B. Brooks

发表

CHARMM: A program for macromolecular energy, minimization, and dynamics calculations

M. Karplus, B. Brooks, R. Bruccoleri, 1983 .

Self-guided Langevin dynamics simulation method

B. Brooks, Xiongwu Wu, 2003 .

Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor.

M. Karplus, B. Brooks, 1983, Proceedings of the National Academy of Sciences of the United States of America.

Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations.

D. Thirumalai, B. Brooks, Wenjun Zheng, 2007, Biophysical journal.

Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme.

M. Karplus, B. Brooks, 1985, Proceedings of the National Academy of Sciences of the United States of America.

CHARMM: The Energy Function and Its Parameterization

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

The effects of truncating long‐range forces on protein dynamics

B. Brooks, R. Loncharich, 1989, Proteins.

Constant pressure molecular dynamics simulation: The Langevin piston method

B. Brooks, R. Pastor, S. Feller, 1995 .

Effect of Electrostatic Force Truncation on Interfacial and Transport Properties of Water

B. Brooks, A. Rojnuckarin, R. Pastor, 1996 .

Langevin dynamics of peptides: The frictional dependence of isomerization rates of N‐acetylalanyl‐N′‐methylamide

B. Brooks, R. Pastor, R. Loncharich, 1992, Biopolymers.

Global organization of a binding site network gives insight into evolution and structure-function relationships of proteins

Janez Konc, D. Janežič, B. Brooks, 2017, Scientific Reports.

An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer.

Alexander D. MacKerell, Jeffery B. Klauda, B. Brooks, 2005, The journal of physical chemistry. B.

Protein conformational transitions explored by mixed elastic network models

G. Hummer, B. Brooks, Wenjun Zheng, 2007, Proteins.

Self‐guided Langevin dynamics study of regulatory interactions in NtrC

Bernard R Brooks, Ana Damjanović, B. Brooks, 2009, Proteins.

Molecular Modeling of Nucleic Acid Structure: Electrostatics and Solvation

P. Kollman, B. Brooks, T. Cheatham, 2001, Current protocols in nucleic acid chemistry.

Recent advances in molecular dynamics simulation towards the realistic representation of biomolecules in solution

Bernard R. Brooks, B. Brooks, T. Cheatham III, 1998 .

Multiscale methods for macromolecular simulations.

B. Brooks, M. Sansom, P. Sherwood, 2008, Current opinion in structural biology.

Theoretical studies of relaxation of a monomeric subunit of HIV‐1 protease in water using molecular dynamics

B. Brooks, R. Venable, F. Carson, 1993, Proteins.

The graphical unitary group approach to the electron correlation problem. Methods and preliminary applications

B. Brooks, H. Schaefer, 1979 .

A 500 ps molecular dynamics simulation study of interleukin-1 beta in water. Correlation with nuclear magnetic resonance spectroscopy and crystallography.

B. Brooks, A. Gronenborn, G. Clore, 1992, Journal of molecular biology.

Simulation-based methods for interpreting x-ray data from lipid bilayers.

Jeffery B. Klauda, B. Brooks, R. Pastor, 2006, Biophysical journal.

Constant pH Molecular Dynamics in Explicit Solvent with Enveloping Distribution Sampling and Hamiltonian Exchange

Benjamin T. Miller, B. Brooks, Juyong Lee, 2014, Journal of chemical theory and computation.

An analysis of the accuracy of Langevin and molecular dynamics algorithms

B. Brooks, R. Pastor, A. Szabó, 1988 .

Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved.

D. Thirumalai, B. Brooks, Wenjun Zheng, 2005, Structure.

Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations

D. Thirumalai, B. Brooks, Wenjun Zheng, 2006, Proceedings of the National Academy of Sciences of the United States of America.

Interactions between hydrophobic and ionic solutes in aqueous guanidinium chloride and urea solutions: lessons for protein denaturation mechanism.

B. Brooks, R. Dima, D. Thirumalai, 2007, Journal of the American Chemical Society.

A temperature of maximum density in soft sticky dipole water

B. Brooks, A. Chandra, T. Ichiye, 2003 .

Probing the local dynamics of nucleotide-binding pocket coupled to the global dynamics: myosin versus kinesin.

B. Brooks, Wenjun Zheng, 2005, Biophysical journal.

Enhancing constant-pH simulation in explicit solvent with a two-dimensional replica exchange method.

Bernard R Brooks, Benjamin T. Miller, Benjamin T Miller, 2015, Journal of chemical theory and computation.

Molecular dynamics simulations of gel (LβI) phase lipid bilayers in constant pressure and constant surface area ensembles

B. Brooks, R. Pastor, R. Venable, 2000 .

A core-weighted fitting method for docking atomic structures into low-resolution maps: application to cryo-electron microscopy.

Bernard R Brooks, Xiongwu Wu, Sriram Subramaniam, 2003, Journal of structural biology.

Engineering Metal Complexes of Chiral Pentaazacrowns as Privileged Reverse‐turn Scaffolds

B. Brooks, G. Marshall, D. Riley, 2007, Chemical biology & drug design.

Protein recognition motifs: design of peptidomimetics of helix surfaces.

B. Brooks, G. Marshall, Ye Che, 2007, Biopolymers.

Molecular Simulation with Discrete Fast Fourier Transform

B. Brooks, Xiongwu Wu, 2012 .

Extracellular complexes of the hematopoietic human and mouse CSF-1 receptor are driven by common assembly principles.

B. Brooks, Xiongwu Wu, S. Savvides, 2011, Structure.

The Atomistic Mechanism of Conformational Transition of Adenylate Kinase Investigated by Lorentzian Structure-Based Potential.

B. Brooks, Jooyoung Lee, K. Joo, 2015, Journal of Chemical Theory and Computation.

Binding and release of cholesterol in the Osh4 protein of yeast

Bernard R Brooks, Jeffery B. Klauda, Rishi P. Singh, 2009, Proteins.

Computer simulation of liquid/liquid interfaces. I. Theory and application to octane/water

Bernard R. Brooks, Richard W. Pastor, B. Brooks, 1995 .

Elastic molecular dynamics with self-consistent flexible constraints

Bernard R. Brooks, Sebastian Reich, S. Reich, 2000 .

Protonation state of the selectivity filter of bacterial voltage‐gated sodium channels is modulated by ions

B. Brooks, Xiongwu Wu, D. Roe, 2020, Proteins.

Efficient Strategy for the Calculation of Solvation Free Energies in Water and Chloroform at the Quantum Mechanical/Molecular Mechanical Level

B. Brooks, Y. Shao, Pengfei Li, 2017, J. Chem. Inf. Model..

Origin of pKa Shifts of Internal Lysine Residues in SNase Studied Via Equal-Molar VMMS Simulations in Explicit Water.

