☰

cached image

Bernard R Brooks, Ph.D. - Publications

Affiliations: 
National Heart, Lung, and Blood Institute National Institutes of Health, Bethesda, MD 
Area:
Computational Biophysics
Website:
http://www.lobos.nih.gov/cbs/
Tree Info Similar researchers PubMed Report error

204/371 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Chen AY, Brooks BR, Damjanovic A. Ion channel selectivity through ion-modulated changes of selectivity filter p values. Proceedings of the National Academy of Sciences of the United States of America. 120: e2220343120. PMID 37339196 DOI: 10.1073/pnas.2220343120  0.763
2022 Hudson PS, Aviat F, Meana-Pañeda R, Warrensford L, Pollard BC, Prasad S, Jones MR, Woodcock HL, Brooks BR. Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches. Journal of Computer-Aided Molecular Design. PMID 35597880 DOI: 10.1007/s10822-022-00443-8  0.776
2022 Chen AY, Lee J, Damjanovic A, Brooks BR. Protein p Prediction by Tree-Based Machine Learning. Journal of Chemical Theory and Computation. 18: 2673-2686. PMID 35289611 DOI: 10.1021/acs.jctc.1c01257  0.755
2021 Choi YK, Kern NR, Kim S, Kanhaiya K, Afshar Y, Jeon SH, Jo S, Brooks BR, Lee J, Tadmor EB, Heinz H, Im W. CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems. Journal of Chemical Theory and Computation. PMID 34871001 DOI: 10.1021/acs.jctc.1c00996  0.31
2021 Chen AY, Brooks BR, Damjanovic A. Determinants of conductance of a bacterial voltage gated sodium channel. Biophysical Journal. PMID 34214541 DOI: 10.1016/j.bpj.2021.06.013  0.785
2021 Ghorbani M, Hudson PS, Jones MR, Aviat F, Meana-Pañeda R, Klauda JB, Brooks BR. A replica exchange umbrella sampling (REUS) approach to predict host-guest binding free energies in SAMPL8 challenge. Journal of Computer-Aided Molecular Design. PMID 33939083 DOI: 10.1007/s10822-021-00385-7  0.78
2020 Wu X, Brooks BR. Reformulation of the self-guided molecular simulation method. The Journal of Chemical Physics. 153: 094112. PMID 32891108 DOI: 10.1063/5.0019086  0.395
2020 Zeindlhofer V, Hudson P, Pálvölgyi ÁM, Welsch M, Almarashi M, Woodcock HL, Brooks B, Bica-Schröder K, Schröder C. Enantiomerization of Axially Chiral Biphenyls: Polarizable MD Simulations in Water and Butylmethylether. International Journal of Molecular Sciences. 21. PMID 32872113 DOI: 10.3390/Ijms21176222  0.782
2020 Roe DR, Brooks BR. A protocol for preparing explicitly solvated systems for stable molecular dynamics simulations. The Journal of Chemical Physics. 153: 054123. PMID 32770927 DOI: 10.1063/5.0013849  0.351
2020 Smith DGA, Burns LA, Simmonett AC, Parrish RM, Schieber MC, Galvelis R, Kraus P, Kruse H, Di Remigio R, Alenaizan A, James AM, Lehtola S, Misiewicz JP, Scheurer M, Shaw RA, ... ... Brooks BR, et al. Psi4 1.4: Open-source software for high-throughput quantum chemistry. The Journal of Chemical Physics. 152: 184108. PMID 32414239 DOI: 10.1063/5.0006002  0.774
2020 Krämer A, Hudson PS, Jones MR, Brooks BR. Multi-phase Boltzmann weighting: accounting for local inhomogeneity in molecular simulations of water-octanol partition coefficients in the SAMPL6 challenge. Journal of Computer-Aided Molecular Design. PMID 32060677 DOI: 10.1007/S10822-020-00285-2  0.773
2020 Patel P, Kuntz DM, Jones MR, Brooks BR, Wilson AK. SAMPL6 logP challenge: machine learning and quantum mechanical approaches. Journal of Computer-Aided Molecular Design. PMID 32002780 DOI: 10.1007/S10822-020-00287-0  0.35
2020 Prasad S, Brooks BR. A deep learning approach for the blind logP prediction in SAMPL6 challenge. Journal of Computer-Aided Molecular Design. PMID 32002779 DOI: 10.1007/S10822-020-00292-3  0.316
2020 Jones MR, Brooks BR. Quantum chemical predictions of water-octanol partition coefficients applied to the SAMPL6 logP blind challenge. Journal of Computer-Aided Molecular Design. PMID 32002778 DOI: 10.1007/S10822-020-00286-1  0.362
2019 Damjanovic A, Chen AY, Rosenberg RL, Roe DR, Wu X, Brooks BR. Protonation state of the selectivity filter of bacterial voltage-gated sodium channels is modulated by ions. Proteins. PMID 31589792 DOI: 10.1002/Prot.25831  0.777
2019 Wu X, Brooks BR. A double exponential potential for van der Waals interaction. Aip Advances. 9: 065304. PMID 31186990 DOI: 10.1063/1.5107505  0.333
2019 Wu X, Brooks BR. The homogeneity condition: A simple way to derive isotropic periodic sum potentials for efficient calculation of long-range interactions in molecular simulation. The Journal of Chemical Physics. 150: 214109. PMID 31176325 DOI: 10.1063/1.5097560  0.364
2019 Tian R, Zhu S, Zeng Q, Lang L, Ma Y, Kiesewetter D, Liu Y, Fu X, Lau J, Zhu G, Jacobson O, Wang Z, Dai Y, Yu G, Brooks B, et al. An albumin sandwich enhances in vivo circulation and stability of metabolically labile peptides. Bioconjugate Chemistry. PMID 31082207 DOI: 10.1021/Acs.Bioconjchem.9B00258  0.305
2019 Krämer A, Pickard FC, Huang J, Venable RM, Simmonett AC, Reith D, Kirschner KN, Pastor RW, Brooks BR. Interactions of Water and Alkanes: Modifying Additive Force Fields to Account for Polarization Effects. Journal of Chemical Theory and Computation. PMID 31002505 DOI: 10.1021/Acs.Jctc.9B00016  0.383
2019 Damjanovic A, Chen AY, Rosenberg RL, Roe D, Brooks BR. Constant pH Study of a Sodium Channel Biophysical Journal. 116: 387a. DOI: 10.1016/J.Bpj.2018.11.2098  0.517
2018 König G, Brooks BR, Thiel W, York DM. On the convergence of multi-scale free energy simulations. Molecular Simulation. 44: 1062-1081. PMID 30581251 DOI: 10.1080/08927022.2018.1475741  0.622
2018 König G, Pickard FC, Huang J, Thiel W, MacKerell AD, Brooks BR, York DM. A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes. Molecules (Basel, Switzerland). 23. PMID 30347691 DOI: 10.3390/Molecules23102695  0.65
2018 Nishikawa N, Han K, Wu X, Tofoleanu F, Brooks BR. Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for SAMPL6 octa-acid host-guest challenges. Journal of Computer-Aided Molecular Design. PMID 30324304 DOI: 10.1007/S10822-018-0166-2  0.38
2018 Prasad S, Huang J, Zeng Q, Brooks BR. An explicit-solvent hybrid QM and MM approach for predicting pKa of small molecules in SAMPL6 challenge. Journal of Computer-Aided Molecular Design. PMID 30276503 DOI: 10.1007/S10822-018-0167-1  0.392
2018 Hudson PS, Han K, Woodcock HL, Brooks BR. Force matching as a stepping stone to QM/MM CB[8] host/guest binding free energies: a SAMPL6 cautionary tale. Journal of Computer-Aided Molecular Design. PMID 30276502 DOI: 10.1007/s10822-018-0165-3  0.798
2018 Narayan B, Herbert C, Yuan Y, Rodriguez BJ, Brooks BR, Buchete NV. Conformational analysis of replica exchange MD: Temperature-dependent Markov networks for FF amyloid peptides. The Journal of Chemical Physics. 149: 072323. PMID 30134732 DOI: 10.1063/1.5027580  0.382
2018 Damjanovic A, Miller BT, Okur A, Brooks BR. Reservoir pH replica exchange. The Journal of Chemical Physics. 149: 072321. PMID 30134701 DOI: 10.1063/1.5027413  0.589
2018 Zeng Q, Jones MR, Brooks BR. Absolute and relative pK predictions via a DFT approach applied to the SAMPL6 blind challenge. Journal of Computer-Aided Molecular Design. PMID 30128926 DOI: 10.1007/S10822-018-0150-X  0.383
2018 Han K, Hudson PS, Jones MR, Nishikawa N, Tofoleanu F, Brooks BR. Prediction of CB[8] host-guest binding free energies in SAMPL6 using the double-decoupling method. Journal of Computer-Aided Molecular Design. PMID 30084077 DOI: 10.1007/S10822-018-0144-8  0.803
2018 Wu X, Brooks BR. Hydronium Ions Accompanying Buried Acidic Residues Lead to High Apparent Dielectric Constants in the Interior of Proteins. The Journal of Physical Chemistry. B. PMID 29771522 DOI: 10.1021/Acs.Jpcb.8B04584  0.37
2018 Pan A, Pan A, Brooks BR, Wu X. New Structure and Energy Cycles of Kinesin Dimers Walking on Microtubules Revealed from Molecular Simulations Biophysical Journal. 114: 510a. DOI: 10.1016/J.Bpj.2017.11.2786  0.369
2017 Leonard AN, Simmonett AC, Pickard FC, Huang J, Venable RM, Klauda JB, Brooks BR, Pastor RW. Comparison of Additive and Polarizable Models with Explicit Treatment of Long-Range Lennard-Jones Interactions using Alkane Simulations. Journal of Chemical Theory and Computation. PMID 29268012 DOI: 10.1021/Acs.Jctc.7B00948  0.374
2017 Huang J, Simmonett AC, Pickard FC, MacKerell AD, Brooks BR. Mapping the Drude polarizable force field onto a multipole and induced dipole model. The Journal of Chemical Physics. 147: 161702. PMID 29096511 DOI: 10.1063/1.4984113  0.338
2017 Wang M, Li P, Jia X, Liu W, Shao Y, Hu W, Zheng J, Brooks BR, Mei Y. An Efficient Strategy for the Calculation of Solvation Free Energies in Water and Chloroform at the Quantum Mechanical/Molecular Mechanical Level. Journal of Chemical Information and Modeling. PMID 28933850 DOI: 10.1021/Acs.Jcim.7B00001  0.446
2017 Li Y, Li H, Pickard FC, Narayanan B, Sen F, Chan MKY, Sankaranarayanan S, Brooks BR, Roux B. Machine Learning Force Field Parameters from Ab Initio Data. Journal of Chemical Theory and Computation. PMID 28800233 DOI: 10.1021/Acs.Jctc.7B00521  0.503
2017 Eastman P, Swails J, Chodera JD, McGibbon RT, Zhao Y, Beauchamp KA, Wang LP, Simmonett AC, Harrigan MP, Stern CD, Wiewiora RP, Brooks BR, Pande VS. OpenMM 7: Rapid development of high performance algorithms for molecular dynamics. Plos Computational Biology. 13: e1005659. PMID 28746339 DOI: 10.1371/Journal.Pcbi.1005659  0.596
2017 Huang J, Mei Y, Koenig G, Simmonett AC, Pickard FC, Wu Q, Wang LP, MacKerell AD, Brooks BR, Shao Y. An Estimation of Hybrid Quantum Mechanical Molecular Mechanical (QM/MM) Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches. Journal of Chemical Theory and Computation. PMID 28081366 DOI: 10.1021/Acs.Jctc.6B01125  0.406
2017 Lee J, Lee I, Joung I, Lee J, Brooks BR. Finding Dominant Reaction Pathways via Global Optimization of Action Biophysical Journal. 112: 290a. DOI: 10.1016/J.Bpj.2016.11.1570  0.328
2016 Wu X, Pickard FC, Brooks BR. Isotropic periodic sum for multipole interactions and a vector relation for calculation of the Cartesian multipole tensor. The Journal of Chemical Physics. 145: 164110. PMID 27802614 DOI: 10.1063/1.4966019  0.374
2016 Wu X, Lee J, Brooks BR. Origin of pKa Shifts of Internal Lysine Residues in SNase Studied via Equal-Molar VMMS Simulations in Explicit Water. The Journal of Physical Chemistry. B. PMID 27700118 DOI: 10.1021/Acs.Jpcb.6B08249  0.404
2016 Tofoleanu F, Lee J, Pickard Iv FC, König G, Huang J, Baek M, Seok C, Brooks BR. Absolute binding free energies for octa-acids and guests in SAMPL5 : Evaluating binding free energies for octa-acid and guest complexes in the SAMPL5 blind challenge. Journal of Computer-Aided Molecular Design. PMID 27696242 DOI: 10.1007/S10822-016-9965-5  0.414
2016 Lee J, Tofoleanu F, Pickard FC, König G, Huang J, Damjanović A, Baek M, Seok C, Brooks BR. Absolute binding free energy calculations of CBClip host-guest systems in the SAMPL5 blind challenge. Journal of Computer-Aided Molecular Design. PMID 27677749 DOI: 10.1007/S10822-016-9968-2  0.672
2016 Pickard FC, König G, Simmonett AC, Shao Y, Brooks BR. An efficient protocol for obtaining accurate hydration free energies using quantum chemistry and reweighting from molecular dynamics simulations. Bioorganic & Medicinal Chemistry. PMID 27667551 DOI: 10.1016/J.Bmc.2016.08.031  0.432
2016 Jones MR, Brooks BR, Wilson AK. Partition coefficients for the SAMPL5 challenge using transfer free energies. Journal of Computer-Aided Molecular Design. PMID 27646287 DOI: 10.1007/S10822-016-9964-6  0.371
2016 Pickard FC, König G, Tofoleanu F, Lee J, Simmonett AC, Shao Y, Ponder JW, Brooks BR. Blind prediction of distribution in the SAMPL5 challenge with QM based protomer and pK a corrections. Journal of Computer-Aided Molecular Design. PMID 27646286 DOI: 10.1007/S10822-016-9955-7  0.412
