| Year |
Citation |
Score |
| 2024 |
Lai TT, Brooks CL. Accuracy and Reproducibility of Lipari-Szabo Order Parameters From Molecular Dynamics. The Journal of Physical Chemistry. B. PMID 39466025 DOI: 10.1021/acs.jpcb.4c04895 |
0.307 |
|
| 2024 |
Hwang W, Austin SL, Blondel A, Boittier ED, Boresch S, Buck M, Buckner J, Caflisch A, Chang HT, Cheng X, Choi YK, Chu JW, Crowley MF, Cui Q, Damjanovic A, ... ... Brooks CL, et al. CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed. The Journal of Physical Chemistry. B. PMID 39303207 DOI: 10.1021/acs.jpcb.4c04100 |
0.768 |
|
| 2024 |
Gartan P, Khorsand F, Mizar P, Vahokovski JI, Cervantes LF, Haug BE, Brenk R, Brooks CL, Reuter N. Investigating Polypharmacology through Targeting Known Human Neutrophil Elastase Inhibitors to Proteinase 3. Journal of Chemical Information and Modeling. PMID 38276895 DOI: 10.1021/acs.jcim.3c01949 |
0.526 |
|
| 2023 |
Buckner J, Liu X, Chakravorty A, Wu Y, Cervantes LF, Lai TT, Brooks CL. pyCHARMM: Embedding CHARMM Functionality in a Python Framework. Journal of Chemical Theory and Computation. PMID 37267404 DOI: 10.1021/acs.jctc.3c00364 |
0.541 |
|
| 2023 |
Liu X, Tsang PK, Soellner MB, Brooks CL. QSAR via Multisite λ-Dynamics in the Orphaned TSSK1B Kinase. Protein Science : a Publication of the Protein Society. e4623. PMID 36906820 DOI: 10.1002/pro.4623 |
0.513 |
|
| 2022 |
Chakravorty A, McCalpin SD, Sahoo BR, Ramamoorthy A, Brooks CL. Free Gangliosides Can Alter Amyloid-β Aggregation. The Journal of Physical Chemistry Letters. 9303-9308. PMID 36174129 DOI: 10.1021/acs.jpclett.2c02362 |
0.404 |
|
| 2022 |
MacKenzie DWS, Schaefer A, Steckner J, Leo CA, Naser D, Artikis E, Broom A, Ko T, Shah P, Ney MQ, Tran E, Smith MTJ, Fuglestad B, Wand AJ, Brooks CL, et al. A fine balance of hydrophobic-electrostatic communication pathways in a pH-switching protein. Proceedings of the National Academy of Sciences of the United States of America. 119: e2119686119. PMID 35737838 DOI: 10.1073/pnas.2119686119 |
0.309 |
|
| 2022 |
Peiffer AL, Garlick JM, Joy ST, Mapp AK, Brooks CL. Allostery in the dynamic coactivator domain KIX occurs through minor conformational micro-states. Plos Computational Biology. 18: e1009977. PMID 35452454 DOI: 10.1371/journal.pcbi.1009977 |
0.302 |
|
| 2021 |
Brooks CL, Case DA, Plimpton S, Roux B, van der Spoel D, Tajkhorshid E. Classical molecular dynamics. The Journal of Chemical Physics. 154: 100401. PMID 33722022 DOI: 10.1063/5.0045455 |
0.406 |
|
| 2020 |
Paul TJ, Vilseck JZ, Hayes RL, Brooks CL. Exploring pH Dependent Host/Guest Binding Affinities. The Journal of Physical Chemistry. B. PMID 32628482 DOI: 10.1021/Acs.Jpcb.0C03671 |
0.362 |
|
| 2020 |
Ding X, Wu Y, Wang Y, Vilseck JZ, Brooks CL. Accelerated CDOCKER with GPUs, parallel simulated annealing and fast Fourier transforms. Journal of Chemical Theory and Computation. PMID 32374996 DOI: 10.1021/Acs.Jctc.0C00145 |
0.365 |
|
| 2020 |
Torabifard H, Panahi A, Brooks CL. M2 amphipathic helices facilitate pH-dependent conformational transition in influenza A virus. Proceedings of the National Academy of Sciences of the United States of America. PMID 32015120 DOI: 10.1073/Pnas.1913385117 |
0.798 |
|
| 2019 |
Gong X, Chiricotto M, Liu X, Nordquist E, Feig M, Brooks CL, Chen J. Accelerating the Generalized Born with Molecular Volume and Solvent Accessible Surface Area Implicit Solvent Model Using Graphics Processing Units. Journal of Computational Chemistry. PMID 31875339 DOI: 10.1002/Jcc.26133 |
0.802 |
|
| 2019 |