B. Brooks, Xiongwu Wu, Juyong Lee, 2017, The journal of physical chemistry. B.

Theoretical study of the ground‐state vibrations of the linear polyenes

M. Karplus, B. Brooks, R. Hemley, 1986 .

The BERKELEY system. III. General configuration‐interaction methods for open‐shell molecular electronic states

B. Brooks, H. Schaefer, 1978 .

Membrane permeability of small molecules from unbiased molecular dynamics simulations.

Jeffery B. Klauda, B. Brooks, R. Pastor, 2020, The Journal of chemical physics.

Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

Alán Aspuru-Guzik, Michael W. Schmidt, Yan Zhao, 2014, Molecular Physics.

Numerical study on the partitioning of the molecular polarizability into fluctuating charge and induced atomic dipole contributions.

Andrew C. Simmonett, Frank C. Pickard, B. Brooks, 2015, The journal of physical chemistry. A.

Computational investigation of the oxidative deboronation of boroglycine, H2N-CH2-B(OH)2, Using H2O and H2O2.

B. Brooks, Joseph D. Larkin, C. Bock, 2009, The journal of physical chemistry. A.

Critical Sequence Hot-spots for Binding of nCOV-2019 to ACE2 as Evaluated by Molecular Simulations

Jeffery B. Klauda, B. Brooks, M. Ghorbani, 2020, bioRxiv.

Reformulation of the self-guided molecular simulation method.

B. Brooks, Xiongwu Wu, 2020, The Journal of chemical physics.

Identification of dynamical correlations within the myosin motor domain by the normal mode analysis of an elastic network model.

Wenjun Zheng, B. Brooks, Wenjun Zheng, 2005, Journal of molecular biology.

transitions explored by mixed elastic network models y

G. Hummer, B. Brooks, Wenjun Zheng, 2007 .

A model transition metal-carbene system MnCH2

B. Brooks, H. Schaefer, 1977 .

Reservoir pH replica exchange.

Benjamin T. Miller, B. Brooks, Asim Okur, 2018, The Journal of chemical physics.

Conformational relaxation and water penetration coupled to ionization of internal groups in proteins.

B. Brooks, A. Damjanovic, B. García-Moreno, 2011, The journal of physical chemistry. A.

Molecular Dynamics of Staphylococcal Nuclease: Comparison of Simulation with 15N and 13C NMR Relaxation Data

Bernard R. Brooks, David C. Chatfield, B. Brooks, 1998 .

Adjacent gauche stabilization in linear alkanes: implications for polymer models and conformational analysis.

Bernard R Brooks, Jeffery B. Klauda, B. Brooks, 2005, The journal of physical chemistry. B.

Molecular Modeling of Nucleic Acid Structure: Energy and Sampling

P. Kollman, B. Brooks, T. Cheatham, 2013, Current protocols in nucleic acid chemistry.

Accurate high-throughput structure mapping and prediction with transition metal ion FRET.

B. Brooks, Xiongwu Wu, J. Taraska, 2013, Structure.

Molecular Multipole Potential Energy Functions for Water.

Andrew C. Simmonett, Kelly N. Tran, Frank C. Pickard, 2016, The journal of physical chemistry. B.

Psi4 1.4: Open-source software for high-throughput quantum chemistry.

Zachary L Glick, Dominic A Sirianni, Jonathan M Waldrop, 2020, The Journal of chemical physics.

Structural Modulation of Human Amylin Protofilaments by Naturally Occurring Mutations.

Frank C. Pickard, N. Buchete, B. Brooks, 2018, The journal of physical chemistry. B.

Probing the "annealing" mechanism of GroEL minichaperone using molecular dynamics simulations.

D. Thirumalai, B. Brooks, G. Stan, 2005, Journal of molecular biology.

Direct global optimization of Onsager-Machlup action using Action-CSA

B. Brooks, Juyong Lee, 2020 .

Dosimeters of human exposure to carcinogens: polycyclic aromatic hydrocarbon-macromolecular adducts.

B. Brooks, J. Willey, D. Mann, 1988, IARC scientific publications.

Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches

Phillip S. Hudson, B. Brooks, Samarjeet Prasad, 2022, Journal of Computer-Aided Molecular Design.

Semi-automated Optimization of the CHARMM36 Lipid Force Field to Include Explicit Treatment of Long-Range Dispersion.

Alexander D. MacKerell, Andrew C. Simmonett, Jeffery B. Klauda, 2020, Journal of chemical theory and computation.

Sudden polarization: pyramidalization of twisted ethylene

B. Brooks, H. Schaefer, 1979 .

Conformational dynamics and aggregation behavior of piezoelectric diphenylalanine peptides in an external electric field.

N. Buchete, B. Brooks, A. Kholkin, 2015, Biophysical chemistry.

Deriving the Open State Structure of Glutamate Receptor through MapSGLD Flexible Fitting into Cryo-Electron Microscopy Maps

B. Brooks, Xiongwu Wu, 2018 .

Structure and Dynamics of Macromolecular Assemblies from Electron Microscopy Maps

B. Brooks, Xiongwu Wu, 2016 .

Deriving atomic structures of macromolecular assemblies from low resolution electron microscopy maps

B. Brooks, Xiongwu Wu, 2014 .

Mutations decouple proton transfer from phosphate cleavage in the dutpase catalytic reaction

B. Brooks, E. Rosta, P. K. Sharma, 2015 .

Structures of some substituted nitrophenols determined by ab initio computation on the origin of heterocliticity in anti-nitrophenol antibodies

B. Brooks, L. Amzel, N. Matsunaga, 1997 .

A computational investigation of the nitrogen-boron interaction in o-(N,N-dialkylaminomethyl)arylboronate systems.

B. Brooks, T. James, J. Fossey, 2010, The journal of physical chemistry. A.

Hydrophobic hydration and the anomalous partial molar volumes in ethanol-water mixtures.

Benjamin T. Miller, B. Brooks, T. Ichiye, 2015, The Journal of chemical physics.

Reactions of carbynes. Potential energy surfaces for the doublet and quartet methylidyne (CH) reactions with molecular hydrogen

B. Brooks, H. Schaefer, 1977 .

Three isomers of the aluminum-acetylene system

B. Brooks, H. Schaefer, M. E. Casida, 1979 .

Hydronium Ions Accompanying Buried Acidic Residues Lead to High Apparent Dielectric Constants in the Interior of Proteins.

B. Brooks, Xiongwu Wu, 2018, The journal of physical chemistry. B.

Isotropic periodic sum for multipole interactions and a vector relation for calculation of the Cartesian multipole tensor.

Frank C. Pickard, B. Brooks, Xiongwu Wu, 2016, The Journal of chemical physics.

Conformational states of a TT mismatch from molecular dynamics simulation of duplex d(CGCGATTCGCG)

B. Brooks, R. Pastor, R. Venable, 1992, Biopolymers.

Quantifying the effects of lossy compression on energies calculated from molecular dynamics trajectories

B. Brooks, D. Roe, 2022, Protein science : a publication of the Protein Society.

Alternate Pathways for Acetic Acid and Acetate ion Release from Acetylcholinesterase: a Molecular Dynamics Study

B. Brooks, I. Enyedy, I. Kovach, 1998 .

Pathways and populations: stereoelectronic insights into the exocyclic torsion of 5-(hydroxymethyl)tetrahydropyran.