2016 König G, Pickard FC, Huang J, Simmonett AC, Tofoleanu F, Lee J, Dral PO, Prasad S, Jones M, Shao Y, Thiel W, Brooks BR. 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. Journal of Computer-Aided Molecular Design. PMID 27577746 DOI: 10.1007/S10822-016-9936-X  0.452
2016 Dybeck EC, König G, Brooks BR, Shirts MR. A Comparison of Methods to Reweight from Classical Molecular Simulations to QM/MM Potentials. Journal of Chemical Theory and Computation. PMID 26928941 DOI: 10.1021/Acs.Jctc.5B01188  0.43
2016 Jia X, Wang M, Shao Y, König G, Brooks BR, Zhang JZ, Mei Y. Calculations of Solvation Free Energy through Energy Reweighting from Molecular Mechanics to Quantum Mechanics. Journal of Chemical Theory and Computation. PMID 26731197 DOI: 10.1021/Acs.Jctc.5B00920  0.44
2015 König G, Mei Y, Pickard FC, Simmonett AC, Miller BT, Herbert JM, Woodcock HL, Brooks BR, Shao Y. Computation of Hydration Free Energies Using the Multiple Environment Single System Quantum Mechanical/Molecular Mechanical (MESS-QM/MM) Method. Journal of Chemical Theory and Computation. PMID 26613419 DOI: 10.1021/Acs.Jctc.5B00874  0.458
2015 Lee J, Joo K, Brooks BR, Lee J. The Atomistic Mechanism of Conformational Transition of Adenylate Kinase Investigated by Lorentzian Structure-Based Potential. Journal of Chemical Theory and Computation. 11: 3211-3224. PMID 26575758 DOI: 10.1021/Acs.Jctc.5B00268  0.33
2015 Lee J, Miller BT, Damjanović A, Brooks BR. Enhancing Constant-pH Simulation in Explicit Solvent with a Two-Dimensional Replica Exchange Method. Journal of Chemical Theory and Computation. 11: 2560-2574. PMID 26575555 DOI: 10.1021/Ct501101F  0.585
2015 Tan ML, Tran K, Pickard FC, Simmonett AC, Brooks BR, Ichiye T. Molecular Multipole Potential Energy Functions for Water. The Journal of Physical Chemistry. B. PMID 26562223 DOI: 10.1021/Acs.Jpcb.5B09565  0.376
2015 Konc J, Miller BT, Štular T, Lešnik S, Woodcock HL, Brooks BR, Janežič D. ProBiS-CHARMMing: Web Interface for Prediction and Optimization of Ligands in Protein Binding Sites. Journal of Chemical Information and Modeling. PMID 26509288 DOI: 10.1021/Acs.Jcim.5B00534  0.322
2015 Wu X, Brooks BR. A Virtual Mixture Approach to the Study of Multistate Equilibrium: Application to Constant pH Simulation in Explicit Water. Plos Computational Biology. 11: e1004480. PMID 26506245 DOI: 10.1371/Journal.Pcbi.1004480  0.395
2015 Joo K, Joung I, Lee J, Lee J, Lee W, Brooks B, Lee SJ, Lee J. Protein structure determination by conformational space annealing using NMR geometric restraints. Proteins. PMID 26454251 DOI: 10.1002/Prot.24941  0.302
2015 Simmonett AC, Pickard FC, Shao Y, Cheatham TE, Brooks BR. Efficient treatment of induced dipoles. The Journal of Chemical Physics. 143: 074115. PMID 26298123 DOI: 10.1063/1.4928530  0.59
2015 Lee J, Miller BT, Brooks BR. Computational scheme for pH-dependent binding free energy calculation with explicit solvent. Protein Science : a Publication of the Protein Society. PMID 26189656 DOI: 10.1002/Pro.2755  0.399
2015 Wu X, Brooks BR, Vanden-Eijnden E. Self-guided Langevin dynamics via generalized Langevin equation. Journal of Computational Chemistry. PMID 26183423 DOI: 10.1002/Jcc.24015  0.345
2015 Mei Y, Simmonett AC, Pickard FC, DiStasio RA, Brooks BR, Shao Y. Numerical study on the partitioning of the molecular polarizability into fluctuating charge and induced atomic dipole contributions. The Journal of Physical Chemistry. A. 119: 5865-82. PMID 25945749 DOI: 10.1021/Acs.Jpca.5B03159  0.323
2015 Kelly CM, Muzard J, Brooks BR, Lee GU, Buchete NV. Structure and dynamics of the fibronectin-III domains of Aplysia californica cell adhesion molecules. Physical Chemistry Chemical Physics : Pccp. 17: 9634-43. PMID 25729787 DOI: 10.1039/C4Cp05307A  0.32
2015 Sodt AJ, Mei Y, König G, Tao P, Steele RP, Brooks BR, Shao Y. Multiple environment single system quantum mechanical/molecular mechanical (MESS-QM/MM) calculations. 1. Estimation of polarization energies. The Journal of Physical Chemistry. A. 119: 1511-23. PMID 25321186 DOI: 10.1021/Jp5072296  0.384
2015 Kelly CM, Northey T, Ryan K, Brooks BR, Kholkin AL, Rodriguez BJ, Buchete NV. Conformational dynamics and aggregation behavior of piezoelectric diphenylalanine peptides in an external electric field. Biophysical Chemistry. 196: 16-24. PMID 25240398 DOI: 10.1016/J.Bpc.2014.08.009  0.301
2015 König G, Brooks BR. Correcting for the free energy costs of bond or angle constraints in molecular dynamics simulations. Biochimica Et Biophysica Acta. 1850: 932-43. PMID 25218695 DOI: 10.1016/J.Bbagen.2014.09.001  0.433
2015 Shao Y, Simmonett A, Pickard F, Koenig G, Brooks B. Quantum Mechanical Molecular Mechanical Calculations using AMOEBA Force Fields Biophysical Journal. 108: 158a. DOI: 10.1016/J.Bpj.2014.11.871  0.37
2015 Damjanovic A, Miller BT, Okur A, Garcia-Moreno B, Brooks BR. Constant pH Simulations with the Double Reservoir pH Replica Exchange Biophysical Journal. 108: 47a. DOI: 10.1016/J.Bpj.2014.11.290  0.576
2015 Tofoleanu F, Brooks B. Computational Studies on the cAMP Modulation of the HCN2 Channel Biophysical Journal. 108: 208a. DOI: 10.1016/J.Bpj.2014.11.1149  0.329
2014 Tao P, Sodt AJ, Shao Y, König G, Brooks BR. Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics. Journal of Chemical Theory and Computation. 10: 4198-4207. PMID 25328492 DOI: 10.1021/Ct500342H  0.422
2014 Lee J, Miller BT, Damjanovi? A, Brooks BR. Constant pH Molecular Dynamics in Explicit Solvent with Enveloping Distribution Sampling and Hamiltonian Exchange. Journal of Chemical Theory and Computation. 10: 2738-2750. PMID 25061443 DOI: 10.1021/Ct500175M  0.39
2014 Perrin BS, Miller BT, Schalk V, Woodcock HL, Brooks BR, Ichiye T. Web-based computational chemistry education with CHARMMing III: Reduction potentials of electron transfer proteins. Plos Computational Biology. 10: e1003739. PMID 25058418 DOI: 10.1371/Journal.Pcbi.1003739  0.348
2014 Pickard FC, Miller BT, Schalk V, Lerner MG, Woodcock HL, Brooks BR. Web-based computational chemistry education with CHARMMing II: Coarse-grained protein folding. Plos Computational Biology. 10: e1003738. PMID 25058338 DOI: 10.1371/Journal.Pcbi.1003738  0.343
2014 Miller BT, Singh RP, Schalk V, Pevzner Y, Sun J, Miller CS, Boresch S, Ichiye T, Brooks BR, Woodcock HL. Web-based computational chemistry education with CHARMMing I: Lessons and tutorial. Plos Computational Biology. 10: e1003719. PMID 25057988 DOI: 10.1371/Journal.Pcbi.1003719  0.646
2014 Simmonett AC, Pickard FC, Schaefer HF, Brooks BR. An efficient algorithm for multipole energies and derivatives based on spherical harmonics and extensions to particle mesh Ewald. The Journal of Chemical Physics. 140: 184101. PMID 24832247 DOI: 10.1063/1.4873920  0.377
2014 Rinschen MM, Wu X, König T, Pisitkun T, Hagmann H, Pahmeyer C, Lamkemeyer T, Kohli P, Schnell N, Schermer B, Dryer S, Brooks BR, Beltrao P, Krueger M, Brinkkoetter PT, et al. Phosphoproteomic analysis reveals regulatory mechanisms at the kidney filtration barrier. Journal of the American Society of Nephrology : Jasn. 25: 1509-22. PMID 24511133 DOI: 10.1681/Asn.2013070760  0.301
2014 König G, Pickard FC, Mei Y, Brooks BR. Predicting hydration free energies with a hybrid QM/MM approach: an evaluation of implicit and explicit solvation models in SAMPL4. Journal of Computer-Aided Molecular Design. 28: 245-57. PMID 24504703 DOI: 10.1007/S10822-014-9708-4  0.471
2013 Wright JD, Sargsyan K, Wu X, Brooks BR, Lim C. Protein-Protein Docking Using EMAP in CHARMM and Support Vector Machine: Application to Ab/Ag Complexes. Journal of Chemical Theory and Computation. 9: 4186-94. PMID 26592408 DOI: 10.1021/Ct400508S  0.322
2013 Wu X, Subramaniam S, Case DA, Wu KW, Brooks BR. Targeted conformational search with map-restrained self-guided Langevin dynamics: application to flexible fitting into electron microscopic density maps. Journal of Structural Biology. 183: 429-40. PMID 23876978 DOI: 10.1016/J.Jsb.2013.07.006  0.324
2013 Okur A, Miller BT, Joo K, Lee J, Brooks BR. Generating reservoir conformations for replica exchange through the use of the conformational space annealing method. Journal of Chemical Theory and Computation. 9: 1115-1124. PMID 23585739 DOI: 10.1021/Ct300996M  0.389
2013 Yu X, Wu X, Bermejo GA, Brooks BR, Taraska JW. Accurate high-throughput structure mapping and prediction with transition metal ion FRET. Structure (London, England : 1993). 21: 9-19. PMID 23273426 DOI: 10.1016/J.Str.2012.11.013  0.343
2013 Wu KW, Liu K, Brooks BR, Wu X. Kinesin Walks on Microtubule through the Conformation-Extension Mechanism Biophysical Journal. 104: 323a. DOI: 10.1016/J.Bpj.2012.11.1790  0.366
2012 König G, Miller BT, Boresch S, Wu X, Brooks BR. Enhanced Sampling in Free Energy Calculations: Combining SGLD with the Bennett's Acceptance Ratio and Enveloping Distribution Sampling Methods. Journal of Chemical Theory and Computation. 8: 3650-62. PMID 26593010 DOI: 10.1021/Ct300116R  0.72
2012 Wu X, Damjanovic A, Brooks BR. Efficient and Unbiased Sampling of Biomolecular Systems in the Canonical Ensemble: A Review of Self-Guided Langevin Dynamics. Advances in Chemical Physics. 150: 255-326. PMID 23913991 DOI: 10.1002/9781118197714.Ch6  0.629
2012 Tao P, Hodoš?ek M, Larkin JD, Shao Y, Brooks BR. Comparison of Three Chain-of-States Methods: Nudged Elastic Band and Replica Path with Restraints or Constraints. Journal of Chemical Theory and Computation. 8: 5035-5051. PMID 23526888 DOI: 10.1021/Ct3006248  0.312
2012 Smith DB, Okur A, Brooks B. MDMS: Molecular Dynamics Meta-Simulator for evaluating exchange type sampling methods. Chemical Physics Letters. 545: 118-124. PMID 23087450 DOI: 10.1016/J.Cplett.2012.07.015  0.402
2012 BorÅ¡tnik U, Miller BT, Brooks BR, Janežič D. Implementation of the force decomposition machine for molecular dynamics simulations. Journal of Molecular Graphics & Modelling. 38: 243-7. PMID 23085166 DOI: 10.1016/J.Jmgm.2012.06.015  0.312
2012 Tao P, Wu X, Brooks BR. Maintain rigid structures in Verlet based cartesian molecular dynamics simulations. The Journal of Chemical Physics. 137: 134110. PMID 23039588 DOI: 10.1063/1.4756796  0.361
2012 Carl N, Hodoš?ek M, Vehar B, Konc J, Brooks BR, Janeži? D. Correlating protein hot spot surface analysis using ProBiS with simulated free energies of protein-protein interfacial residues. Journal of Chemical Information and Modeling. 52: 2541-9. PMID 23009716 DOI: 10.1021/Ci3003254  0.369
2012 Ghysels A, Miller BT, Pickard FC, Brooks BR. Comparing normal modes across different models and scales: Hessian reduction versus coarse-graining. Journal of Computational Chemistry. 33: 2250-75. PMID 22941785 DOI: 10.1002/Jcc.23076  0.318
2012 Wu X, Hodoscek M, Brooks BR. Replica exchanging self-guided Langevin dynamics for efficient and accurate conformational sampling. The Journal of Chemical Physics. 137: 044106. PMID 22852596 DOI: 10.1063/1.4737094  0.354
2012 Biswas PK, Vellore NA, Yancey JA, Kucukkal TG, Collier G, Brooks BR, Stuart SJ, Latour RA. Simulation of multiphase systems utilizing independent force fields to control intraphase and interphase behavior. Journal of Computational Chemistry. 33: 1458-66. PMID 22488548 DOI: 10.1002/Jcc.22979  0.393
2012 König G, Brooks BR. Predicting binding affinities of host-guest systems in the SAMPL3 blind challenge: the performance of relative free energy calculations. Journal of Computer-Aided Molecular Design. 26: 543-50. PMID 22198474 DOI: 10.1007/S10822-011-9525-Y  0.419
2012 O'Brien EP, Brooks BR, Thirumalai D. Effects of pH on proteins: predictions for ensemble and single-molecule pulling experiments. Journal of the American Chemical Society. 134: 979-87. PMID 22148729 DOI: 10.1021/Ja206557Y  0.649
