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/

180 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
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  0.4
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  0.4
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  0.6
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  0.6
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  0.6
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  0.4
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  0.6
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  0.32
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  0.4
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  0.4
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  0.6
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  0.6
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  0.6
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  0.44
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  0.6
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  0.44
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  0.6
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  0.6
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  0.6
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  0.4
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  0.6
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.6
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  0.44
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  0.44
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  0.4
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  0.44
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  0.68
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  0.68
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  0.44
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  0.44
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  0.68
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  0.44
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  0.68
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  0.68
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  0.44
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  0.68
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  0.68
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  0.44
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  0.68
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  0.44
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  0.44
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.4
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  0.68
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  0.68
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  0.68
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  0.68
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  0.6
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.44
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  0.4
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  0.68
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  0.68
2011 Itoh SG, Damjanovi? A, Brooks BR. pH replica-exchange method based on discrete protonation states. Proteins. 79: 3420-36. PMID 22002801 DOI: 10.1002/prot.23176  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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.  0.68
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  0.4
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.4
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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+  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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 0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
2005 Wu X, Brooks BR. Isotropic periodic sum: A method for the calculation of long-range interactions Journal of Chemical Physics. 122. DOI: 10.1063/1.1836733  0.68
2005 Klauda JB, Brooks BR, Pastor RW. Structure and dynamics of lipid membranes: How can simulations aid experiments? Aiche Annual Meeting, Conference Proceedings. 10460.  0.68
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.  0.68
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  0.68
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  0.68
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  0.68
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.  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.68
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  0.72
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  0.68
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  0.72
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  0.72
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  0.68
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  0.68
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  0.68
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