B. Brooks, R. Pastor, H. Woodcock, 2008, Journal of the American Chemical Society.

Deep attention based variational autoencoder for antimicrobial peptide discovery

Jeffery B. Klauda, B. Brooks, Samarjeet Prasad, 2022, bioRxiv.

A computational characterization of boron-oxygen multiple bonding in HN=CH-CH=CH-NH-BO.

B. Brooks, K. Bhat, T. James, 2008, The journal of physical chemistry. A.

Structures of human TGFα fragments using two-dimensional proton magnetic resonance spectroscopy and computer simulation

B. Brooks, J. Ferretti, Kyou-Hoon Han, 1988 .

Comparison of Three Chain-of-States Methods: Nudged Elastic Band and Replica Path with Restraints or Constraints.

Bernard R Brooks, Joseph D Larkin, Milan Hodošček, 2012, Journal of chemical theory and computation.

Enantiomerization of Axially Chiral Biphenyls: Polarizable MD Simulations in Water and Butylmethylether

Phillip S. Hudson, B. Brooks, H. Woodcock, 2020, International journal of molecular sciences.

The Loop-Driven Graphical Unitary Group Approach: A Powerful Method for the Variational Description of Electron Correlation

Bernard R. Brooks, Henry F. Schaefer, Nicholas C. Handy, 1980 .

An ab initio study of amide proton shift tensor dependence on local protein structure.

B. Brooks, N. Tjandra, O. Kwon, 2002, Journal of the American Chemical Society.

Normal modes for large molecules with arbitrary link constraints in the mobile block Hessian approach.

V Van Speybroeck, M Waroquier, B. Brooks, 2009, The Journal of chemical physics.

A Quantum Chemical Study of the Ground and Excited State Electronic Structures of Carbazole Oligomers with and without Triarylborane Substitutes.

B. Brooks, Y. Shao, Zexing Qu, 2012, The journal of physical chemistry. C, Nanomaterials and interfaces.

Structure of the boronic acid dimer and the relative stabilities of its conformers.

B. Brooks, H. Schaefer, K. Bhat, 2006, The journal of physical chemistry. A.

Molecular architecture and mechanism of an icosahedral pyruvate dehydrogenase complex: a multifunctional catalytic machine

Bernard R Brooks, Xiongwu Wu, Richard Henderson, 2002, The EMBO journal.

Protein pKa Prediction by Tree-Based Machine Learning.

B. Brooks, Juyong Lee, A. Damjanovic, 2022, Journal of chemical theory and computation.

Protein pKa Prediction by Tree-Based Machine Learning.

B. Brooks, Juyong Lee, A. Damjanovic, 2021, Journal of chemical theory and computation.

A parallel implementation of the analytic nuclear gradient for time-dependent density functional theory within the Tamm–Dancoff approximation

Benjamin T. Miller, M. Head‐Gordon, B. Brooks, 1999 .

Removal of pressure and free energy artifacts in charged periodic systems via net charge corrections to the Ewald potential

Bernard R. Brooks, Thomas E. Cheatham, B. Brooks, 1998 .

New spherical‐cutoff methods for long‐range forces in macromolecular simulation

Bernard R. Brooks, Peter J. Steinbach, B. Brooks, 1994, J. Comput. Chem..

A protocol for preparing explicitly solvated systems for stable molecular dynamics simulations.

Bernard R Brooks, Daniel R Roe, B. Brooks, 2020, The Journal of chemical physics.

CHARMM: The biomolecular simulation program

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

Harmonic analysis of large systems. I. Methodology

Dusanka Janezic, Bernard R. Brooks, Martin Karplus, 1995, J. Comput. Chem..

Finding multiple reaction pathways via global optimization of action

In-Ho Lee, Bernard R. Brooks, Juyong Lee, 2017, Nature Communications.

Coupling between allosteric transitions in GroEL and assisted folding of a substrate protein

Bernard R Brooks, D Thirumalai, George H Lorimer, 2007, Proceedings of the National Academy of Sciences.

Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package

Daniel S. Levine, Run R. Li, K. B. Whaley, 2021, The Journal of chemical physics.

Development of small molecules designed to modulate protein–protein interactions

Garland R. Marshall, Bernard R. Brooks, Ye Che, 2006, J. Comput. Aided Mol. Des..

Carbene stabilization by aryl substituents. Is bigger better?

B. Brooks, H. Schaefer, P. Schleyer, 2007, Journal of the American Chemical Society.

Molecular dynamics simulations of human rhinovirus and an antiviral compound.

B. Brooks, B. Speelman, C. Post, 2001, Biophysical journal.

Measurement of NH-C.alpha.H coupling constants in staphylococcal nuclease by two-dimensional NMR and comparison with x-ray crystallographic results

B. Brooks, L. Kay, A. Bax, 1989 .

Temperature dependence of diffusion properties of soft sticky dipole water

B. Brooks, T. Ichiye, M. Tan, 2006 .

Inverse Resolution Limit of Partition Density and Detecting Overlapping Communities by Link-Surprise

B. Brooks, Yong-Yeol Ahn, Juyong Lee, 2017, Scientific Reports.

Molecular Modeling of Nucleic Acid Structure

P. Kollman, B. Brooks, T. Cheatham, 2001, Current protocols in nucleic acid chemistry.

Dynamics of DNA oligomers.

M Karplus, B Tidor, M. Karplus, 1983, Journal of biomolecular structure & dynamics.

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

Vijay S. Pande, Matthew P. Harrigan, Bernard R. Brooks, 2016, bioRxiv.

CHARMM36 Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for PE, PG, and Ether Lipids

Jeffery B. Klauda, B. Brooks, R. Pastor, 2020 .

The effects of environment and hydration on protein dynamics: A simulation study of myoglobin

Bernard R. Brooks, Peter J. Steinbach, B. Brooks, 1991 .

Comparison of Additive and Polarizable Models with Explicit Treatment of Long-Range Lennard-Jones Interactions Using Alkane Simulations.

Andrew C Simmonett, Bernard R Brooks, Jing Huang, 2018, Journal of chemical theory and computation.

Analytic gradients from correlated wave functions via the two‐particle density matrix and the unitary group approach

Bernard R. Brooks, Henry F. Schaefer, John D. Goddard, 1980 .

How accurate are polymer models in the analysis of Förster resonance energy transfer experiments on proteins?

B. Brooks, D. Thirumalai, E. O’Brien, 2009, The Journal of chemical physics.

The ubiquitin ligase Ubr4 controls stability of podocin/MEC-2 supercomplexes.

Markus M. Rinschen, B. Brooks, Xiongwu Wu, 2016, Human molecular genetics.