2012 König G, Miller BT, Boresch S, Wu X, Brooks BR. Enhanced sampling in free energy calculations: Combining SGLD with the Bennett's acceptance ratio and enveloping distribution sampling methods Journal of Chemical Theory and Computation. 8: 3650-3662. DOI: 10.1021/ct300116r  0.641
2012 Wu X, Hodoscek M, Brooks BR. Replica Exchange of Self-Guided Langevin Dynamics Simulation Biophysical Journal. 102: 171a. DOI: 10.1016/J.Bpj.2011.11.930  0.379
2011 Ghysels A, Woodcock HL, Larkin JD, Miller BT, Shao Y, Kong J, Neck DV, Speybroeck VV, Waroquier M, Brooks BR. Efficient Calculation of QM/MM Frequencies with the Mobile Block Hessian. Journal of Chemical Theory and Computation. 7: 496-514. PMID 26596169 DOI: 10.1021/Ct100473F  0.337
2011 Wu X, Brooks BR. Force-momentum-based self-guided Langevin dynamics: a rapid sampling method that approaches the canonical ensemble. The Journal of Chemical Physics. 135: 204101. PMID 22128922 DOI: 10.1063/1.3662489  0.446
2011 BorÅ¡tnik U, Miller BT, Brooks BR, Janežič D. The distributed diagonal force decomposition method for parallelizing molecular dynamics simulations. Journal of Computational Chemistry. 32: 3005-13. PMID 21793007 DOI: 10.1002/Jcc.21882  0.374
2011 Woodcock HL, Miller BT, Hodoscek M, Okur A, Larkin JD, Ponder JW, Brooks BR. MSCALE: A General Utility for Multiscale Modeling. Journal of Chemical Theory and Computation. 7: 1208-1219. PMID 21691425 DOI: 10.1021/Ct100738H  0.393
2011 O'Brien EP, Straub JE, Brooks BR, Thirumalai D. Influence of Nanoparticle Size and Shape on Oligomer Formation of an Amyloidogenic Peptide. The Journal of Physical Chemistry Letters. 2: 1171-1177. PMID 21691423 DOI: 10.1021/Jz200330K  0.663
2011 Wu X, Brooks BR. Toward canonical ensemble distribution from self-guided Langevin dynamics simulation. The Journal of Chemical Physics. 134: 134108. PMID 21476744 DOI: 10.1063/1.3574397  0.347
2011 Damjanovi? A, Brooks BR, García-Moreno B. Conformational relaxation and water penetration coupled to ionization of internal groups in proteins. The Journal of Physical Chemistry. A. 115: 4042-53. PMID 21428436 DOI: 10.1021/Jp110373F  0.322
2011 Damjanovic A, Wu X, Garcia-Moreno B, Brooks BR. Conformational Relaxation and Water Penetration Triggered by the Ionization of Internal Groups in Proteins Biophysical Journal. 100: 309a. DOI: 10.1016/J.Bpj.2010.12.1890  0.599
2010 Larkin JD, Fossey JS, James TD, Brooks BR, Bock CW. A computational investigation of the nitrogen-boron interaction in o-(N,N-dialkylaminomethyl)arylboronate systems. The Journal of Physical Chemistry. A. 114: 12531-9. PMID 21050022 DOI: 10.1021/Jp1087674  0.311
2010 Pendse PY, Brooks BR, Klauda JB. Probing the periplasmic-open state of lactose permease in response to sugar binding and proton translocation. Journal of Molecular Biology. 404: 506-21. PMID 20875429 DOI: 10.1016/J.Jmb.2010.09.045  0.386
2010 Liu F, Gan Z, Shao Y, Hsu CP, Dreuw A, Head-Gordon M, Miller BT, Brooks BR, Yu JG, Furlani TR, Kong J. A parallel implementation of the analytic nuclear gradient for time-dependent density functional theory within the Tamm-Dancoff approximation Molecular Physics. 108: 2791-2800. DOI: 10.1080/00268976.2010.526642  0.344
2009 Ghysels A, Van Speybroeck V, Pauwels E, Van Neck D, Brooks BR, Waroquier M. Mobile Block Hessian Approach with Adjoined Blocks: An Efficient Approach for the Calculation of Frequencies in Macromolecules. Journal of Chemical Theory and Computation. 5: 1203-15. PMID 26609711 DOI: 10.1021/Ct800489R  0.347
2009 O'Brien EP, Okamoto Y, Straub JE, Brooks BR, Thirumalai D. Thermodynamic perspective on the dock-lock growth mechanism of amyloid fibrils. The Journal of Physical Chemistry. B. 113: 14421-30. PMID 19813700 DOI: 10.1021/Jp9050098  0.716
2009 Wu X, Brooks BR. Isotropic periodic sum of electrostatic interactions for polar systems. The Journal of Chemical Physics. 131: 024107. PMID 19603970 DOI: 10.1063/1.3160730  0.3
2009 Rosta E, Woodcock HL, Brooks BR, Hummer G. Artificial reaction coordinate "tunneling" in free-energy calculations: the catalytic reaction of RNase H. Journal of Computational Chemistry. 30: 1634-41. PMID 19462398 DOI: 10.1002/Jcc.21312  0.356
2009 Brooks BR, Brooks CL, Mackerell AD, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, et al. CHARMM: the biomolecular simulation program. Journal of Computational Chemistry. 30: 1545-614. PMID 19444816 DOI: 10.1002/Jcc.21287  0.767
2009 Damjanovi? A, García-Moreno E B, Brooks BR. Self-guided Langevin dynamics study of regulatory interactions in NtrC. Proteins. 76: 1007-19. PMID 19384996 DOI: 10.1002/Prot.22439  0.355
2009 O'Brien EP, Morrison G, Brooks BR, Thirumalai D. How accurate are polymer models in the analysis of Förster resonance energy transfer experiments on proteins? The Journal of Chemical Physics. 130: 124903. PMID 19334885 DOI: 10.1063/1.3082151  0.629
2009 O'Brien EP, Brooks BR, Thirumalai D. Molecular origin of constant m-values, denatured state collapse, and residue-dependent transition midpoints in globular proteins. Biochemistry. 48: 3743-54. PMID 19278261 DOI: 10.1021/bi8021119  0.599
2009 Ghysels A, Van Neck D, Brooks BR, Van Speybroeck V, Waroquier M. Normal modes for large molecules with arbitrary link constraints in the mobile block Hessian approach. The Journal of Chemical Physics. 130: 084107. PMID 19256597 DOI: 10.1063/1.3071261  0.329
2009 Buch I, Brooks BR, Wolfson HJ, Nussinov R. Computational validation of protein nanotubes. Nano Letters. 9: 1096-102. PMID 19199488 DOI: 10.1021/Nl803521J  0.331
2009 Singh RP, Brooks BR, Klauda JB. Binding and release of cholesterol in the Osh4 protein of yeast. Proteins. 75: 468-77. PMID 18937371 DOI: 10.1002/Prot.22263  0.348
2009 Rosta E, Woodcock HL, Brooks BR, Hummer G. Artificial Reaction Coordinate “Tunneling” In Free Energy Calculations: Nucleic Acid Cleavage By Ribonuclease-H Biophysical Journal. 96: 573a. DOI: 10.1016/J.Bpj.2008.12.3750  0.344
2009 Pendse PY, Brooks BR, Klauda JB. An Atomic-level Model for the Periplasmic Open State of Lactose Permease Biophysical Journal. 96: 430a. DOI: 10.1016/J.Bpj.2008.12.2201  0.369
2009 Biswas PK, O'Brien CO, Stuart SJ, Latour RA, Brooks BR. Simultaneous Use Of Class-i And Class-ii Force Fields In CHARMM For Solid-liquid Multiphase Simulation Of Protein-surface Interaction Biophysical Journal. 96: 405a-406a. DOI: 10.1016/J.Bpj.2008.12.2065  0.313
2008 Klauda JB, Brooks BR. CHARMM Force Field Parameters for Nitroalkanes and Nitroarenes. Journal of Chemical Theory and Computation. 4: 107-15. PMID 26619984 DOI: 10.1021/Ct700191V  0.385
2008 Woodcock HL, Zheng W, Ghysels A, Shao Y, Kong J, Brooks BR. Vibrational subsystem analysis: A method for probing free energies and correlations in the harmonic limit. The Journal of Chemical Physics. 129: 214109. PMID 19063546 DOI: 10.1063/1.3013558  0.386
2008 Wu X, Brooks BR. Using the isotropic periodic sum method to calculate long-range interactions of heterogeneous systems. The Journal of Chemical Physics. 129: 154115. PMID 19045184 DOI: 10.1063/1.2992601  0.342
2008 Damjanović A, Miller BT, Wenaus TJ, Maksimović P, García-Moreno E B, Brooks BR. Open science grid study of the coupling between conformation and water content in the interior of a protein. Journal of Chemical Information and Modeling. 48: 2021-9. PMID 18834189 DOI: 10.1021/Ci800263C  0.385
2008 O'Brien EP, Stan G, Thirumalai D, Brooks BR. Factors governing helix formation in peptides confined to carbon nanotubes. Nano Letters. 8: 3702-8. PMID 18817452 DOI: 10.1021/Nl8019328  0.618
2008 O'Brien EP, Ziv G, Haran G, Brooks BR, Thirumalai D. Effects of denaturants and osmolytes on proteins are accurately predicted by the molecular transfer model. Proceedings of the National Academy of Sciences of the United States of America. 105: 13403-8. PMID 18757747 DOI: 10.1073/Pnas.0802113105  0.636
2008 Sherwood P, Brooks BR, Sansom MS. Multiscale methods for macromolecular simulations. Current Opinion in Structural Biology. 18: 630-40. PMID 18721882 DOI: 10.1016/J.Sbi.2008.07.003  0.394
2008 Miller BT, Singh RP, Klauda JB, Hodoscek M, Brooks BR, Woodcock HL. CHARMMing: a new, flexible web portal for CHARMM. Journal of Chemical Information and Modeling. 48: 1920-9. PMID 18698840 DOI: 10.1021/Ci800133B  0.365
2008 Damjanovi? A, Wu X, García-Moreno E B, Brooks BR. Backbone relaxation coupled to the ionization of internal groups in proteins: a self-guided Langevin dynamics study. Biophysical Journal. 95: 4091-101. PMID 18641078 DOI: 10.1529/Biophysj.108.130906  0.35
2008 Rosales T, Xu J, Wu X, Hodoscek M, Callis P, Brooks BR, Knutson JR. Molecular dynamics simulations of perylene and tetracene librations: comparison with femtosecond upconversion data. The Journal of Physical Chemistry. A. 112: 5593-7. PMID 18507364 DOI: 10.1021/Jp7117289  0.311
2008 Klauda JB, Roberts MF, Redfield AG, Brooks BR, Pastor RW. Rotation of lipids in membranes: molecular dynamics simulation, 31P spin-lattice relaxation, and rigid-body dynamics. Biophysical Journal. 94: 3074-83. PMID 18192349 DOI: 10.1529/Biophysj.107.121806  0.314
2008 Klauda JB, Eldho NV, Gawrisch K, Brooks BR, Pastor RW. Collective and noncollective models of NMR relaxation in lipid vesicles and multilayers. The Journal of Physical Chemistry. B. 112: 5924-9. PMID 18179193 DOI: 10.1021/Jp075641W  0.318
2008 Larkin JD, Milkevitch M, Bhat KL, Markham GD, Brooks BR, Bock CW. Dimers of boroglycine and methylamine boronic acid: a computational comparison of the relative importance of dative versus hydrogen bonding. The Journal of Physical Chemistry. A. 112: 125-33. PMID 18072757 DOI: 10.1021/Jp076537H  0.349
2007 Woodcock HL, Moran D, Pastor RW, MacKerell AD, Brooks BR. Ab initio modeling of glycosyl torsions and anomeric effects in a model carbohydrate: 2-ethoxy tetrahydropyran. Biophysical Journal. 93: 1-10. PMID 17554075 DOI: 10.1529/Biophysj.106.099986  0.349
2007 O'Brien EP, Dima RI, Brooks B, Thirumalai D. Interactions between hydrophobic and ionic solutes in aqueous guanidinium chloride and urea solutions: Lessons for protein denaturation mechanism Journal of the American Chemical Society. 129: 7346-7353. PMID 17503819 DOI: 10.1021/Ja069232+  0.632
2007 Klauda JB, Wu X, Pastor RW, Brooks BR. Long-range Lennard-Jones and electrostatic interactions in interfaces: application of the isotropic periodic sum method. The Journal of Physical Chemistry. B. 111: 4393-400. PMID 17425357 DOI: 10.1021/Jp068767M  0.319
2007 Woodcock HL, Moran D, Brooks BR, Schleyer PVR, Schaefer HF. Carbene stabilization by aryl substituents. Is bigger better? Journal of the American Chemical Society. 129: 3763-3770. PMID 17326641 DOI: 10.1021/Ja068899T  0.323
2007 Klauda JB, Brooks BR. Sugar binding in lactose permease: anomeric state of a disaccharide influences binding structure. Journal of Molecular Biology. 367: 1523-34. PMID 17320103 DOI: 10.1016/J.Jmb.2007.02.001  0.351
2006 Stan G, Brooks BR, Lorimer GH, Thirumalai D. Residues in substrate proteins that interact with GroEL in the capture process are buried in the native state Proceedings of the National Academy of Sciences of the United States of America. 103: 4433-4438. PMID 16537402 DOI: 10.1073/Pnas.0600433103  0.308
2006 Klauda JB, Kucerka N, Brooks BR, Pastor RW, Nagle JF. Simulation-based methods for interpreting x-ray data from lipid bilayers. Biophysical Journal. 90: 2796-807. PMID 16443652 DOI: 10.1529/Biophysj.105.075697  0.348
2005 Klauda JB, Brooks BR, MacKerell AD, Venable RM, Pastor RW. An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer. The Journal of Physical Chemistry. B. 109: 5300-11. PMID 16863197 DOI: 10.1021/Jp0468096  0.407
