| 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 |
0.382 |
|
| 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 |
0.504 |
|
| 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 |
0.597 |
|
| 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 |
0.429 |
|
| 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 |
0.421 |
|
| 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 |
0.648 |
|
| 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 |
0.722 |
|
| 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, JanežiÄ 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 |
0.653 |
|
| 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 |
0.644 |
|
| 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, JanežiÄ 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 |
0.666 |
|
| 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 |
0.718 |
|
| 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 |
0.633 |
|
| 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 |
0.604 |
|
| 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, GarcÃa-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 |
0.622 |
|
| 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 |
0.64 |
|
| 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+ |
0.636 |
|
| 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 |
0.372 |
|
| 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 |
|
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