Phosphoproteomic analysis reveals regulatory mechanisms at the kidney filtration barrier.

Markus M. Rinschen, B. Brooks, Xiongwu Wu, 2014, Journal of the American Society of Nephrology : JASN.

Targeted conformational search with map-restrained self-guided Langevin dynamics: application to flexible fitting into electron microscopic density maps.

Xiongwu Wu, Sriram Subramaniam, S. Subramaniam, 2013, Journal of structural biology.

A new model defines the minimal set of polymorphism in HLA-DQ and -DR that determines susceptibility and resistance to autoimmune diabetes

B. Brooks, C. Parry, 2008, Biology Direct.

Theoretically determined three-dimensional structures for amphipathic segments of the HIV-1 gp41 envelope protein.

B. Brooks, R. Pastor, R. Venable, 1989, AIDS research and human retroviruses.

Toward the mechanism of dynamical couplings and translocation in hepatitis C virus NS3 helicase using elastic network model

Sebastian Doniach, Bernard R Brooks, Jung-Chi Liao, 2007, Proteins.

Inelastic neutron scattering analysis of low frequency motion in proteins: A normal mode study of the bovine pancreatic trypsin inhibitor

Bernard R. Brooks, Martin Karplus, Jeremy C. Smith, 1986 .

Global organization of a binding site network gives insight into evolution and structure-function relationships of proteins

Janez Konc, D. Janežič, B. Brooks, 2017, Scientific Reports.

Molecular Structure of a 9-MDa Icosahedral Pyruvate Dehydrogenase Subcomplex Containing the E2 and E3 Enzymes Using Cryoelectron Microscopy*

Bernard R Brooks, Xiongwu Wu, Sriram Subramaniam, 2006, Journal of Biological Chemistry.

Theoretically determined three-dimensional structure for the repeating tetrapeptide unit of the circumsporozoite coat protein of the malaria parasite Plasmodium falciparum.

B. Brooks, R. Pastor, F. Carson, 1987, Proceedings of the National Academy of Sciences of the United States of America.

CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems.

Nathan R. Kern, Nathan R Kern, B. Brooks, 2021, Journal of chemical theory and computation.

Interaction of DNA with bifunctional aldehydes.

B. Brooks, O. Klamerth, 1968, European journal of biochemistry.

Self‐guided Langevin dynamics via generalized Langevin equation

Bernard R. Brooks, Eric Vanden-Eijnden, Xiongwu Wu, 2016, J. Comput. Chem..

Critical Sequence Hotspots for Binding of Novel Coronavirus to Angiotensin Converter Enzyme as Evaluated by Molecular Simulations

Jeffery B. Klauda, B. Brooks, M. Ghorbani, 2020, The journal of physical chemistry. B.

Effects of denaturants and osmolytes on proteins are accurately predicted by the molecular transfer model

Bernard R Brooks, Guy Ziv, Gilad Haran, 2008, Proceedings of the National Academy of Sciences.

Metabolism-based transformation of myoglobin to an oxidase by BrCCl3 and molecular modeling of the oxidase form.

B. Brooks, P. J. Steinbach, J. Darbyshire, 1993, The Journal of biological chemistry.

Ab initio modeling of glycosyl torsions and anomeric effects in a model carbohydrate: 2-ethoxy tetrahydropyran.

Alexander D. MacKerell, Bernard R Brooks, H Lee Woodcock, 2007, Biophysical journal.

An efficient protocol for obtaining accurate hydration free energies using quantum chemistry and reweighting from molecular dynamics simulations.

Andrew C Simmonett, Bernard R Brooks, Gerhard König, 2016, Bioorganic & medicinal chemistry.

Partition coefficients for the SAMPL5 challenge using transfer free energies

Bernard R Brooks, Angela K Wilson, Michael R Jones, 2016, Journal of Computer-Aided Molecular Design.

Reaction Path Optimization and Sampling Methods and Their Applications for Rare Events

B. Brooks, Peng Tao, J. Larkin, 2012 .

Interfacing Q‐Chem and CHARMM to perform QM/MM reaction path calculations

Bernard R. Brooks, H. Lee Woodcock, Milan Hodoscek, 2007, J. Comput. Chem..

A three-dimensional model of an anti-lysozyme antibody.

B. Brooks, S. Smith‐Gill, B R Brooks, 1987, Journal of molecular biology.

Extended polypeptide linkers establish the spatial architecture of a pyruvate dehydrogenase multienzyme complex.

S. Subramaniam, B. Brooks, Xiongwu Wu, 2008, Structure.

The Local Maximum ClusteringMethod and Its Application in Microarray Gene Expression Data Analysis

Yan A. Su, B. Brooks, 2004 .

Rotation of lipids in membranes: molecular dynamics simulation, 31P spin-lattice relaxation, and rigid-body dynamics.

Bernard R Brooks, Jeffery B. Klauda, Mary F Roberts, 2008, Biophysical journal.

Collective and noncollective models of NMR relaxation in lipid vesicles and multilayers.

Jeffery B. Klauda, B. Brooks, R. Pastor, 2008, The journal of physical chemistry. B.

Molecular dynamics simulations of native and substrate-bound lysozyme. A study of the average structures and atomic fluctuations.

M. Karplus, B. Brooks, C. Dobson, 1986, Journal of molecular biology.

A compression strategy for particle mesh Ewald theory.

Andrew C. Simmonett, B. Brooks, 2021, The Journal of chemical physics.

Residues in substrate proteins that interact with GroEL in the capture process are buried in the native state.

Bernard R Brooks, D Thirumalai, George H Lorimer, 2006, Proceedings of the National Academy of Sciences of the United States of America.

Efficient High Accuracy Non-Bonded Interactions in the CHARMM Simulation Package

Andrew C. Simmonett, Frank C. Pickard, B. Brooks, 2015 .

Dynamical motions of lipids and a finite size effect in simulations of bilayers.

Jeffery B. Klauda, B. Brooks, R. Pastor, 2006, The Journal of chemical physics.

Models of δ‐hemolysin membrane channels and crystal structures

H. Guy, P. Seetharamulu, B. Brooks, 1991 .

Models of delta-hemolysin membrane channels and crystal structures.

H. Guy, P. Seetharamulu, B. Brooks, 1990, Proteins.

Beta-hairpin folding mechanism of a nine-residue peptide revealed from molecular dynamics simulations in explicit water.

Bernard R Brooks, Xiongwu Wu, B. Brooks, 2004, Biophysical journal.

Variational embedding of protein folding simulations using gaussian mixture variational autoencoders pdf

Bernard R. Brooks, Samarjeet Prasad, Mahdi Ghorbani, 2021, The Journal of chemical physics.

Protein hydration elucidated by molecular dynamics simulation.

B. Brooks, P J Steinbach, B R Brooks, 1993, Proceedings of the National Academy of Sciences of the United States of America.

Sigma-RF: prediction of the variability of spatial restraints in template-based modeling by random forest

Keehyoung Joo, Jooyoung Lee, Bernard R. Brooks, 2015, BMC Bioinformatics.