2005 Klauda JB, Pastor RW, Brooks BR. Adjacent gauche stabilization in linear alkanes: implications for polymer models and conformational analysis. The Journal of Physical Chemistry. B. 109: 15684-6. PMID 16852989 DOI: 10.1021/Jp0527608  0.387
2005 Stan G, Brooks BR, Thirumalai D. Probing the "annealing" mechanism of GroEL minichaperone using molecular dynamics simulations Journal of Molecular Biology. 350: 817-829. PMID 15967467 DOI: 10.1016/J.Jmb.2005.05.012  0.345
2005 Zheng W, Brooks BR. Probing the local dynamics of nucleotide-binding pocket coupled to the global dynamics: myosin versus kinesin. Biophysical Journal. 89: 167-78. PMID 15879477 DOI: 10.1529/Biophysj.105.063305  0.302
2005 Zheng W, Brooks BR. Normal-modes-based prediction of protein conformational changes guided by distance constraints. Biophysical Journal. 88: 3109-17. PMID 15722427 DOI: 10.1529/Biophysj.104.058453  0.338
2005 Zheng W, Brooks B. Identification of dynamical correlations within the myosin motor domain by the normal mode analysis of an elastic network model. Journal of Molecular Biology. 346: 745-59. PMID 15713460 DOI: 10.1016/J.Jmb.2004.12.020  0.329
2004 Chu JW, Brooks BR, Trout BL. Oxidation of methionine residues in aqueous solutions: free methionine and methionine in granulocyte colony-stimulating factor. Journal of the American Chemical Society. 126: 16601-7. PMID 15600366 DOI: 10.1021/Ja0467059  0.36
2004 Wu X, Brooks BR. β-Hairpin Folding Mechanism of a Nine-Residue Peptide Revealed from Molecular Dynamics Simulations in Explicit Water Biophysical Journal. 86: 1946-1958. PMID 15041639 DOI: 10.1016/S0006-3495(04)74258-7  0.328
2004 Lagüe P, Pastor RW, Brooks BR. Pressure-based long-range correction for Lennard-Jones interactions in molecular dynamics simulations: Application to alkanes and interfaces Journal of Physical Chemistry B. 108: 363-368. DOI: 10.1021/Jp030458Y  0.345
2003 Stan G, Thirumalai D, Lorimer GH, Brooks BR. Annealing function of GroEL: Structural and bioinformatic analysis Biophysical Chemistry. 100: 453-467. PMID 12646383 DOI: 10.1016/S0301-4622(02)00298-3  0.302
2003 Petrella RJ, Andricioaei I, Brooks BR, Karplus M. An improved method for nonbonded list generation: rapid determination of near-neighbor pairs. Journal of Computational Chemistry. 24: 222-31. PMID 12497601 DOI: 10.1002/Jcc.10123  0.685
2003 Wu X, Brooks BR. Self-guided Langevin dynamics simulation method Chemical Physics Letters. 381: 512-518. DOI: 10.1016/J.Cplett.2003.10.013  0.354
2003 Woodcock HL, Hodošček M, Sherwood P, Lee YS, Schaefer HF, Brooks BR. Exploring the quantum mechanical/molecular mechanical replica path method: A pathway optimization of the chorismate to prephenate Claisen rearrangement catalyzed by chorismate mutase Theoretical Chemistry Accounts. 109: 140-148. DOI: 10.1007/S00214-002-0421-3  0.373
2002 Wu X, Wang S, Brooks BR. Direct observation of the folding and unfolding of a β-hairpin in explicit water through computer simulation Journal of the American Chemical Society. 124: 5282-5283. PMID 11996565 DOI: 10.1021/Ja0257321  0.336
2002 Das D, Eurenius KP, Billings EM, Sherwood P, Chatfield DC, Hodoŝĉek M, Brooks BR. Optimization of quantum mechanical molecular mechanical partitioning schemes: Gaussian delocalization of molecular mechanical charges and the double link atom method Journal of Chemical Physics. 117: 10534-10547. DOI: 10.1063/1.1520134  0.351
2001 Cheatham TE, Brooks BR, Kollman PA. Molecular modeling of nucleic acid structure: electrostatics and solvation. Current Protocols in Nucleic Acid Chemistry / Edited by Serge L. Beaucage ... [Et Al.]. Unit 7.9. PMID 18428877 DOI: 10.1002/0471142700.Nc0709S05  0.636
2001 Cheatham TE, Brooks BR, Kollman PA. Molecular modeling of nucleic acid structure: energy and sampling. Current Protocols in Nucleic Acid Chemistry / Edited by Serge L. Beaucage ... [Et Al.]. Unit 7.8. PMID 18428876 DOI: 10.1002/0471142700.Nc0708S04  0.697
2001 Cheatham TE, Brooks BR, Kollman PA. Molecular modeling of nucleic acid structure. Current Protocols in Nucleic Acid Chemistry / Edited by Serge L. Beaucage ... [Et Al.]. Unit 7.5. PMID 18428873 DOI: 10.1002/0471142700.Nc0705S06  0.631
2001 Cheatham TE, Brooks BR, Kollman PA. Molecular modeling of nucleic acid structure: setup and analysis. Current Protocols in Nucleic Acid Chemistry / Edited by Serge L. Beaucage ... [Et Al.]. Unit 7.10. PMID 18428869 DOI: 10.1002/0471142700.Nc0710S06  0.656
2001 Speelman B, Brooks BR, Post CB. Molecular dynamics simulations of human rhinovirus and an antiviral compound. Biophysical Journal. 80: 121-9. PMID 11159387 DOI: 10.1016/S0006-3495(01)75999-1  0.351
2000 Zhou J, Reich S, Brooks BR. Elastic molecular dynamics with self-consistent flexible constraints The Journal of Chemical Physics. 112: 7919-7929. DOI: 10.1063/1.481393  0.422
2000 Venable RM, Brooks BR, Pastor RW. Molecular dynamics simulations of gel (LβI) phase lipid bilayers in constant pressure and constant surface area ensembles The Journal of Chemical Physics. 112: 4822-4832. DOI: 10.1063/1.481085  0.348
1998 Lee YS, Hodoscek M, Brooks BR, Kador PF. Catalytic mechanism of aldose reductase studied by the combined potentials of quantum mechanics and molecular mechanics. Biophysical Chemistry. 70: 203-16. PMID 9546197 DOI: 10.1016/S0301-4622(97)00115-4  0.31
1998 Bogusz S, Cheatham TE, Brooks BR. Removal of pressure and free energy artifacts in charged periodic systems via net charge corrections to the Ewald potential The Journal of Chemical Physics. 108: 7070-7084. DOI: 10.1063/1.476320  0.564
1998 Enyedy IJ, Kovach IM, Brooks BR. Alternate Pathways for Acetic Acid and Acetate ion Release from Acetylcholinesterase:  a Molecular Dynamics Study Journal of the American Chemical Society. 120: 8043-8050. DOI: 10.1021/Ja973131H  0.36
1998 Chatfield DC, Szabo A, Brooks BR. Molecular dynamics of staphylococcal nuclease: Comparison of simulation with 15N and 13C NMR relaxation data Journal of the American Chemical Society. 120: 5301-5311. DOI: 10.1021/Ja972215N  0.344
1998 Chatfield DC, P. Eurenius K, Brooks BR. HIV-1 protease cleavage mechanism: A theoretical investigation based on classical MD simulation and reaction path calculations using a hybrid QM/MM potential Journal of Molecular Structure: Theochem. 423: 79-92. DOI: 10.1016/S0166-1280(96)04875-0  0.336
1998 Cheatham III. TE, Brooks BR. Recent advances in molecular dynamics simulation towards the realistic representation of biomolecules in solution Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta). 99: 279-288. DOI: 10.1007/S002140050337  0.407
1997 Parry CS, Brooks BR, Matsunaga N, Amzel LM. Structures of some substituted nitrophenols determined by ab initio computation on the origin of heterocliticity in anti-nitrophenol antibodies Journal of Molecular Structure-Theochem. 555-563. DOI: 10.1016/S0166-1280(97)00033-X  0.32
1996 Steinbach PJ, Brooks BR. Hydrated myoglobin's anharmonic fluctuations are not primarily due to dihedral transitions. Proceedings of the National Academy of Sciences of the United States of America. 93: 55-9. PMID 8552674 DOI: 10.1073/Pnas.93.1.55  0.315
1996 Feller SE, Pastor RW, Rojnuckarin A, Bogusz S, Brooks BR. Effect of Electrostatic Force Truncation on Interfacial and Transport Properties of Water The Journal of Physical Chemistry. 100: 17011-17020. DOI: 10.1021/Jp9614658  0.351
1996 Eurenius KP, Chatfield DC, Brooks BR, Hodoscek M. Enzyme mechanisms with hybrid quantum and molecular mechanical potentials. I. Theoretical considerations International Journal of Quantum Chemistry. 60: 1189-1200. DOI: 10.1002/(Sici)1097-461X(1996)60:6<1189::Aid-Qua7>3.0.Co;2-W  0.328
1995 Feller SE, Zhang Y, Pastor RW, Brooks BR. Constant pressure molecular dynamics simulation: The Langevin piston method The Journal of Chemical Physics. 103: 4613-4621. DOI: 10.1063/1.470648  0.341
1995 Zhang Y, Feller SE, Brooks BR, Pastor RW. Computer simulation of liquid/liquid interfaces. I. Theory and application to octane/water The Journal of Chemical Physics. 103: 10252-10266. DOI: 10.1063/1.469927  0.31
1995 Chatfield DC, Brooks BR. HIV-1 protease cleavage mechanism elucidated with molecular dynamics simulation Journal of the American Chemical Society. 117: 5561-5572. DOI: 10.1021/Ja00125A018  0.326
1995 Jane?i? D, Venable RM, Brooks BR. Harmonic analysis of large systems. III. Comparison with molecular dynamics Journal of Computational Chemistry. 16: 1554-1566. DOI: 10.1002/Jcc.540161211  0.391
1995 Jane?i? D, Brooks BR. Harmonic analysis of large systems. II. Comparison of different protein models Journal of Computational Chemistry. 16: 1543-1553. DOI: 10.1002/Jcc.540161210  0.325
1995 Brooks BR, Jane?i? D, Karplus M. Harmonic analysis of large systems. I. Methodology Journal of Computational Chemistry. 16: 1522-1542. DOI: 10.1002/Jcc.540161209  0.439
1994 Durell SR, Brooks BR, Ben-Naim A. Solvent-Induced Forces between Two Hydrophilic Groups The Journal of Physical Chemistry. 98: 2198-2202. DOI: 10.1021/J100059A038  0.362
1994 Steinbach PJ, Brooks BR. Protein simulation below the glass-transition temperature. Dependence on cooling protocol Chemical Physics Letters. 226: 447-452. DOI: 10.1016/0009-2614(94)00754-3  0.309
1994 Steinbach PJ, Brooks BR. New spherical-cutoff methods for long-range forces in macromolecular simulation Journal of Computational Chemistry. 15: 667-683. DOI: 10.1002/Jcc.540150702  0.407
1994 Derreumaux P, Zhang G, Schlick T, Brooks B. A truncated Newton minimizer adapted for CHARMM and biomolecular applications Journal of Computational Chemistry. 15: 532-552. DOI: 10.1002/Jcc.540150506  0.326
1993 Venable RM, Brooks BR, Carson FW. Theoretical studies of relaxation of a monomeric subunit of HIV-1 protease in water using molecular dynamics. Proteins. 15: 374-84. PMID 8460108 DOI: 10.1002/Prot.340150405  0.354
1993 Steinbach PJ, Brooks BR. Protein hydration elucidated by molecular dynamics simulation. Proceedings of the National Academy of Sciences of the United States of America. 90: 9135-9. PMID 8415667 DOI: 10.1073/Pnas.90.19.9135  0.332
1992 Loncharich RJ, Brooks BR, Pastor RW. Langevin dynamics of peptides: the frictional dependence of isomerization rates of N-acetylalanyl-N'-methylamide. Biopolymers. 32: 523-35. PMID 1515543 DOI: 10.1002/Bip.360320508  0.342
1992 Venable RM, Widmalm G, Brooks BR, Egan W, Pastor RW. Conformational states of a TT mismatch from molecular dynamics simulation of duplex d (CGCGATTCGCG). Biopolymers. 32: 783-94. PMID 1391631 DOI: 10.1002/Bip.360320707  0.301
1991 Steinbach PJ, Loncharich RJ, Brooks BR. The effects of environment and hydration on protein dynamics: A simulation study of myoglobin Chemical Physics. 158: 383-394. DOI: 10.1016/0301-0104(91)87078-A  0.341
1990 Loncharich RJ, Brooks BR. The effects of truncating long-range forces on protein dynamics. Proteins. 6: 32-45. PMID 2608658 DOI: 10.1002/Prot.340060104  0.341
1989 Venable RM, Pastor RW, Brooks BR, Carson FW. Theoretically determined three-dimensional structures for amphipathic segments of the HIV-1 gp41 envelope protein. Aids Research and Human Retroviruses. 5: 7-22. PMID 2541749 DOI: 10.1089/Aid.1989.5.7  0.317
1989 Reid RH, Hooper CA, Brooks BR. Computer simulations of a tumor surface octapeptide epitope. Biopolymers. 28: 525-30. PMID 2470439 DOI: 10.1002/Bip.360280146  0.363
1988 Pastor RW, Brooks BR, Szabo A. An analysis of the accuracy of Langevin and molecular dynamics algorithms Molecular Physics. 65: 1409-1419. DOI: 10.1080/00268978800101881  0.3