Ding X, Zou Z, Brooks CL. Deciphering protein evolution and fitness landscapes with latent space models Nature Communications. 10: 5644. PMID 31822668 DOI: 10.1038/S41467-019-13633-0 |
0.325 |
|
| 2019 |
Wang Y, Brooks CL. Enhanced Sampling Applied to Modeling Allosteric Regulation in Transcription. The Journal of Physical Chemistry Letters. PMID 31535860 DOI: 10.1021/Acs.Jpclett.9B02226 |
0.358 |
|
| 2019 |
Deng H, Ke S, Callender R, Balakrishnan G, Spiro TG, May ER, Brooks CL. Computational Studies of Catalytic Loop Dynamics in Protein Tyrosine Phosphatase Using Pathway Optimization Methods. The Journal of Physical Chemistry. B. PMID 31437399 DOI: 10.1021/Acs.Jpcb.9B06759 |
0.7 |
|
| 2019 |
Vilseck JZ, Sohail N, Hayes RL, Brooks CL. Overcoming Challenging Substituent Perturbations with Multisite λ-Dynamics: A Case Study Targeting β-Secretase 1. The Journal of Physical Chemistry Letters. PMID 31386370 DOI: 10.1021/Acs.Jpclett.9B02004 |
0.39 |
|
| 2019 |
Halloran KT, Wang Y, Arora K, Chakravarthy S, Irving TC, Bilsel O, Brooks CL, Matthews CR. Frustration and folding of a TIM barrel protein. Proceedings of the National Academy of Sciences of the United States of America. PMID 31346089 DOI: 10.1073/Pnas.1900880116 |
0.421 |
|
| 2019 |
Artikis E, Brooks CL. Modeling pH-Dependent NMR Chemical Shift Perturbations in Peptides. Biophysical Journal. PMID 31255294 DOI: 10.1016/J.Bpj.2019.06.003 |
0.382 |
|
| 2019 |
Ding X, Vilseck JZ, Brooks CL. A Fast Solver for Large Scale Multistate Bennett Acceptance Ratio Equations. Journal of Chemical Theory and Computation. PMID 30689377 DOI: 10.1021/Acs.Jctc.8B01010 |
0.303 |
|
| 2018 |
Zou X, Wei S, Badieyan S, Schroeder M, Jasensky J, Brooks CL, Marsh ENG, Chen Z. Investigating the Effect of Two-point Surface Attachment on Enzyme Stability and Activity. Journal of the American Chemical Society. PMID 30403342 DOI: 10.1021/Jacs.8B08138 |
0.308 |
|
| 2018 |
Widom JR, Nedialkov YA, Rai V, Hayes RL, Brooks CL, Artsimovitch I, Walter NG. Ligand Modulates Cross-Coupling between Riboswitch Folding and Transcriptional Pausing. Molecular Cell. 72: 541-552.e6. PMID 30388413 DOI: 10.1016/J.Molcel.2018.08.046 |
0.302 |
|
| 2018 |
Ho PT, Montiel-Garcia DJ, Wong JJ, Carrillo-Tripp M, Brooks CL, Johnson JE, Reddy VS. VIPERdb: A Tool for Virus Research. Annual Review of Virology. 5: 477-488. PMID 30265627 DOI: 10.1146/Annurev-Virology-092917-043405 |
0.301 |
|
| 2018 |
Hayes RL, Vilseck JZ, Brooks CL. Approaching Protein Design with Multisite λ Dynamics: Accurate and Scalable Mutational Folding Free Energies in T4 Lysozyme. Protein Science : a Publication of the Protein Society. PMID 30175503 DOI: 10.1002/Pro.3500 |
0.369 |
|
| 2018 |
Henderson AR, Henley MJ, Foster NJ, Peiffer AL, Beyersdorf MS, Stanford KD, Sturlis SM, Linhares BM, Hill ZB, Wells JA, Cierpicki T, Brooks CL, Fierke CA, Mapp AK. Conservation of coactivator engagement mechanism enables small-molecule allosteric modulators. Proceedings of the National Academy of Sciences of the United States of America. PMID 30127017 DOI: 10.1073/Pnas.1806202115 |
0.378 |
|
| 2018 |
Vilseck JZ, Armacost KA, Hayes RL, Goh GB, Brooks CL. Predicting Binding Free Energies in a Large Combinatorial Chemical Space Using Multisite Lambda Dynamics. The Journal of Physical Chemistry Letters. PMID 29847134 DOI: 10.1021/Acs.Jpclett.8B01284 |
0.77 |
|
| 2017 |
Ding X, Hayes RL, Vilseck JZ, Charles MK, Brooks CL. CDOCKER and [Formula: see text]-dynamics for prospective prediction in D3R Grand Challenge 2. Journal of Computer-Aided Molecular Design. PMID 28884249 DOI: 10.1007/S10822-017-0050-5 |