Structural Characterization of Arginine Fingers: Identification of an Arginine Finger for the Pyrophosphatase dUTPases.

B. Brooks, E. Rosta, B. Vértessy, 2016, Journal of the American Chemical Society.

Normal-modes-based prediction of protein conformational changes guided by distance constraints.

Bernard R Brooks, Wenjun Zheng, B. Brooks, 2005, Biophysical journal.

HIV-1 protease cleavage mechanism: A theoretical investigation based on classical MD simulation and reaction path calculations using a hybrid QM/MM potential

Bernard R. Brooks, David C. Chatfield, B. Brooks, 1998 .

Allosteric transitions in biological nanomachines are described by robust normal modes of elastic networks.

Bernard R Brooks, D Thirumalai, Wenjun Zheng, 2009, Current protein & peptide science.

CHARMM36 Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Phosphatidylethanolamine, Phosphatidylglycerol, and Ether Lipids.

Jeffery B. Klauda, B. Brooks, R. Pastor, 2021, Journal of chemical theory and computation.

Machine Learning Force Field Parameters from Ab Initio Data.

Bernard R Brooks, Benoît Roux, Ying Li, 2017, Journal of chemical theory and computation.

Backbone relaxation coupled to the ionization of internal groups in proteins: a self-guided Langevin dynamics study.

Bernard R Brooks, Xiongwu Wu, Ana Damjanović, 2008, Biophysical journal.

Identifying natural substrates for chaperonins using a sequence‐based approach

D. Thirumalai, B. Brooks, G. Stan, 2005, Protein science : a publication of the Protein Society.

Annealing function of GroEL: structural and bioinformatic analysis.

D. Thirumalai, B. Brooks, G. Stan, 2002, Biophysical chemistry.

An Albumin Sandwich Enhances in Vivo Circulation and Stability of Metabolically Labile Peptides.

B. Brooks, Xiaoyuan Chen, G. Niu, 2019, Bioconjugate chemistry.

A deep learning approach for the blind logP prediction in SAMPL6 challenge

Bernard R. Brooks, Samarjeet Prasad, B. Brooks, 2020, Journal of Computer-Aided Molecular Design.

Molecular origin of constant m-values, denatured state collapse, and residue-dependent transition midpoints in globular proteins.

D. Thirumalai, B. Brooks, E. O’Brien, 2009, Biochemistry.

N (1Ag), T (3B1u), and V (1B1u) states of vertical ethylene

B. Brooks, H. Schaefer, 1978 .

Multiple Environment Single System Quantum Mechanical/Molecular Mechanical (MESS-QM/MM) Calculations. 1. Estimation of Polarization Energies

Ye Mei, Bernard R. Brooks, Gerhard König, 2014, The journal of physical chemistry. A.

New Directions for the Loop-Driven Graphical Unitary Group Approach: Analytic Gradients and an MCSCF Procedure

B. Brooks, H. Schaefer, Paul Saxe, 1981 .

BERKELEY: An “open ended” Configuration Interaction (CI) program designed for minicomputers

Henry F. Schaefer, Bernard R. Brooks, Robert R. Lucchese, 1978 .

Quantum chemical predictions of water–octanol partition coefficients applied to the SAMPL6 logP blind challenge

Bernard R. Brooks, Michael R. Jones, B. Brooks, 2020, Journal of Computer-Aided Molecular Design.

A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes

Alexander D. MacKerell, Bernard R Brooks, Walter Thiel, 2018, Molecules.

Prediction of CB[8] host–guest binding free energies in SAMPL6 using the double-decoupling method

Bernard R. Brooks, Naohiro Nishikawa, Phillip S. Hudson, 2018, Journal of Computer-Aided Molecular Design.

Optimization of quantum mechanical molecular mechanical partitioning schemes: Gaussian delocalization of molecular mechanical charges and the double link atom method

Bernard R. Brooks, Milan Hodošček, Eric M. Billings, 2002 .

A comprehensive picture of non-site specific oxidation of methionine residues by peroxides in protein pharmaceuticals.

Bernard R Brooks, Bernhardt L Trout, Jhih-Wei Chu, 2004, Journal of pharmaceutical sciences.

Analytical Hessians for Ewald and particle mesh Ewald electrostatics.

Andrew C. Simmonett, B. Brooks, 2021, The Journal of chemical physics.

Mapping the Drude polarizable force field onto a multipole and induced dipole model.

Alexander D. MacKerell, Andrew C Simmonett, Bernard R Brooks, 2017, The Journal of chemical physics.

Molecular Modeling of Nucleic Acid Structure: Setup and Analysis

P. Kollman, B. Brooks, T. Cheatham, 2014, Current protocols in nucleic acid chemistry.

Exploring dynamics and network analysis of spike glycoprotein of SARS-COV-2

Jeffery B. Klauda, B. Brooks, M. Ghorbani, 2021, Biophysical Journal.

Molecular dynamics simulations of perylene and tetracene librations: comparison with femtosecond upconversion data.

B. Brooks, Xiongwu Wu, Jianhua Xu, 2008, The journal of physical chemistry. A.

Simulations of membranes and other interfacial systems using P2(1) and Pc periodic boundary conditions.

Bernard R Brooks, B. Brooks, R. Pastor, 2002, Biophysical journal.

Efficient and Unbiased Sampling of Biomolecular Systems in the Canonical Ensemble: A Review of Self-Guided Langevin Dynamics.

Bernard R Brooks, Xiongwu Wu, Ana Damjanovic, 2012, Advances in chemical physics.

Force-momentum-based self-guided Langevin dynamics: a rapid sampling method that approaches the canonical ensemble.

Bernard R Brooks, Xiongwu Wu, B. Brooks, 2011, The Journal of chemical physics.

Protein simulation below the glass-transition temperature. Dependence on cooling protocol

Bernard R. Brooks, Peter J. Steinbach, B. Brooks, 1994 .

An explicit-solvent hybrid QM and MM approach for predicting pKa of small molecules in SAMPL6 challenge

Bernard R. Brooks, Samarjeet Prasad, Jing Huang, 2018, Journal of Computer-Aided Molecular Design.

Absolute and relative pKa predictions via a DFT approach applied to the SAMPL6 blind challenge

Bernard R. Brooks, Qiao Zeng, Michael R. Jones, 2018, Journal of Computer-Aided Molecular Design.

Temperature dependence of dynamics of hydrated myoglobin. Comparison of force field calculations with neutron scattering data.

B. Brooks, R. Loncharich, B R Brooks, 1990, Journal of molecular biology.

Protein-Protein Docking Using EMAP in CHARMM and Support Vector Machine: Application to Ab/Ag Complexes.

Bernard R Brooks, Xiongwu Wu, Carmay Lim, 2013, Journal of chemical theory and computation.

Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics

Bernard R. Brooks, Gerhard König, Yihan Shao, 2014, Journal of chemical theory and computation.

