the American Chemical Society.

A rapid solvent accessible surface area estimator for coarse grained molecular simulations

Charles L. Brooks, Shuai Wei, Aaron T. Frank, 2017, J. Comput. Chem..

Residue-level resolution of alphavirus envelope protein interactions in pH-dependent fusion

C. Brooks, S. Mukhopadhyay, Xiancheng Zeng, 2015, Proceedings of the National Academy of Sciences.

Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism

C. Brooks, Huiqing Zhou, Garrett B. Goh, 2014, Proteins.

VIRUS PARTICLE EXPLORER (VIPER): A REPOSITORY OF VIRUS CAPSID STRUCTURES

John E. Johnson, Chunxu Qu, C. Brooks, 2004 .

De novo prediction of the structures of M. tuberculosis membrane proteins.

C. Brooks, L. Bu, 2008, Journal of the American Chemical Society.

Sekikaic acid and lobaric acid target a dynamic interface of the coactivator CBP/p300.

Jessica K. Gagnon, Chinmay Y. Majmudar, C. Brooks, 2012, Angewandte Chemie.

Protein-Protein Interfaces in Viral Capsids Are Structurally Unique.

C. Brooks, Shanshan Cheng, 2015, Journal of molecular biology.

Characterizing the protonation state of cytosine in transient G·C Hoogsteen base pairs in duplex DNA.

C. Brooks, H. Al‐Hashimi, Garrett B. Goh, 2013, Journal of the American Chemical Society.

Conformational substates modulate hydride transfer in dihydrofolate reductase.

Ian F. Thorpe, C. Brooks, 2005, Journal of the American Chemical Society.

Application of solid-state NMR restraint potentials in membrane protein modeling.

C. Brooks, Jianhan Chen, W. Im, 2008, Journal of magnetic resonance.

Molecular interactions between single layered MoS2 and biological molecules† †Electronic supplementary information (ESI) available: SFG data analysis methods, spectral fitting parameters, additional spectra, CD spectrum, and details about MD simulation methods. See DOI: 10.1039/c7sc04884j

C. Brooks, Shuai Wei, Junjie Chen, 2017, Chemical science.

CapsidMaps: protein-protein interaction pattern discovery platform for the structural analysis of virus capsids using Google Maps.

C. Brooks, V. Reddy, M. Carrillo-Tripp, 2015, Journal of structural biology.

Modulation of frustration in folding by sequence permutation

C. Brooks, T. Irving, C. Matthews, 2014, Proceedings of the National Academy of Sciences.