0.358 |
|
| 2017 |
Kamgar-Parsi K, Hong L, Naito A, Brooks CL, Ramamoorthy A. Growth-incompetent monomers of human calcitonin lead to a non-canonical direct relationship between peptide concentration and lag time. The Journal of Biological Chemistry. PMID 28739873 DOI: 10.1074/Jbc.M117.791236 |
0.487 |
|
| 2017 |
Ding X, Vilseck JZ, Hayes RL, Brooks CL. Gibbs Sampler Based λ-Dynamics and Rao-Blackwell Estimator for Alchemical Free Energy Calculation. Journal of Chemical Theory and Computation. PMID 28510433 DOI: 10.1021/Acs.Jctc.7B00204 |
0.358 |
|
| 2017 |
Kim S, Lee J, Jo S, Brooks CL, Lee HS, Im W. CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules. Journal of Computational Chemistry. PMID 28497616 DOI: 10.1002/Jcc.24829 |
0.349 |
|
| 2017 |
Su M, Guo EZ, Ding X, Li Y, Tarrasch JT, Brooks CL, Xu Z, Skiniotis G. Mechanism of Vps4 hexamer function revealed by cryo-EM. Science Advances. 3: e1700325. PMID 28439563 DOI: 10.1126/Sciadv.1700325 |
0.331 |
|
| 2017 |
Wei S, Brooks CL, Frank AT. A rapid solvent accessible surface area estimator for coarse grained molecular simulations. Journal of Computational Chemistry. PMID 28419507 DOI: 10.1002/Jcc.24709 |
0.709 |
|
| 2017 |
Wei S, Ahlstrom LS, Brooks CL. Exploring Protein-Nanoparticle Interactions with Coarse-Grained Protein Folding Models. Small (Weinheim An Der Bergstrasse, Germany). PMID 28266786 DOI: 10.1002/Smll.201603748 |
0.325 |
|
| 2017 |
Hayes RL, Armacost KA, Vilseck JZ, Brooks CL. Adaptive Landscape Flattening Accelerates Sampling of Alchemical Space in Multisite λ Dynamics. The Journal of Physical Chemistry. B. PMID 28112940 DOI: 10.1021/Acs.Jpcb.6B09656 |
0.776 |
|
| 2017 |
Gichana E, Brooks CL. Investigating the Influence of Sequence on Protein Folding Mechanism using a Structure Based Model Biophysical Journal. 112: 287a. DOI: 10.1016/J.Bpj.2016.11.1552 |
0.356 |
|
| 2016 |
Won SJ, Davda D, Labby KJ, Hwang SY, Pricer RE, Majmudar JD, Armacost KA, Rodriguez LA, Rodriguez CL, Chong FS, Torossian KA, Palakurthi J, Hur ES, Meagher JL, Brooks CL, et al. Molecular mechanism for isoform-selective inhibition of acyl protein thioesterases 1 and 2 (APT1 and APT2). Acs Chemical Biology. PMID 27748579 DOI: 10.1021/Acschembio.6B00720 |
0.779 |
|
| 2016 |
Salmon L, Ahlstrom LS, Horowitz S, Dickson A, Brooks CL, Bardwell JC. Capturing a dynamic chaperone-substrate interaction using NMR-informed molecular modeling. Journal of the American Chemical Society. PMID 27415450 DOI: 10.1021/Jacs.6B02382 |
0.638 |
|
| 2016 |
Arthur EJ, Brooks CL. Efficient implementation of constant pH molecular dynamics on modern graphics processors. Journal of Computational Chemistry. PMID 27405884 DOI: 10.1002/Jcc.24435 |
0.435 |
|
| 2016 |
Soteras Gutiérrez I, Lin FY, Vanommeslaeghe K, Lemkul JA, Armacost KA, Brooks CL, MacKerell AD. Parametrization of halogen bonds in the CHARMM general force field: Improved treatment of ligand-protein interactions. Bioorganic & Medicinal Chemistry. PMID 27353885 DOI: 10.1016/J.Bmc.2016.06.034 |
0.8 |
|
| 2016 |
Horowitz S, Salmon L, Koldewey P, Ahlstrom LS, Martin R, Quan S, Afonine PV, van den Bedem H, Wang L, Xu Q, Trievel RC, Brooks CL, Bardwell JC. Visualizing chaperone-assisted protein folding. Nature Structural & Molecular Biology. PMID 27239796 DOI: 10.1038/Nsmb.3237 |
0.401 |
|
| 2016 |
Aggarwal A, May ER, Brooks CL, Klug WS. Nonuniform elastic properties of macromolecules and effect of prestrain on their continuum nature. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 93: 012417. PMID 26871111 DOI: 10.1103/Physreve.93.012417 |