A super-linear minimization scheme for the nudged elastic band method

B. Brooks, B. Trout, J. Chu, 2003 .

Exploring the quantum mechanical/molecular mechanical replica path method: a pathway optimization of the chorismate to prephenate Claisen rearrangement catalyzed by chorismate mutase

Bernard R. Brooks, Milan Hodošček, Paul Sherwood, 2003 .

The distributed diagonal force decomposition method for parallelizing molecular dynamics simulations

Dusanka Janezic, Bernard R. Brooks, Benjamin T. Miller, 2011, J. Comput. Chem..

Web-Based Computational Chemistry Education with CHARMMing III: Reduction Potentials of Electron Transfer Proteins

Bernard R. Brooks, Benjamin T. Miller, H. Lee Woodcock, 2014, PLoS Comput. Biol..

Influence of Nanoparticle Size and Shape on Oligomer Formation of an Amyloidogenic Peptide.

Bernard R Brooks, John E Straub, Edward P O'Brien, 2011, The journal of physical chemistry letters.

MSCALE: A General Utility for Multiscale Modeling.

Asim Okur, Bernard R Brooks, Benjamin T. Miller, 2011, Journal of chemical theory and computation.

Determinants of conductance of a bacterial voltage gated sodium channel.

B. Brooks, A. Damjanovic, Ada Y. Chen, 2021, Biophysical journal.

Computational scheme for pH‐dependent binding free energy calculation with explicit solvent

Bernard R Brooks, Benjamin T. Miller, Benjamin T Miller, 2015, Protein science : a publication of the Protein Society.

Absolute binding free energy calculations of CBClip host–guest systems in the SAMPL5 blind challenge

Chaok Seok, Bernard R. Brooks, Juyong Lee, 2016, Journal of Computer-Aided Molecular Design.

ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites

Dusanka Janezic, Bernard R. Brooks, Benjamin T. Miller, 2015, J. Chem. Inf. Model..

Generating reservoir conformations for replica exchange through the use of the conformational space annealing method.

Keehyoung Joo, Jooyoung Lee, Asim Okur, 2013, Journal of chemical theory and computation.

Replica exchanging self-guided Langevin dynamics for efficient and accurate conformational sampling.

Bernard R Brooks, Xiongwu Wu, Milan Hodoscek, 2012, The Journal of chemical physics.

Enhanced Sampling in Free Energy Calculations: Combining SGLD with the Bennett's Acceptance Ratio and Enveloping Distribution Sampling Methods.

Bernard R Brooks, Xiongwu Wu, Benjamin T. Miller, 2012, Journal of chemical theory and computation.

pH replica‐exchange method based on discrete protonation states

Bernard R Brooks, Ana Damjanović, B. Brooks, 2011, Proteins.

CHARMMing: A New, Flexible Web Portal for CHARMM

Bernard R. Brooks, Benjamin T. Miller, H. Lee Woodcock, 2008, J. Chem. Inf. Model..

Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for SAMPL6 octa-acid host–guest challenges

Xiongwu Wu, Bernard R. Brooks, Naohiro Nishikawa, 2018, Journal of Computer-Aided Molecular Design.

Absolute binding free energies for octa-acids and guests in SAMPL5

Chaok Seok, Bernard R. Brooks, Juyong Lee, 2016, Journal of Computer-Aided Molecular Design.

Albumin-chaperoned cyanine dye yields superbright NIR-II fluorophore with enhanced pharmacokinetics

B. Brooks, Xiaoyuan Chen, G. Niu, 2019, Science Advances.

Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical Method.

Andrew C Simmonett, Bernard R Brooks, Ye Mei, 2016, Journal of chemical theory and computation.

Predicting hydration free energies with a hybrid QM/MM approach: an evaluation of implicit and explicit solvation models in SAMPL4

Ye Mei, Bernard R. Brooks, Gerhard König, 2014, Journal of Computer-Aided Molecular Design.

Molecular mechanics and antibody binding in the structural analysis of polycyclic aromatic hydrocarbon-diol-epoxide--DNA adducts.

B. Brooks, D. Mann, A. Weston, 1990, Carcinogenesis.

Langevin network model of myosin.

Bernard R Brooks, Benjamin T. Miller, Benjamin T Miller, 2008, The journal of physical chemistry. B.

Calculations of Solvation Free Energy through Energy Reweighting from Molecular Mechanics to Quantum Mechanics.

Bernard R Brooks, Ye Mei, John Z H Zhang, 2016, Journal of chemical theory and computation.

Pressure-Based Long-Range Correction for Lennard-Jones Interactions in Molecular Dynamics Simulations: Application to Alkanes and Interfaces

Bernard R. Brooks, Richard W. Pastor, Patrick Lagüe, 2004 .

An efficient algorithm for multipole energies and derivatives based on spherical harmonics and extensions to particle mesh Ewald.

Andrew C Simmonett, Bernard R Brooks, Andrew C. Simmonett, 2014, The Journal of chemical physics.

Efficient Calculation of QM/MM Frequencies with the Mobile Block Hessian.

Michel Waroquier, Veronique Van Speybroeck, Bernard R Brooks, 2011, Journal of chemical theory and computation.

Correlation Between Water Molecules Identified in Atomic Models of Beta-Galactosidase Determined by Cryo-EM and X-Ray Crystallography

Frank C. Pickard, B. Brooks, L. Earl, 2020 .

An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches.

Alexander D. MacKerell, Andrew C Simmonett, Bernard R Brooks, 2017, Journal of chemical theory and computation.

GraphVAMPNet, using graph neural networks and variational approach to markov processes for dynamical modeling of biomolecules pdf

Bernard R. Brooks, Mahdi Ghorbani, Jeffery B. Klauda, 2022, The Journal of chemical physics.

Improving the speed of volumetric density map generation via cubic spline interpolation.

Bernard R. Brooks, Daniel R. Roe, B. Brooks, 2021, Journal of molecular graphics & modelling.

Protein-Protein Docking Using Map Objects

B. Brooks, Xiongwu Wu, 2019, Molecular Docking and Molecular Dynamics.

Solvent-Induced Forces between Two Hydrophilic Groups

Bernard R. Brooks, Arieh Ben-Naim, B. Brooks, 1994 .

Inverse Resolution Limit of Partition Density and Detecting Overlapping Communities by Link-Surprise pdf

Jooyoung Lee, Yong-Yeol Ahn, Bernard R. Brooks, 2016, Scientific Reports.

Catalytic mechanism of aldose reductase studied by the combined potentials of quantum mechanics and molecular mechanics.

M Hodoscek, B. Brooks, M. Hodošček, 1998, Biophysical chemistry.

ENZYME MECHANISMS WITH HYBRID QUANTUM AND MOLECULAR MECHANICAL POTENTIALS.I. THEORETICAL CONSIDERATIONS

Bernard R. Brooks, Milan Hodošček, David C. Chatfield, 1996 .