1987 Smith-Gill SJ, Mainhart C, Lavoie TB, Feldmann RJ, Drohan W, Brooks BR. A three-dimensional model of an anti-lysozyme antibody. Journal of Molecular Biology. 194: 713-24. PMID 3656404 DOI: 10.1016/0022-2836(87)90249-X  0.323
1986 Post CB, Brooks BR, Karplus M, Dobson CM, Artymiuk PJ, Cheetham JC, Phillips DC. Molecular dynamics simulations of native and substrate-bound lysozyme. A study of the average structures and atomic fluctuations. Journal of Molecular Biology. 190: 455-79. PMID 3783708 DOI: 10.1016/0022-2836(86)90015-X  0.5
1986 Hemley RJ, Brooks BR, Karplus M. Theoretical study of the ground‐state vibrations of the linear polyenes The Journal of Chemical Physics. 85: 6550-6564. DOI: 10.1063/1.451437  0.574
1986 Smith J, Cusack S, Pezzeca U, Brooks B, Karplus M. Inelastic neutron scattering analysis of low frequency motion in proteins: A normal mode study of the bovine pancreatic trypsin inhibitor The Journal of Chemical Physics. 85: 3636-3654. DOI: 10.1063/1.450935  0.56
1985 Brooks B, Karplus M. Normal modes for specific motions of macromolecules: application to the hinge-bending mode of lysozyme. Proceedings of the National Academy of Sciences of the United States of America. 82: 4995-9. PMID 3860838 DOI: 10.1073/Pnas.82.15.4995  0.464
1985 Irikura KK, Tidor B, Brooks BR, Karplus M. Transition from B to Z DNA: contribution of internal fluctuations to the configurational entropy difference. Science (New York, N.Y.). 229: 571-2. PMID 3839596 DOI: 10.1126/Science.3839596  0.591
1983 Brooks B, Karplus M. Harmonic dynamics of proteins: normal modes and fluctuations in bovine pancreatic trypsin inhibitor. Proceedings of the National Academy of Sciences of the United States of America. 80: 6571-5. PMID 6579545 DOI: 10.1073/Pnas.80.21.6571  0.485
1983 Tidor B, Irikura KK, Brooks BR, Karplus M. Dynamics of DNA oligomers. Journal of Biomolecular Structure & Dynamics. 1: 231-52. PMID 6400872 DOI: 10.1080/07391102.1983.10507437  0.628
1983 Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations Journal of Computational Chemistry. 4: 187-217. DOI: 10.1002/Jcc.540040211  0.707
1980 Brooks BR, Laidig WD, Saxe P, Handy NC, Schaefer HF. The loop-driven graphical unitary group approach: A powerful method for the variational description of electron correlation Physica Scripta. 21: 312-322. DOI: 10.1088/0031-8949/21/3-4/013  0.644
1980 Brooks BR, Laidig WD, Saxe P, Goddard JD, Yamaguchi Y, Schaefer HF. Analytic gradients from correlated wave functions via the two‐particle density matrix and the unitary group approach The Journal of Chemical Physics. 72: 4652-4653. DOI: 10.1063/1.439707  0.583
1980 Brooks BR, Laidig WD, Saxe P, Schaefer HF. A multiconfiguration self‐consistent‐field formalism utilizing the two‐particle density matrix and the unitary group approach The Journal of Chemical Physics. 72: 3837-3838. DOI: 10.1063/1.439599  0.583
1979 Trenary M, Casida ME, Brooks BR, Schaefer HF. Three isomers of the aluminum-acetylene system Journal of the American Chemical Society. 101: 1638-1639. DOI: 10.1021/Ja00500A067  0.31
1978 Brooks BR, Schaefer HF. N(1Ag),T(3B1u), andV(1B1u) states of vertical ethylene The Journal of Chemical Physics. 68: 4839-4847. DOI: 10.1063/1.435637  0.315
1978 Lucchese RR, Brooks BR, Meadows JH, Swope WC, Schaefer HF. BERKELEY: An "open ended" Configuration Interaction (CI) program designed for minicomputers Journal of Computational Physics. 26: 243-251. DOI: 10.1016/0021-9991(78)90095-5  0.558
Low-probability matches (unlikely to be authored by this person)
2018 Tofoleanu F, Yuan Y, Pickard FC, Tywoniuk B, Brooks BR, Buchete NV. Structural Modulation of Human Amylin Protofilaments by Naturally-Occurring Mutations. The Journal of Physical Chemistry. B. PMID 29406755 DOI: 10.1021/Acs.Jpcb.7B12083  0.3
2007 Zheng W, Liao JC, Brooks BR, Doniach S. Toward the mechanism of dynamical couplings and translocation in hepatitis C virus NS3 helicase using elastic network model. Proteins. 67: 886-96. PMID 17373706 DOI: 10.1002/Prot.21326  0.299
1987 Brooks BR, Pastor RW, Carson FW. Theoretically determined three-dimensional structure for the repeating tetrapeptide unit of the circumsporozoite coat protein of the malaria parasite Plasmodium falciparum. Proceedings of the National Academy of Sciences of the United States of America. 84: 4470-4. PMID 3299369 DOI: 10.1073/Pnas.84.13.4470  0.299
2008 Woodcock HL, Brooks BR, Pastor RW. Pathways and populations: stereoelectronic insights into the exocyclic torsion of 5-(hydroxymethyl)tetrahydropyran. Journal of the American Chemical Society. 130: 6345-7. PMID 18444612 DOI: 10.1021/Ja077633Z  0.298
2015 Lopata A, Jambrina PG, Sharma PK, Brooks BR, Toth J, Vertessy BG, Rosta E. Mutations decouple proton transfer from phosphate cleavage in the dutpase catalytic reaction Acs Catalysis. 5: 3225-3237. DOI: 10.1021/Cs502087F  0.296
2016 Simmonett AC, Pickard FC, Ponder JW, Brooks BR. An empirical extrapolation scheme for efficient treatment of induced dipoles. The Journal of Chemical Physics. 145: 164101. PMID 27802661 DOI: 10.1063/1.4964866  0.294
2003 Wu X, Milne JLS, Borgnia MJ, Rostapshov AV, Subramaniam S, Brooks BR. A core-weighted fitting method for docking atomic structures into low-resolution maps: Application to cryo-electron microscopy Journal of Structural Biology. 141: 63-76. PMID 12576021 DOI: 10.1016/S1047-8477(02)00570-1  0.294
1991 Raghunathan G, Seetharamulu P, Brooks BR, Guy HR. Models of delta-hemolysin membrane channels and crystal structures. Proteins. 8: 213-25. PMID 2281085 DOI: 10.1002/Prot.340080304  0.294
1979 Brooks BR, Schaefer HF. The graphical unitary group approach to the electron correlation problem. Methods and preliminary applications The Journal of Chemical Physics. 70: 5092-5106. DOI: 10.1063/1.437351  0.294
2018 Tywoniuk B, Yuan Y, McCartan S, Szydlowska BM, Tofoleanu F, Brooks BR, Buchete NV. Amyloid Fibril Design: Limiting Structural Polymorphism in Alzheimer's Aβ Protofilaments. The Journal of Physical Chemistry. B. PMID 30335383 DOI: 10.1021/Acs.Jpcb.8B07423  0.292
2020 Lee J, Brooks BR. Direct global optimization of Onsager-Machlup action using Action-CSA Chemical Physics. 535: 110768. DOI: 10.1016/J.Chemphys.2020.110768  0.291
2003 Chu JW, Trout BL, Brooks BR. A super-linear minimization scheme for the nudged elastic band method Journal of Chemical Physics. 119: 12708-12717. DOI: 10.1063/1.1627754  0.291
2007 Che Y, Brooks BR, Riley DP, Reaka AJ, Marshall GR. Engineering metal complexes of chiral pentaazacrowns as privileged reverse-turn scaffolds. Chemical Biology & Drug Design. 69: 99-110. PMID 17381723 DOI: 10.1111/J.1747-0285.2007.00484.X  0.284
2015 Tan ML, Miller BT, Te J, Cendagorta JR, Brooks BR, Ichiye T. Hydrophobic hydration and the anomalous partial molar volumes in ethanol-water mixtures. The Journal of Chemical Physics. 142: 064501. PMID 25681917 DOI: 10.1063/1.4906750  0.283
2003 Tan ML, Fischer JT, Chandra A, Brooks BR, Ichiye T. A temperature of maximum density in soft sticky dipole water Chemical Physics Letters. 376: 646-652. DOI: 10.1016/S0009-2614(03)01044-3  0.282
2015 Lee J, Lee K, Joung I, Joo K, Brooks BR, Lee J. Sigma-RF: prediction of the variability of spatial restraints in template-based modeling by random forest. Bmc Bioinformatics. 16: 94. PMID 25886990 DOI: 10.1186/S12859-015-0526-Z  0.282
1990 Loncharich RJ, Brooks BR. Temperature dependence of dynamics of hydrated myoglobin. Comparison of force field calculations with neutron scattering data. Journal of Molecular Biology. 215: 439-55. PMID 2231714 DOI: 10.1016/S0022-2836(05)80363-8  0.28
2006 Che Y, Brooks BR, Marshall GR. Development of small molecules designed to modulate protein-protein interactions. Journal of Computer-Aided Molecular Design. 20: 109-30. PMID 16622794 DOI: 10.1007/S10822-006-9040-8  0.28
1987 Sklenár V, Brooks BR, Zon G, Bax A. Absorption mode two-dimensional NOE spectroscopy of exchangeable protons in oligonucleotides. Febs Letters. 216: 249-52. PMID 3034676 DOI: 10.1016/0014-5793(87)80699-3  0.279
2019 Krämer A, Venable RM, Wang EZ, Brooks BR, Pastor RW. Membrane Permeability from Conventional MD Simulations: Counting Transitions vs. Bayesian Analysis Biophysical Journal. 116: 166a. DOI: 10.1016/J.Bpj.2018.11.921  0.279
2002 Dolan EA, Venable RM, Pastor RW, Brooks BR. Simulations of membranes and other interfacial systems using P21 and Pc periodic boundary conditions Biophysical Journal. 82: 2317-2325. PMID 11964222 DOI: 10.1016/S0006-3495(02)75577-X  0.278
2009 Zheng W, Brooks BR, Thirumalai D. Allosteric transitions in biological nanomachines are described by robust normal modes of elastic networks. Current Protein & Peptide Science. 10: 128-32. PMID 19355980 DOI: 10.2174/138920309787847608  0.278
2004 Chu JW, Yin J, Brooks BR, Wang DI, Ricci MS, Brems DN, Trout BL. A comprehensive picture of non-site specific oxidation of methionine residues by peroxides in protein pharmaceuticals. Journal of Pharmaceutical Sciences. 93: 3096-102. PMID 15514984 DOI: 10.1002/Jps.20207  0.278
2010 Wu X, Zhang P, Khursigara CM, Subramaniam S, Brooks BR. Electron Tomography and Molecular Modeling Study of Chemoreceptor Organization Biophysical Journal. 98: 383a. DOI: 10.1016/J.Bpj.2009.12.2064  0.275
2006 Tan ML, Brooks BR, Ichiye T. Temperature dependence of diffusion properties of soft sticky dipole water Chemical Physics Letters. 421: 166-170. DOI: 10.1016/J.Cplett.2006.01.048  0.274
2002 Lee YS, Worthington SE, Krauss M, Brooks BR. Reaction mechanism of chorismate mutase studied by the combined potentials of quantum mechanics and molecular mechanics Journal of Physical Chemistry B. 106: 12059-12065. DOI: 10.1021/Jp0268718  0.274
2005 Stan G, Brooks BR, Lorimer GH, Thirumalai D. Identifying natural substrates for chaperonins using a sequence-based approach Protein Science. 14: 193-201. PMID 15576562 DOI: 10.1110/Ps.04933205  0.273
1977 Brooks BR, Schaefer HF. Reactions of carbynes. Potential energy surfaces for the doublet and quartet methylidyne (CH) reactions with molecular hydrogen The Journal of Chemical Physics. 67: 5146-5151. DOI: 10.1063/1.434743  0.273
2007 Zheng W, Brooks BR, Thirumalai D. Allosteric transitions in the chaperonin GroEL are captured by a dominant normal mode that is most robust to sequence variations. Biophysical Journal. 93: 2289-99. PMID 17557788 DOI: 10.1529/Biophysj.107.105270  0.272
2016 Nagy GN, Suardiaz R, Lopata A, Ozohanics O, Vékey K, Brooks BR, Leveles I, Toth J, Vertessy BG, Rosta E. Structural Characterization of Arginine Fingers: Identification of an Arginine Finger for the Pyrophosphatase dUTPases. Journal of the American Chemical Society. PMID 27740761 DOI: 10.1021/Jacs.6B09012  0.271
2015 Tofoleanu F, Brooks BR, Buchete NV. Modulation of Alzheimer's Aβ protofilament-membrane interactions by lipid headgroups. Acs Chemical Neuroscience. 6: 446-55. PMID 25581460 DOI: 10.1021/Cn500277F  0.27
2010 Ghysels A, Van Speybroeck V, Pauwels E, Catak S, Brooks BR, Van Neck D, Waroquier M. Comparative study of various normal mode analysis techniques based on partial Hessians. Journal of Computational Chemistry. 31: 994-1007. PMID 19813181 DOI: 10.1002/Jcc.21386  0.269
2016 Rinschen MM, Bharill P, Wu X, Kohli P, Reinert MJ, Kretz O, Martinez IS, Schermer B, Höhne M, Bartram MP, Aravamudhan S, Brooks BR, Vilchez D, Huber TB, Müller RU, et al. The ubiquitin ligase Ubr4 controls stability of podocin/MEC-2 supercomplexes. Human Molecular Genetics. PMID 26792178 DOI: 10.1093/Hmg/Ddw016  0.268
2022 Roe DR, Brooks BR. Quantifying the Effects of Lossy Compression on Energies Calculated from Molecular Dynamics Trajectories. Protein Science : a Publication of the Protein Society. e4511. PMID 36382864 DOI: 10.1002/pro.4511  0.265