Finding Dominant Reaction Pathways via Global Optimization of Action

B. Brooks, In-Ho Lee, Juyong Lee, 2016, 1610.02652.

Isotropic periodic sum: a method for the calculation of long-range interactions.

Bernard R Brooks, Xiongwu Wu, B. Brooks, 2005, The Journal of chemical physics.

Oxidation of methionine residues in aqueous solutions: free methionine and methionine in granulocyte colony-stimulating factor.

B. Brooks, B. Trout, J. Chu, 2004, Journal of the American Chemical Society.

Exploring dynamics and network analysis of spike glycoprotein of SARS-COV-2

Jeffery B. Klauda, B. Brooks, M. Ghorbani, 2020, bioRxiv.

Factors governing helix formation in peptides confined to carbon nanotubes.

D. Thirumalai, B. Brooks, G. Stan, 2008, Nano letters.

Thermodynamic perspective on the dock-lock growth mechanism of amyloid fibrils.

Yuko Okamoto, Bernard R Brooks, John E Straub, 2009, The journal of physical chemistry. B.

Effects of pH on proteins: predictions for ensemble and single-molecule pulling experiments.

D. Thirumalai, B. Brooks, E. O’Brien, 2012, Journal of the American Chemical Society.

An empirical extrapolation scheme for efficient treatment of induced dipoles.

Andrew C Simmonett, Bernard R Brooks, Jay W Ponder, 2016, The Journal of chemical physics.

Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit.

Bernard R Brooks, H Lee Woodcock, Yihan Shao, 2008, The Journal of chemical physics.

Interactions of Water and Alkanes: Modifying Additive Force Fields to Account for Polarization Effects.

Andrew C Simmonett, Bernard R Brooks, Jing Huang, 2019, Journal of chemical theory and computation.

Efficient treatment of induced dipoles.

Andrew C Simmonett, Bernard R Brooks, Yihan Shao, 2015, The Journal of chemical physics.

Isotropic periodic sum of electrostatic interactions for polar systems.

Bernard R Brooks, Xiongwu Wu, B. Brooks, 2009, The Journal of chemical physics.

A multiconfiguration self‐consistent‐field formalism utilizing the two‐particle density matrix and the unitary group approach

Bernard R. Brooks, Henry F. Schaefer, B. Brooks, 1980 .

Comparative study of various normal mode analysis techniques based on partial Hessians

Michel Waroquier, Veronique Van Speybroeck, Bernard R. Brooks, 2009, J. Comput. Chem..

Mobile Block Hessian Approach with Adjoined Blocks: An Efficient Approach for the Calculation of Frequencies in Macromolecules.

V Van Speybroeck, M Waroquier, B. Brooks, 2009, Journal of chemical theory and computation.

Absorption mode two‐dimensional NOE spectroscopy of exchangeable protons in oligonucleotides

B. Brooks, A. Bax, G. Zon, 1987, FEBS letters.

Maintain rigid structures in Verlet based cartesian molecular dynamics simulations.

Bernard R Brooks, Xiongwu Wu, Peng Tao, 2012, The Journal of chemical physics.

Replica Exchange Molecular Dynamics of Diphenylalanine Amyloid Peptides in Electric Fields

N. Buchete, B. Brooks, B. Rodriguez, 2021, The journal of physical chemistry. B.

Modulation of Alzheimer's Aβ protofilament-membrane interactions by lipid headgroups.

Bernard R Brooks, Florentina Tofoleanu, Nicolae-Viorel Buchete, 2015, ACS chemical neuroscience.

Transition from B to Z DNA: contribution of internal fluctuations to the configurational entropy difference.

M Karplus, B Tidor, M. Karplus, 1985, Science.

The homogeneity condition: A simple way to derive isotropic periodic sum potentials for efficient calculation of long-range interactions in molecular simulation.

B. Brooks, Xiongwu Wu, 2019, The Journal of chemical physics.

A Virtual Mixture Approach to the Study of Multistate Equilibrium: Application to Constant pH Simulation in Explicit Water

Xiongwu Wu, Bernard R. Brooks, B. Brooks, 2015, PLoS Comput. Biol..

Using the isotropic periodic sum method to calculate long-range interactions of heterogeneous systems.

Bernard R Brooks, Xiongwu Wu, B. Brooks, 2008, The Journal of chemical physics.

Long-range Lennard-Jones and electrostatic interactions in interfaces: application of the isotropic periodic sum method.

Bernard R Brooks, Xiongwu Wu, Jeffery B. Klauda, 2007, The journal of physical chemistry. B.

Reaction Mechanism of Chorismate Mutase Studied by the Combined Potentials of Quantum Mechanics and Molecular Mechanics

Bernard R. Brooks, Sharon E. Worthington, B. Brooks, 2002 .

Modeling protein conformational changes by iterative fitting of distance constraints using reoriented normal modes.

Bernard R Brooks, Wenjun Zheng, B. Brooks, 2006, Biophysical journal.

Artificial reaction coordinate “tunneling” in free‐energy calculations: The catalytic reaction of RNase H

Bernard R. Brooks, H. Lee Woodcock, Gerhard Hummer, 2009, J. Comput. Chem..

Web-Based Computational Chemistry Education with CHARMMing I: Lessons and Tutorial

Bernard R. Brooks, Benjamin T. Miller, Yuri Pevzner, 2014, PLoS Comput. Biol..

Probing the periplasmic-open state of lactose permease in response to sugar binding and proton translocation.

Bernard R Brooks, Jeffery B. Klauda, B. Brooks, 2010, Journal of molecular biology.

Multi-phase Boltzmann weighting: accounting for local inhomogeneity in molecular simulations of water–octanol partition coefficients in the SAMPL6 challenge

Bernard R. Brooks, Phillip S. Hudson, Michael R. Jones, 2020, Journal of Computer-Aided Molecular Design.

Computer simulations of a tumor surface octapeptide epitope

R H Reid, B. Brooks, B R Brooks, 1989, Biopolymers.

Conformational analysis of replica exchange MD: Temperature-dependent Markov networks for FF amyloid peptides.

Bernard R Brooks, Brajesh Narayan, Nicolae-Viorel Buchete, 2018, The Journal of chemical physics.

SAMPL6 logP challenge: machine learning and quantum mechanical approaches

Bernard R. Brooks, Michael R. Jones, Prajay Patel, 2020, Journal of Computer-Aided Molecular Design.

Force matching as a stepping stone to QM/MM CB[8] host/guest binding free energies: a SAMPL6 cautionary tale

Bernard R. Brooks, H. Lee Woodcock, Phillip S. Hudson, 2018, Journal of Computer-Aided Molecular Design.

Hydrogen bonding in high-resolution protein structures: a new method to assess NMR protein geometry.

B. Brooks, R. Lipsitz, N. Tjandra, 2002, Journal of the American Chemical Society.

Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

Michael W. Schmidt, Shawn T. Brown, Igor Ying Zhang, 2014, Molecular Physics.