2007 Larkin JD, Bhat KL, Markham GD, Brooks BR, Lai JH, Bock CW. A computational investigation of the geometrical structure and protodeboronation of boroglycine, H2N-CH2-B(OH)2. The Journal of Physical Chemistry. A. 111: 6489-500. PMID 17595064 DOI: 10.1021/Jp0700682  0.263
2002 Lipsitz RS, Sharma Y, Brooks BR, Tjandra N. Hydrogen bonding in high-resolution protein structures: a new method to assess NMR protein geometry. Journal of the American Chemical Society. 124: 10621-6. PMID 12197765 DOI: 10.1021/Ja020676P  0.263
2008 Miller BT, Zheng W, Venable RM, Pastor RW, Brooks BR. Langevin network model of myosin. The Journal of Physical Chemistry. B. 112: 6274-81. PMID 18311963 DOI: 10.1021/Jp077042V  0.263
2006 Zheng W, Brooks BR, Thirumalai D. Low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations. Proceedings of the National Academy of Sciences of the United States of America. 103: 7664-9. PMID 16682636 DOI: 10.1073/Pnas.0510426103  0.262
2006 Larkin JD, Bhat KL, Markham GD, Brooks BR, Schaefer HF, Bock CW. Structure of the boronic acid dimer and the relative stabilities of its conformers. The Journal of Physical Chemistry. A. 110: 10633-42. PMID 16956246 DOI: 10.1021/jp062407h  0.261
2009 Larkin JD, Markham GD, Milkevitch M, Brooks BR, Bock CW. Computational investigation of the oxidative deboronation of boroglycine, H2N-CH2-B(OH)2, Using H2O and H2O2. The Journal of Physical Chemistry. A. 113: 11028-34. PMID 19810757 DOI: 10.1021/Jp904149W  0.261
2017 Lee J, Konc J, Janežič D, Brooks BR. Global organization of a binding site network gives insight into evolution and structure-function relationships of proteins. Scientific Reports. 7: 11652. PMID 28912495 DOI: 10.1038/S41598-017-10412-Z  0.26
2007 Woodcock HL, Hodoscek M, Gilbert AT, Gill PM, Schaefer HF, Brooks BR. Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations. Journal of Computational Chemistry. 28: 1485-502. PMID 17334987 DOI: 10.1002/Jcc.20587  0.26
2005 Zheng W, Brooks BR, Doniach S, Thirumalai D. Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved. Structure (London, England : 1993). 13: 565-77. PMID 15837195 DOI: 10.1016/J.Str.2005.01.017  0.258
2020 Krämer A, Ghysels A, Wang E, Venable RM, Klauda JB, Brooks BR, Pastor RW. Membrane permeability of small molecules from unbiased molecular dynamics simulations. The Journal of Chemical Physics. 153: 124107. PMID 33003739 DOI: 10.1063/5.0013429  0.256
2021 Ghorbani M, Prasad S, Klauda JB, Brooks BR. Variational embedding of protein folding simulations using Gaussian mixture variational autoencoders. The Journal of Chemical Physics. 155: 194108. PMID 34800961 DOI: 10.1063/5.0069708  0.255
2002 Milne JL, Shi D, Rosenthal PB, Sunshine JS, Domingo GJ, Wu X, Brooks BR, Perham RN, Henderson R, Subramaniam S. Molecular architecture and mechanism of an icosahedral pyruvate dehydrogenase complex: a multifunctional catalytic machine. The Embo Journal. 21: 5587-98. PMID 12411477 DOI: 10.1093/Emboj/Cdf574  0.255
2008 Parry CS, Brooks BR. A new model defines the minimal set of polymorphism in HLA-DQ and -DR that determines susceptibility and resistance to autoimmune diabetes. Biology Direct. 3: 42. PMID 18854049 DOI: 10.1186/1745-6150-3-42  0.252
2015 Weidlich IE, Pevzner Y, Miller BT, Filippov IV, Woodcock HL, Brooks BR. Development and implementation of (Q)SAR modeling within the CHARMMing web-user interface. Journal of Computational Chemistry. 36: 62-7. PMID 25362883 DOI: 10.1002/Jcc.23765  0.252
2016 Pickard F, Koenig G, Brooks B. Difficult lessons learned fromQM-NBB & p K a calculations in SAMPL5 F1000research. 5. DOI: 10.7490/F1000Research.1112482.1  0.246
2018 Nishikawa N, Lee J, Brooks BR. Parameter Optimization for a New Reaction Pathway Sampling Method: Action-CSA Biophysical Journal. 114: 578a. DOI: 10.1016/J.Bpj.2017.11.3161  0.242
2008 Larkin JD, Bhat KL, Markham GD, James TD, Brooks BR, Bock CW. A computational characterization of boron-oxygen multiple bonding in HN=CH-CH=CH-NH-BO. The Journal of Physical Chemistry. A. 112: 8446-54. PMID 18707068 DOI: 10.1021/Jp800125P  0.242
2007 Che Y, Brooks BR, Marshall GR. Protein recognition motifs: design of peptidomimetics of helix surfaces. Biopolymers. 86: 288-97. PMID 17443711 DOI: 10.1002/Bip.20744  0.24
2011 Wu E, Su YA, Billings E, Brooks BR, Wu X. Automatic Spot Identification for High Throughput Microarray Analysis. Journal of Bioengineering & Biomedical Science. PMID 24298393 DOI: 10.4172/2155-9538.S5-005  0.239
2017 Lee J, Zhang ZY, Lee J, Brooks BR, Ahn YY. Inverse Resolution Limit of Partition Density and Detecting Overlapping Communities by Link-Surprise. Scientific Reports. 7: 12399. PMID 28963540 DOI: 10.1038/S41598-017-12432-1  0.237
2008 Lengyel JS, Stott KM, Wu X, Brooks BR, Balbo A, Schuck P, Perham RN, Subramaniam S, Milne JL. Extended polypeptide linkers establish the spatial architecture of a pyruvate dehydrogenase multienzyme complex. Structure (London, England : 1993). 16: 93-103. PMID 18184587 DOI: 10.1016/J.Str.2007.10.017  0.235
2011 Elegheert J, Desfosses A, Shkumatov AV, Wu X, Bracke N, Verstraete K, Van Craenenbroeck K, Brooks BR, Svergun DI, Vergauwen B, Gutsche I, Savvides SN. Extracellular complexes of the hematopoietic human and mouse CSF-1 receptor are driven by common assembly principles. Structure (London, England : 1993). 19: 1762-72. PMID 22153499 DOI: 10.1016/J.Str.2011.10.012  0.229
2019 Tian R, Zeng Q, Zhu S, Lau J, Chandra S, Ertsey R, Hettie KS, Teraphongphom T, Hu Z, Niu G, Kiesewetter DO, Sun H, Zhang X, Antaris AL, Brooks BR, et al. Albumin-chaperoned cyanine dye yields superbright NIR-II fluorophore with enhanced pharmacokinetics. Science Advances. 5: eaaw0672. PMID 31548981 DOI: 10.1126/Sciadv.Aaw0672  0.228
2004 Wu X, Chen Y, Brooks BR, Su YA. The Local Maximum Clustering Method and Its Application in Microarray Gene Expression Data Analysis Eurasip Journal On Applied Signal Processing. 2004: 53-63. DOI: 10.1155/S1110865704309145  0.228
2012 Smith DB, Okur A, Brooks BR. MDMS: Molecular dynamics meta-simulator for evaluating exchange type sampling methods Chemical Physics Letters. 545: 118-124. DOI: 10.1016/j.cplett.2012.07.015  0.223
2006 Zheng W, Brooks BR. Modeling protein conformational changes by iterative fitting of distance constraints using reoriented normal modes. Biophysical Journal. 90: 4327-36. PMID 16565046 DOI: 10.1529/Biophysj.105.076836  0.222
1996 Bhattacharyya D, Brooks BR, Callahan L. Positioning of positively charged residues in the V3 loop correlates with HIV type 1 syncytium-inducing phenotype. Aids Research and Human Retroviruses. 12: 83-90. PMID 8834457 DOI: 10.1089/Aid.1996.12.83  0.22
2020 Ghorbani M, Klauda JB, Brooks BR. Mechanism of Degradation of Histatin 5 Peptide by Secreted Aspartic Proteases (SAPS) of C. Albicans Biophysical Journal. 118: 534a-535a. DOI: 10.1016/J.Bpj.2019.11.2932  0.217
1989 Kay LE, Brooks B, Sparks SW, Torchia DA, Bax A. Measurement of NH-C.alpha.H coupling constants in staphylococcal nuclease by two-dimensional NMR and comparison with x-ray crystallographic results Journal of the American Chemical Society. 111: 5488-5490. DOI: 10.1021/Ja00196A078  0.216
2023 Roe DR, Brooks BR. MPI-parallelization of the grid inhomogeneous solvation theory calculation. Journal of Computational Chemistry. PMID 38071482 DOI: 10.1002/jcc.27278  0.216
2021 Man VH, Wu X, He X, Xie XQ, Brooks BR, Wang J. Determination of van der Waals Parameters Using a Double Exponential Potential for Nonbonded Divalent Metal Cations in TIP3P Solvent. Journal of Chemical Theory and Computation. PMID 33503371 DOI: 10.1021/acs.jctc.0c01267  0.215
2007 Woodcock HL, Hodoscek M, Brooks BR. Exploring SCC-DFTB paths for mapping QM/MM reaction mechanisms. The Journal of Physical Chemistry. A. 111: 5720-8. PMID 17555303 DOI: 10.1021/jp0714217  0.213
2017 Wu X, Brooks BR. Glutamate Receptor Ion Channel Activation Mechanism Revealed by Cryo-EM Maps Biophysical Journal. 112: 545a. DOI: 10.1016/J.Bpj.2016.11.2943  0.21
2021 Narayan B, Herbert C, Rodriguez BJ, Brooks BR, Buchete NV. Replica Exchange Molecular Dynamics of Diphenylalanine Amyloid Peptides in Electric Fields. The Journal of Physical Chemistry. B. PMID 33990140 DOI: 10.1021/acs.jpcb.1c01939  0.207
2006 Wu X, Brooks BR. Isotropic periodic sum: a method for the calculation of long-range interactions. The Journal of Chemical Physics. 122: 44107. PMID 15740235 DOI: 10.1063/1.1836733  0.205
2006 Wu X, Brooks BR. Isotropic periodic sum: a method for the calculation of long-range interactions. The Journal of Chemical Physics. 122: 44107. PMID 15740235 DOI: 10.1063/1.1836733  0.205
2021 Prasad S, Simmonett AC, Meana-Pañeda R, Brooks BR. The Extended Eighth-Shell method for periodic boundary conditions with rotational symmetry. Journal of Computational Chemistry. PMID 33977553 DOI: 10.1002/jcc.26545  0.204
2012 Zhang S, Qu Z, Tao P, Brooks B, Shao Y, Chen X, Liu C. A Quantum Chemical Study of the Ground and Excited State Electronic Structures of Carbazole Oligomers with and without Triarylborane Substitutes. The Journal of Physical Chemistry. C, Nanomaterials and Interfaces. 116: 12434-12442. PMID 22754601 DOI: 10.1021/Jp3027447  0.201
2021 Simmonett AC, Brooks BR. Analytical Hessians for Ewald and particle mesh Ewald electrostatics. The Journal of Chemical Physics. 154: 104101. PMID 33722046 DOI: 10.1063/5.0044166  0.198
2021 Yu Y, Krämer A, Venable RM, Simmonett AC, MacKerell AD, Klauda JB, Pastor RW, Brooks BR. Semi-automated Optimization of the CHARMM36 Lipid Force Field to Include Explicit Treatment of Long-Range Dispersion. Journal of Chemical Theory and Computation. PMID 33620214 DOI: 10.1021/acs.jctc.0c01326  0.198
2011 Itoh SG, Damjanovi? A, Brooks BR. pH replica-exchange method based on discrete protonation states. Proteins. 79: 3420-36. PMID 22002801 DOI: 10.1016/J.Bpj.2011.11.246  0.194
2007 Zheng W, Brooks BR, Hummer G. Protein conformational transitions explored by mixed elastic network models. Proteins. 69: 43-57. PMID 17596847 DOI: 10.1002/Prot.21465  0.193
2015 Lee J, Miller BT, Damjanovi? A, Brooks BR. Enhancing constant-pH simulation in explicit solvent with a two-dimensional replica exchange method Journal of Chemical Theory and Computation. 11: 2560-2574. DOI: 10.1021/ct501101f  0.193
2006 Klauda JB, Brooks BR, Pastor RW. Dynamical motions of lipids and a finite size effect in simulations of bilayers. The Journal of Chemical Physics. 125: 144710. PMID 17042634 DOI: 10.1063/1.2354486  0.188
2021 Epifanovsky E, Gilbert ATB, Feng X, Lee J, Mao Y, Mardirossian N, Pokhilko P, White AF, Coons MP, Dempwolff AL, Gan Z, Hait D, Horn PR, Jacobson LD, Kaliman I, ... ... Brooks BR, et al. Software for the frontiers of quantum chemistry: An overview of developments in the Q-Chem 5 package. The Journal of Chemical Physics. 155: 084801. PMID 34470363 DOI: 10.1063/5.0055522  0.187
1992 Chandrasekhar I, Clore GM, Szabo A, Gronenborn AM, Brooks BR. A 500 ps molecular dynamics simulation study of interleukin-1 beta in water. Correlation with nuclear magnetic resonance spectroscopy and crystallography. Journal of Molecular Biology. 226: 239-50. PMID 1619653 DOI: 10.1016/0022-2836(92)90136-8  0.18
2021 Simmonett AC, Brooks BR. A compression strategy for particle mesh Ewald theory. The Journal of Chemical Physics. 154: 054112. PMID 33557541 DOI: 10.1063/5.0040966  0.179
2024 Amin M, Kaur D, Brudvig GW, Brooks BR. Mapping the Oxygens in the Oxygen-Evolving Complex of Photosystem II by Their Nucleophilicity Using Quantum Descriptors. Journal of Chemical Theory and Computation. PMID 38306696 DOI: 10.1021/acs.jctc.3c00926  0.174
2017 Lee J, Lee IH, Joung I, Lee J, Brooks BR. Finding multiple reaction pathways via global optimization of action. Nature Communications. 8: 15443. PMID 28548089 DOI: 10.1038/ncomms15443  0.172