The Extended Eighth‐Shell method for periodic boundary conditions with rotational symmetry

Andrew C. Simmonett, B. Brooks, Samarjeet Prasad, 2021, J. Comput. Chem..

Automatic Spot Identification for High Throughput Microarray Analysis.

Bernard R Brooks, Xiongwu Wu, Yan A. Su, 2011, Journal of bioengineering & biomedical science.

Development and implementation of (Q)SAR modeling within the CHARMMing web‐user interface

Igor V. Filippov, Bernard R. Brooks, Benjamin T. Miller, 2015, J. Comput. Chem..

Conformational Fluctuations in β2-Microglubulin Using Markov State Modeling and Molecular Dynamics.

Jeffery B. Klauda, B. Brooks, M. Ghorbani, 2023, Journal of Physical Chemistry B.

Comparing normal modes across different models and scales: Hessian reduction versus coarse‐graining

Bernard R. Brooks, Benjamin T. Miller, IV FrankC.Pickard, 2012, J. Comput. Chem..

An improved method for nonbonded list generation: Rapid determination of near‐neighbor pairs

Bernard R. Brooks, Ioan Andricioaei, Robert J. Petrella, 2003, J. Comput. Chem..

A new model defines the minimal set of polymorphism in HLA-DQ and -DR that determines susceptibility and resistance to autoimmune diabetes

B. Brooks, C. Parry, 2008, Biology Direct.

HIV-1 Protease Cleavage Mechanism Elucidated with Molecular Dynamics Simulation

B. Brooks, D. Chatfield, 1995 .

Web-Based Computational Chemistry Education with CHARMMing II: Coarse-Grained Protein Folding

Bernard R. Brooks, Benjamin T. Miller, H. Lee Woodcock, 2014, PLoS Comput. Biol..

Amyloid Fibril Design: Limiting Structural Polymorphism in Alzheimer's Aβ Protofilaments.

B. Brooks, B. Szydłowska, F. Tofoleanu, 2018, The journal of physical chemistry. B.

Phosphoproteomic analysis reveals regulatory mechanisms at the kidney filtration barrier.

Markus M. Rinschen, B. Brooks, Xiongwu Wu, 2014, Journal of the American Society of Nephrology : JASN.

Numerical study on the partitioning of the molecular polarizability into fluctuating charge and induced atomic dipole contributions.

Andrew C. Simmonett, Frank C. Pickard, B. Brooks, 2015, The journal of physical chemistry. A.

A computational investigation of the geometrical structure and protodeboronation of boroglycine, H2N-CH2-B(OH)2.

B. Brooks, K. Bhat, J. Lai, 2007, The journal of physical chemistry. A.

Backbone relaxation coupled to the ionization of internal groups in proteins: a self-guided Langevin dynamics study.

B. Brooks, Xiongwu Wu, A. Damjanovic, 2008, Biophysical journal.

A truncated Newton minimizer adapted for CHARMM and biomolecular applications

Tamar Schlick, Bernard R. Brooks, Philippe Derreumaux, 1994, J. Comput. Chem..

Self-guided molecular dynamics simulation based on concerted movement.

B. Brooks, Xiongwu Wu, 2023, Biophysical journal.

On the convergence of multi-scale free energy simulations

Bernard R Brooks, Walter Thiel, Gerhard König, 2018, Molecular simulation.

Calculating distribution coefficients based on multi-scale free energy simulations: an evaluation of MM and QM/MM explicit solvent simulations of water-cyclohexane transfer in the SAMPL5 challenge

Bernard R. Brooks, Juyong Lee, Walter Thiel, 2016, Journal of Computer-Aided Molecular Design.

The Heat is On: Temperature Increase Mimics Allosteric Signaling in Imidazole-Glycerol Phosphate Synthase

B. Brooks, J. P. Loria, I. Rivalta, 2022 .

Effects of denaturants and osmolytes on proteins are accurately predicted by the molecular transfer model

B. Brooks, G. Ziv, D. Thirumalai, 2008, Proceedings of the National Academy of Sciences.

Structure and dynamics of the fibronectin-III domains of Aplysia californica cell adhesion molecules.

Gil U. Lee, B. Brooks, J. Muzard, 2015, Physical chemistry chemical physics : PCCP.

A replica exchange umbrella sampling (REUS) approach to predict host–guest binding free energies in SAMPL8 challenge

Phillip S. Hudson, Jeffery B. Klauda, B. Brooks, 2021, Journal of Computer-Aided Molecular Design.

Molecular Modeling of Nucleic Acid Structure: Energy and Sampling

P. Kollman, B. Brooks, T. Cheatham, 2001, Current protocols in nucleic acid chemistry.

MDMS: Molecular Dynamics Meta-Simulator for evaluating exchange type sampling methods.

Asim Okur, Bernard Brooks, Daniel B Smith, 2012, Chemical physics letters.

Web-Based Computational Chemistry Education with CHARMMing I: Lessons and Tutorial

Benjamin T. Miller, Rishi P. Singh, B. Brooks, 2014, PLoS Comput. Biol..

Direct observation of the folding and unfolding of a beta-hairpin in explicit water through computer simulation.

Bernard R Brooks, Xiongwu Wu, B. Brooks, 2002, Journal of the American Chemical Society.

A parallel implementation of the analytic nuclear gradient for time-dependent density functional theory within the Tamm–Dancoff approximation

Benjamin T. Miller, M. Head‐Gordon, B. Brooks, 2010 .

Accurate High-Throughput Structure Mapping and Prediction with Transition Metal Ion FRET

B. Brooks, Xiongwu Wu, G. Bermejo, 2013 .

Sugar binding in lactose permease: anomeric state of a disaccharide influences binding structure.

Jeffery B. Klauda, B. Brooks, 2007, Journal of molecular biology.

Molecular Simulation with Discrete Fast Fourier Transform

Xiongwu Wu, Bernard R. Brooks, B. Brooks, 2012 .

Medicine Open Access book publisher

B. Brooks, Xiongwu Wu, 2017 .

Toward canonical ensemble distribution from self-guided Langevin dynamics simulation.

Bernard R Brooks, Xiongwu Wu, B. Brooks, 2011, The Journal of chemical physics.

Open Science Grid Study of the Coupling between Conformation and Water Content in the Interior of a Protein

Bernard R. Brooks, Ana Damjanovic, Benjamin T. Miller, 2008, J. Chem. Inf. Model..

Mapping the Drude polarizable force field onto a multipole and induced dipole model.

Alexander D. MacKerell, Andrew C. Simmonett, Frank C. Pickard, 2017, Journal of Chemical Physics.

Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and pKa corrections

Bernard R. Brooks, Juyong Lee, Gerhard König, 2016, Journal of Computer-Aided Molecular Design.

Electron Spin Resonance Studies on the Photolysis of Azo Compounds at -196°

H. Evans, B. Brooks, P. Ayscough, 1964 .