2023 Ghorbani M, Brooks BR, Klauda JB. Conformational Fluctuations in β2-Microglubulin Using Markov State Modeling and Molecular Dynamics. The Journal of Physical Chemistry. B. PMID 37527428 DOI: 10.1021/acs.jpcb.3c02473  0.172
1990 Han KH, Syi JL, Brooks BR, Ferretti JA. Solution conformations of the B-loop fragments of human transforming growth factor alpha and epidermal growth factor by 1H nuclear magnetic resonance and restrained molecular dynamics. Proceedings of the National Academy of Sciences of the United States of America. 87: 2818-22. PMID 2320585 DOI: 10.1073/pnas.87.7.2818  0.171
1978 Brooks BR, Schaefer HF. The BERKELEY system. III. General configuration-interaction methods for open-shell molecular electronic states International Journal of Quantum Chemistry. 14: 603-612. DOI: 10.1002/qua.560140507  0.163
2007 Stan G, Lorimer GH, Thirumalai D, Brooks BR. Coupling between allosteric transitions in GroEL and assisted folding of a substrate protein Proceedings of the National Academy of Sciences of the United States of America. 104: 8803-8808. PMID 17496143 DOI: 10.1073/Pnas.0700607104  0.162
2023 Maschietto F, Morzan UN, Tofoleanu F, Gheeraert A, Chaudhuri A, Kyro GW, Nekrasov P, Brooks B, Loria JP, Rivalta I, Batista VS. Turning up the heat mimics allosteric signaling in imidazole-glycerol phosphate synthase. Nature Communications. 14: 2239. PMID 37076500 DOI: 10.1038/s41467-023-37956-1  0.162
2014 Brooks BR, Swash M. Theodore Leon 'Ted' Munsat MD (1930-2013). Amyotrophic Lateral Sclerosis & Frontotemporal Degeneration. 15: 473-4. PMID 24809967 DOI: 10.3109/21678421.2014.909492  0.16
2022 Ghorbani M, Prasad S, Klauda JB, Brooks BR. GraphVAMPNet, using graph neural networks and variational approach to Markov processes for dynamical modeling of biomolecules. The Journal of Chemical Physics. 156: 184103. PMID 35568532 DOI: 10.1063/5.0085607  0.158
2021 Roe DR, Brooks BR. Improving the speed of volumetric density map generation via cubic spline interpolation. Journal of Molecular Graphics & Modelling. 104: 107832. PMID 33444979 DOI: 10.1016/j.jmgm.2021.107832  0.157
2020 Ghorbani M, Brooks BR, Klauda JB. Critical Sequence Hotspots for Binding of Novel Coronavirus to Angiotensin Converter Enzyme as Evaluated by Molecular Simulations. The Journal of Physical Chemistry. B. PMID 33112147 DOI: 10.1021/acs.jpcb.0c05994  0.154
2020 Ghorbani M, Brooks BR, Klauda JB. Critical Sequence Hot-spots for Binding of nCOV-2019 to ACE2 as Evaluated by Molecular Simulations. Biorxiv : the Preprint Server For Biology. PMID 32637962 DOI: 10.1101/2020.06.27.175448  0.15
2005 Klauda JB, Brooks BR, Pastor RW. Structure and dynamics of lipid membranes: How can simulations aid experiments? Aiche Annual Meeting, Conference Proceedings. 10460.  0.139
2021 Yu Y, Krämer A, Venable RM, Brooks BR, Klauda JB, Pastor RW. CHARMM36 Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Phosphatidylethanolamine, Phosphatidylglycerol, and Ether Lipids. Journal of Chemical Theory and Computation. PMID 33620194 DOI: 10.1021/acs.jctc.0c01327  0.139
2005 Klauda JB, Wu X, Pastor RW, Brooks BR. Importance of including long-range interactions in simulations of biologically relevant 2d surfaces Aiche Annual Meeting, Conference Proceedings. 10436.  0.133
2021 Ghorbani M, Brooks BR, Klauda JB. Exploring dynamics and network analysis of spike glycoprotein of SARS-COV-2. Biophysical Journal. PMID 33705760 DOI: 10.1016/j.bpj.2021.02.047  0.133
2020 Ghorbani M, Brooks BR, Klauda JB. Exploring dynamics and network analysis of spike glycoprotein of SARS-COV-2. Biorxiv : the Preprint Server For Biology. PMID 33024973 DOI: 10.1101/2020.09.28.317206  0.133
2002 Lipsitz RS, Sharma Y, Brooks BR, Tjandra N. Hydrogen bonding in high-resolution protein structures: A new method to assess NMR protein geometry Journal of the American Chemical Society. 124: 10621-10626. DOI: 10.1021/ja020676p  0.124
2007 Klauda J, Wu X, Pastor RW, Brooks BR. Long-range Lennard-Jones and electrostatic interactions in interfaces: Application and development of the isotropic periodic sum method 2007 Aiche Annual Meeting.  0.12
2011 Ghysels A, Woodcock HL, Larkin JD, Miller BT, Shao Y, Kong J, Neck DV, Speybroeck VV, Waroquier M, Brooks BR. Efficient calculation of QM/MM frequencies with the mobile Block Hessian Journal of Chemical Theory and Computation. 7: 496-514. DOI: 10.1021/ct100473f  0.116
1995 Hwang YS, Das R, Saltz JH, Hodošček M, Brooks BR. Parallelizing Molecular Dynamics Programs for Distributed-Memory Machines Ieee Computational Science and Engineering. 2: 18-29. DOI: 10.1109/99.388949  0.11
2012 Baciu C, Thompson KJ, Mougeot JL, Brooks BR, Weller JW. The LO-BaFL method and ALS microarray expression analysis. Bmc Bioinformatics. 13: 244. PMID 23006766 DOI: 10.1186/1471-2105-13-244  0.109
2009 Ghysels A, Van Speybroeck V, Pauwels E, Van Neck D, Brooks BR, Waroquier M. Mobile block Hessian approach with adjoined blocks: An efficient approach for the calculation of frequencies in macromolecules Journal of Chemical Theory and Computation. 5: 1203-1215. DOI: 10.1021/ct800489r  0.109
2008 Klauda JB, Brooks BR. CHARMM force field parameters for nitroalkanes and nitroarenes Journal of Chemical Theory and Computation. 4: 107-115. DOI: 10.1021/ct700191v  0.105
2008 Basener W, Brooks B, Radin M, Wiandt T. Dynamics of a discrete population model for extinction and sustainability in ancient civilizations. Nonlinear Dynamics, Psychology, and Life Sciences. 12: 29-53. PMID 18157926  0.093
2006 Milne JL, Wu X, Borgnia MJ, Lengyel JS, Brooks BR, Shi D, Perham RN, Subramaniam S. Molecular structure of a 9-MDa icosahedral pyruvate dehydrogenase subcomplex containing the E2 and E3 enzymes using cryoelectron microscopy. The Journal of Biological Chemistry. 281: 4364-70. PMID 16308322 DOI: 10.1074/Jbc.M504363200  0.092
2011 Basener W, Brooks B, Radin M, Wiandt T. Spatial effects and turing instabilities in the invasive species model. Nonlinear Dynamics, Psychology, and Life Sciences. 15: 455-64. PMID 21933514  0.091
2013 Wright JD, Sargsyan K, Wu X, Brooks BR, Lim C. Protein-protein docking using EMAP in CHARMM and support vector machine: Application to Ab/Ag complexes Journal of Chemical Theory and Computation. 9: 4186-4194. DOI: 10.1021/ct400508s  0.081
1990 Weston A, Newman MJ, Mann DL, Brooks BR. Molecular mechanics and antibody binding in the structural analysis of polycyclic aromatic hydrocarbon-diol-epoxide--DNA adducts. Carcinogenesis. 11: 859-64. PMID 1692267 DOI: 10.1093/carcin/11.5.859  0.079
2001 Wolinsky JS, Narayana PA, Johnson KP, Pruitt AA, Kolson D, Gonzalez-Scarano F, Bird SJ, Pfohl D, Grossman R, Mannon L, Ford CC, Greinel E, Padilla R, Lisak RP, Khan O, ... ... Brooks BR, et al. United States open-label glatiramer acetate extension trial for relapsing multiple sclerosis: MRI and clinical correlates Multiple Sclerosis. 7: 33-41. PMID 11321192 DOI: 10.1191/135245801667520627  0.073
2004 Sanjak M, Konopacki R, Capasso R, Roelke KA, Peper SM, Houdek AM, Waclawik A, Brooks BR. Dissociation between mechanical and myoelectrical manifestation of muscle fatigue in amyotrophic lateral sclerosis Amyotrophic Lateral Sclerosis and Other Motor Neuron Disorders. 5: 26-32. PMID 15204021 DOI: 10.1080/14660820310017551  0.072
2009 Saybasili AB, Tzannes A, Brooks BR, Vishkin U. Highly parallel multi-dimensional fast fourier transform on fine- and coarse-grained many-core approaches Proceedings of the Iasted International Conference On Parallel and Distributed Computing and Systems. 107-113.  0.067
2014 Bozik ME, Mitsumoto H, Brooks BR, Rudnicki SA, Moore DH, Zhang B, Ludolph A, Cudkowicz ME, van den Berg LH, Mather J, Petzinger T, Archibald D. A post hoc analysis of subgroup outcomes and creatinine in the phase III clinical trial (EMPOWER) of dexpramipexole in ALS. Amyotrophic Lateral Sclerosis & Frontotemporal Degeneration. 15: 406-13. PMID 25125035 DOI: 10.3109/21678421.2014.943672  0.062
2013 Ravits J, Appel S, Baloh RH, Barohn R, Brooks BR, Elman L, Floeter MK, Henderson C, Lomen-Hoerth C, Macklis JD, McCluskey L, Mitsumoto H, Przedborski S, Rothstein J, Trojanowski JQ, et al. Deciphering amyotrophic lateral sclerosis: what phenotype, neuropathology and genetics are telling us about pathogenesis. Amyotrophic Lateral Sclerosis & Frontotemporal Degeneration. 14: 5-18. PMID 23678876 DOI: 10.3109/21678421.2013.778548  0.061
2008 Basener W, Brooks B, Radin M, Wiandt T. Rat instigated human population collapse on easter island. Nonlinear Dynamics, Psychology, and Life Sciences. 12: 227-40. PMID 18510835  0.06
2007 Brooks BR. Involuntary emotional expression disorder: Treating the untreated Cns Spectrums. 12: 23-27. PMID 17426672  0.06
2009 Mougeot JL, Richardson-Milazi S, Brooks BR. Whole-genome association studies of sporadic amyotrophic lateral sclerosis: are retroelements involved? Trends in Molecular Medicine. 15: 148-58. PMID 19332388 DOI: 10.1016/j.molmed.2009.02.005  0.057
2013 Brooks BR, Crumpacker D, Fellus J, Kantor D, Kaye RE. PRISM: a novel research tool to assess the prevalence of pseudobulbar affect symptoms across neurological conditions. Plos One. 8: e72232. PMID 23991068 DOI: 10.1371/journal.pone.0072232  0.056
2010 Pioro EP, Brooks BR, Cummings J, Schiffer R, Thisted RA, Wynn D, Hepner A, Kaye R. Dextromethorphan plus ultra low-dose quinidine reduces pseudobulbar affect. Annals of Neurology. 68: 693-702. PMID 20839238 DOI: 10.1002/Ana.22093  0.054
2001 Bushara KO, Wheat JM, Khan A, Mock BJ, Turski PA, Sorenson J, Brooks BR. Multiple tactile maps in the human cerebellum. Neuroreport. 12: 2483-6. PMID 11496134  0.054
2001 Johnson KP, Brooks BR, Cohen JA, Ford CC, Goldstein J, Lisak RP, Myers LW, Panitch HS, Rose JW, Schiffer RB, Vollmer T, Weiner LP, Wolinsky JS. Extended use of glatiramer acetate (Copaxone) is well tolerated and maintains its clinical effect on multiple sclerosis relapse rate and degree of disability. 1998 [classical article]. Neurology. 57: S46-53. PMID 11902595  0.051
2009 Brooks BR. Managing amyotrophic lateral sclerosis: slowing disease progression and improving patient quality of life. Annals of Neurology. 65: S17-23. PMID 19191306 DOI: 10.1002/ana.21544  0.051
2006 Konrad C, Jansen A, Henningsen H, Sommer J, Turski PA, Brooks BR, Knecht S. Subcortical reorganization in amyotrophic lateral sclerosis. Experimental Brain Research. 172: 361-9. PMID 16463149 DOI: 10.1007/s00221-006-0352-7  0.051
2001 Sanjak M, Brinkmann J, Belden DS, Roelke K, Waclawik A, Neville HE, Ringel SP, Murphy JR, Brooks BR. Quantitative assessment of motor fatigue in amyotrophic lateral sclerosis. Journal of the Neurological Sciences. 191: 55-9. PMID 11676992 DOI: 10.1016/S0022-510X(01)00624-4  0.051
2004 Brooks BR, Thisted RA, Appel SH, Bradley WG, Olney RK, Berg JE, Pope LE, Smith RA. Treatment of pseudobulbar affect in ALS with dextromethorphan/quinidine: a randomized trial. Neurology. 63: 1364-70. PMID 15505150 DOI: 10.1212/01.Wnl.0000142042.50528.2F  0.05
2010 Sanjak M, Salachas F, Frija-Orvoen E, Theys P, Hutchinson D, Verheijde J, Pianta T, Stewart H, Brooks BR, Meininger V, Douillet P. Quality control of vital capacity as a primary outcome measure during phase III therapeutic clinical trial in amyotrophic lateral sclerosis. Amyotrophic Lateral Sclerosis : Official Publication of the World Federation of Neurology Research Group On Motor Neuron Diseases. 11: 383-8. PMID 20192884 DOI: 10.3109/17482960903486083  0.05
2010 Panov A, Kubalik N, Brooks BR, Shaw CA. In vitro effects of cholesterol β-D-glucoside, cholesterol and cycad phytosterol glucosides on respiration and reactive oxygen species generation in brain mitochondria. The Journal of Membrane Biology. 237: 71-7. PMID 20938651 DOI: 10.1007/s00232-010-9307-9  0.049
2011 Panov AV, Kubalik N, Zinchenko N, Ridings DM, Radoff DA, Hemendinger R, Brooks BR, Bonkovsky HL. Metabolic and functional differences between brain and spinal cord mitochondria underlie different predisposition to pathology. American Journal of Physiology. Regulatory, Integrative and Comparative Physiology. 300: R844-54. PMID 21248309 DOI: 10.1152/ajpregu.00528.2010  0.049
2013 Abdelnour-Mallet M, Tezenas Du Montcel S, Cazzolli PA, Assouline A, Pointon C, Leveque N, Dominique H, Elmazria H, Rothmayer M, Lenglet T, Bruneteau G, le Forestier N, Delanian S, Gonzalez-Bermejo J, Salachas F, ... Brooks BR, et al. Validation of robust tools to measure sialorrhea in amyotrophic lateral sclerosis: a study in a large French cohort. Amyotrophic Lateral Sclerosis & Frontotemporal Degeneration. 14: 302-7. PMID 23134507 DOI: 10.3109/21678421.2012.735238  0.048
2009 Panov A, Schonfeld P, Dikalov S, Hemendinger R, Bonkovsky HL, Brooks BR. The neuromediator glutamate, through specific substrate interactions, enhances mitochondrial ATP production and reactive oxygen species generation in nonsynaptic brain mitochondria. The Journal of Biological Chemistry. 284: 14448-56. PMID 19304986 DOI: 10.1074/jbc.M900985200  0.048
1979 TRENARY M, CASIDA ME, BROOKS BR, SCHAEFER HFI. ChemInform Abstract: THREE ISOMERS OF THE ALUMINUM-ACETYLENE SYSTEM Chemischer Informationsdienst. 10. DOI: 10.1002/chin.197926310  0.046
2011 Gallagher CL, Johnson SC, Bendlin BB, Chung MK, Holden JE, Oakes TR, Brooks BR, Konopacki RA, Dogan S, Abbs JH, Xu G, Nickles RJ, Pyzalski RW, Dejesus OT, Brown WD. A longitudinal study of motor performance and striatal [18F]fluorodopa uptake in Parkinson's disease. Brain Imaging and Behavior. 5: 203-11. PMID 21556744 DOI: 10.1007/S11682-011-9124-5  0.041
2003 Johnson KP, Brooks BR, Ford CC, Goodman AD, Lisak RP, Myers LW, Pruitt AA, Rizzo MA, Rose JW, Weiner LP, Wolinsky JS. Glatiramer acetate (Copaxone): Comparison of continuous versus delayed therapy in a six-year organized multiple sclerosis trial Multiple Sclerosis. 9: 585-591. PMID 14664471 DOI: 10.1191/1352458503ms961oa  0.041
2012 Hemendinger RA, Armstrong EJ, Radio N, Brooks BR. Neurotoxic injury pathways in differentiated mouse motor neuron-neuroblastoma hybrid (NSC-34D) cells in vitro--limited effect of riluzole on thapsigargin, but not staurosporine, hydrogen peroxide and homocysteine neurotoxicity. Toxicology and Applied Pharmacology. 258: 208-15. PMID 22108590 DOI: 10.1016/j.taap.2011.10.022  0.041
2011 Mougeot JL, Li Z, Price AE, Wright FA, Brooks BR. Microarray analysis of peripheral blood lymphocytes from ALS patients and the SAFE detection of the KEGG ALS pathway. Bmc Medical Genomics. 4: 74. PMID 22027401 DOI: 10.1186/1755-8794-4-74  0.041
1979 Brooks BR, Schaefer HF. Sudden polarization: pyramidalization of twisted ethylene Journal of the American Chemical Society. 101: 307-311. DOI: 10.1021/ja00496a005  0.041
2014 Mitsumoto H, Brooks BR, Silani V. Clinical trials in amyotrophic lateral sclerosis: why so many negative trials and how can trials be improved? The Lancet. Neurology. 13: 1127-38. PMID 25316019 DOI: 10.1016/S1474-4422(14)70129-2  0.04
2023 Maschietto F, Morzan UN, Tofoleanu F, Gheeraert A, Chaudhuri A, Kyro GW, Nekrasov P, Brooks B, Loria JP, Rivalta I, Batista VS. Author Correction: Turning up the heat mimics allosteric signaling in imidazole-glycerol phosphate synthase. Nature Communications. 14: 2611. PMID 37147327 DOI: 10.1038/s41467-023-38370-3  0.039
2009 Miller RG, Anderson F, Brooks BR, Mitsumoto H, Bradley WG, Ringel SP. Outcomes research in amyotrophic lateral sclerosis: lessons learned from the amyotrophic lateral sclerosis clinical assessment, research, and education database. Annals of Neurology. 65: S24-8. PMID 19191307 DOI: 10.1002/Ana.21556  0.038
2004 Meininger V, Bensimon G, Bradley WG, Brooks BR, Douillet P, Eisen AA, Lacomblez L, Leigh PN, Robberecht W. Efficacy and safety of xaliproden in amyotrophic lateral sclerosis: Results of two phase III trials Amyotrophic Lateral Sclerosis and Other Motor Neuron Disorders. 5: 107-117. PMID 15204012 DOI: 10.1080/14660820410019602  0.037
2012 Stark MS, Woods SL, Gartside MG, Bonazzi VF, Dutton-Regester K, Aoude LG, Chow D, Sereduk C, Niemi NM, Tang N, Ellis JJ, Reid J, Zismann V, Tyagi S, Muzny D, ... ... Brooks BR, et al. Frequent somatic mutations in MAP3K5 and MAP3K9 in metastatic melanoma identified by exome sequencing. Nature Genetics. 44: 165-9. PMID 22197930 DOI: 10.1038/Ng.1041  0.036
2011 Deng HX, Chen W, Hong ST, Boycott KM, Gorrie GH, Siddique N, Yang Y, Fecto F, Shi Y, Zhai H, Jiang H, Hirano M, Rampersaud E, Jansen GH, Donkervoort S, ... ... Brooks BR, et al. Mutations in UBQLN2 cause dominant X-linked juvenile and adult-onset ALS and ALS/dementia. Nature. 477: 211-5. PMID 21857683 DOI: 10.1038/Nature10353  0.036
1977 Brooks BR, Schaefer HF. A model transition metal-carbene system MnCH2 Molecular Physics. 34: 193-213. DOI: 10.1080/00268977700101631  0.034
2005 O'Brien TJ, Brooks BR, Patierno SR. Nucleotide excision repair functions in the removal of chromium-induced DNA damage in mammalian cells Molecular and Cellular Biochemistry. 279: 85-95. PMID 16283517 DOI: 10.1007/S11010-005-8225-0  0.033
2002 Brooks BR. Functional scales: Summary Amyotrophic Lateral Sclerosis and Other Motor Neuron Disorders. 3: S13-S18. PMID 12396795  0.032
2004 Nix WA, Berger MM, Oberste MS, Brooks BR, McKenna-Yasek DM, Brown RH, Roos RP, Pallansch MA. Failure to detect enterovirus in the spinal cord of ALS patients using a sensitive RT-PCR method Neurology. 62: 1372-1377. PMID 15111676 DOI: 10.1212/01.Wnl.0000123258.86752.51  0.032
2013 Turner MR, Hardiman O, Benatar M, Brooks BR, Chio A, de Carvalho M, Ince PG, Lin C, Miller RG, Mitsumoto H, Nicholson G, Ravits J, Shaw PJ, Swash M, Talbot K, et al. Controversies and priorities in amyotrophic lateral sclerosis. The Lancet. Neurology. 12: 310-22. PMID 23415570 DOI: 10.1016/S1474-4422(13)70036-X  0.031
2013 Miller RG, Brooks BR, Swain-Eng RJ, Basner RC, Carter GT, Casey P, Cohen AB, Dubinsky R, Forshew D, Jackson CE, Kasarskis E, Procaccini NJ, Sanjak M, Tolin FP. Quality improvement in neurology: amyotrophic lateral sclerosis quality measures: report of the quality measurement and reporting subcommittee of the American Academy of Neurology. Neurology. 81: 2136-40. PMID 24271651 DOI: 10.1212/01.wnl.0000437305.37850.f9  0.031
2011 Hemendinger RA, Armstrong EJ, Brooks BR. Methyl Vitamin B12 but not methylfolate rescues a motor neuron-like cell line from homocysteine-mediated cell death. Toxicology and Applied Pharmacology. 251: 217-25. PMID 21237187 DOI: 10.1016/j.taap.2011.01.003  0.03
2001 Johnson KP, Brooks BR, Cohen JA, Ford CC, Goldstein J, Lisak RP, Myers LW, Panitch HS, Rose JW, Schiffer RB, Vollmer T, Weiner LP, Wolinsky JS. Copolymer 1 reduces relapse rate and improves disability in relapsing-remitting multiple sclerosis: results of a phase III multicenter, double-blind, placebo-controlled trial. 1995. Neurology. 57: S16-24. PMID 11902590  0.03
2010 Ward AL, Sanjak M, Duffy K, Bravver E, Williams N, Nichols M, Brooks BR. Power wheelchair prescription, utilization, satisfaction, and cost for patients with amyotrophic lateral sclerosis: preliminary data for evidence-based guidelines. Archives of Physical Medicine and Rehabilitation. 91: 268-72. PMID 20159132 DOI: 10.1016/j.apmr.2009.10.023  0.029
2014 Cudkowicz ME, Titus S, Kearney M, Yu H, Sherman A, Schoenfeld D, Hayden D, Shui A, Brooks B, Conwit R, Felsenstein D, Greenblatt DJ, Keroack M, Kissel JT, Miller R, et al. Safety and efficacy of ceftriaxone for amyotrophic lateral sclerosis: a multi-stage, randomised, double-blind, placebo-controlled trial. The Lancet. Neurology. 13: 1083-91. PMID 25297012 DOI: 10.1016/S1474-4422(14)70222-4  0.027
2002 Szurek PF, Vann JM, Brooks BR. Letter to the editor: Sequence analysis of a neuropathogenic variant of Moloney murine leukemia virus ts1: Evidence for recombination Virus Genes. 25: 343-344. PMID 12881645 DOI: 10.1023/A:1020996529014  0.027
2004 Brooks BR, Sanjak M. Disease-modifying drug therapies Amyotrophic Lateral Sclerosis and Other Motor Neuron Disorders. 5: 68-75. PMID 15512878 DOI: 10.1080/17434470410019898  0.025
2010 Panov AV, Vavilin VA, Lyakhovich VV, Brooks BR, Bonkovsky HL. Effect of bovine serum albumin on mitochondrial respiration in the brain and liver of mice and rats. Bulletin of Experimental Biology and Medicine. 149: 187-90. PMID 21113488 DOI: 10.1007/s10517-010-0904-5  0.024
2007 Liao JP, Waclawik AJ, Lotz BP, Salamat SM, Beinlich BR, Brooks BR. Myopathic dropped head syndrome: an expanding clinicopathological spectrum. American Journal of Physical Medicine & Rehabilitation / Association of Academic Physiatrists. 86: 970-6. PMID 18090438 DOI: 10.1097/PHM.0b013e3181588331  0.022
1996 Upton T, Brooks B. Managing change in the NHS Page Kogan In association with NAHAT Managing change in the NHS £12.95 paperback 0 7494 1485 50749414855134 pages Nursing Management. 2: 28-28. DOI: 10.7748/nm.2.9.28.s21  0.02
2010 Sanjak M, Bravver E, Bockenek WL, Norton HJ, Brooks BR. Supported treadmill ambulation for amyotrophic lateral sclerosis: a pilot study. Archives of Physical Medicine and Rehabilitation. 91: 1920-9. PMID 21112435 DOI: 10.1016/j.apmr.2010.08.009  0.018
2014 Brooks BR. ALS-Plus - where does it begin, where does it end? Journal of the Neurological Sciences. 345: 1-2. PMID 25073572 DOI: 10.1016/j.jns.2014.07.027  0.017
2006 Cummings JL, Arciniegas DB, Brooks BR, Herndon RM, Lauterbach EC, Pioro EP, Robinson RG, Scharre DW, Schiffer RB, Weintraub D. Defining and diagnosing involuntary emotional expression disorder. Cns Spectrums. 11: 1-7. PMID 16816786 DOI: 10.1017/S1092852900026614  0.016
2015 Ward AL, Hammond S, Holsten S, Bravver E, Brooks BR. Power Wheelchair Use in Persons with Amyotrophic Lateral Sclerosis: Changes over Time Assistive Technology. 27: 238-245. DOI: 10.1080/10400435.2015.1040896  0.015
2014 Miller RG, Brooks BR, Swain-Eng RJ, Basner RC, Carter GT, Casey P, Cohen AB, Dubinsky R, Forshew D, Jackson CE, Kasarskis E, Procaccini NJ, Sanjak M, Tolin FP. Quality improvement in neurology: amyotrophic lateral sclerosis quality measures. Report of the Quality Measurement and Reporting Subcommittee of the American Academy of Neurology. Amyotrophic Lateral Sclerosis & Frontotemporal Degeneration. 15: 165-8. PMID 24707820 DOI: 10.3109/21678421.2013.875706  0.015
2001 Mandler RN, Anderson FA, Miller RG, Clawson L, Cudkowicz M, Del Bene M, Bradley WG, Boynton de Sepulveda LI, Brooks BR, Cashman NR, Graves M, Harati Y, Heiman-Patterson T, Lyon M, Mitsumoto H, et al. The ALS patient care database: Insights into end-of-life care in ALS Amyotrophic Lateral Sclerosis and Other Motor Neuron Disorders. 2: 203-208. PMID 11958732 DOI: 10.1080/14660820152882214  0.012
2014 Sanjak M, Hirsch MA, Bravver EK, Bockenek WL, Norton HJ, Brooks BR. Vestibular deficits leading to disequilibrium and falls in ambulatory amyotrophic lateral sclerosis. Archives of Physical Medicine and Rehabilitation. 95: 1933-9. PMID 24946083 DOI: 10.1016/j.apmr.2014.05.024  0.01
2005 Smith RA, Brooks BR. Treatment of pseudobulbar affect in ALS Lancet Neurology. 4: 270. PMID 15847840 DOI: 10.1016/S1474-4422(05)70058-2  0.01
1984 Brooks B, Schuster FL. Oral Protozoa: Survey, Isolation, and Ultrastructure of Trichomonas tenax from Clinical Practice Transactions of the American Microscopical Society. 103: 376. DOI: 10.2307/3226474  0.01
Hide low-probability matches.