0.674 |
|
| 2016 |
Arthur EJ, Brooks CL. Parallelization and improvements of the generalized born model with a simple sWitching function for modern graphics processors. Journal of Computational Chemistry. PMID 26786647 DOI: 10.1002/Jcc.24280 |
0.398 |
|
| 2016 |
Morriss-Andrews A, Mustoe AM, Brooks CL. Junction Topological Constraints in Hairpin Ribozyme Folding Biophysical Journal. 110: 408a. DOI: 10.1016/J.Bpj.2015.11.2206 |
0.372 |
|
| 2016 |
Ahlstrom LS, Salmon L, Horowitz S, Dickson A, Brooks CL, Bardwell JC. NMR-Informed Molecular Modeling Uncovers the Conformational Landscape of Chaperone Binding with Unfolded Substrate Biophysical Journal. 110: 369a. DOI: 10.1016/J.Bpj.2015.11.1989 |
0.644 |
|
| 2015 |
Gagnon JK, Law SM, Brooks CL. Flexible CDOCKER: Development and application of a pseudo-explicit structure-based docking method within CHARMM. Journal of Computational Chemistry. PMID 26691274 DOI: 10.1002/Jcc.24259 |
0.81 |
|
| 2015 |
Lee J, Cheng X, Swails JM, Yeom MS, Eastman PK, Lemkul JA, Wei S, Buckner J, Jeong JC, Qi Y, Jo S, Pande VS, Case DA, Brooks CL, MacKerell AD, et al. CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. Journal of Chemical Theory and Computation. PMID 26631602 DOI: 10.1021/Acs.Jctc.5B00935 |
0.555 |
|
| 2015 |
Armacost KA, Goh GB, Brooks CL. Biasing Potential Replica Exchange Multisite λ-Dynamics for Efficient Free Energy Calculations. Journal of Chemical Theory and Computation. 11: 1267-77. PMID 26579773 DOI: 10.1021/Ct500894K |
0.792 |
|
| 2015 |
Mustoe AM, Al-Hashimi HM, Brooks CL. Secondary structure encodes a cooperative tertiary folding funnel in the Azoarcus ribozyme. Nucleic Acids Research. PMID 26481360 DOI: 10.1093/Nar/Gkv1055 |
0.422 |
|
| 2015 |
Cheng S, Brooks CL. Protein-protein interfaces in viral capsids are structurally unique. Journal of Molecular Biology. PMID 26375252 DOI: 10.1016/J.Jmb.2015.09.008 |
0.356 |
|
| 2015 |
Dickson A, Ahlstrom LS, Brooks CL. Coupled folding and binding with 2D Window-Exchange Umbrella Sampling. Journal of Computational Chemistry. PMID 26250657 DOI: 10.1002/Jcc.24004 |
0.582 |
|
| 2015 |
Ding B, Panahi A, Ho JJ, Laaser JE, Brooks CL, Zanni MT, Chen Z. Probing Site-Specific Structural Information of Peptides at Model Membrane Interface In Situ. Journal of the American Chemical Society. 137: 10190-8. PMID 26241117 DOI: 10.1021/Jacs.5B04024 |
0.618 |
|
| 2015 |
Ogorzalek TL, Wei S, Liu Y, Wang Q, Brooks CL, Chen Z, Marsh EN. Molecular-Level Insights into Orientation-Dependent Changes in the Thermal Stability of Enzymes Covalently Immobilized on Surfaces. Langmuir : the Acs Journal of Surfaces and Colloids. 31: 6145-53. PMID 25973638 DOI: 10.1021/Acs.Langmuir.5B01735 |
0.324 |
|
| 2015 |
Goh GB, Eike DM, Murch BP, Brooks CL. Accurate modeling of ionic surfactants at high concentration. The Journal of Physical Chemistry. B. 119: 6217-24. PMID 25913469 DOI: 10.1021/Acs.Jpcb.5B01765 |
0.383 |
|
| 2015 |
Panahi A, Brooks CL. Membrane environment modulates the pKa values of transmembrane helices. The Journal of Physical Chemistry. B. 119: 4601-7. PMID 25734901 DOI: 10.1021/Acs.Jpcb.5B00289 |
0.599 |
|
| 2015 |
Mustoe AM, Liu X, Lin PJ, Al-Hashimi HM, Fierke CA, Brooks CL. Noncanonical secondary structure stabilizes mitochondrial tRNA(Ser(UCN)) by reducing the entropic cost of tertiary folding. Journal of the American Chemical Society. 137: 3592-9. PMID 25705930 DOI: 10.1021/Ja5130308 |
0.33 |
|
| 2015 |
Carrillo-Tripp M, Montiel-García DJ, Brooks CL, Reddy VS. CapsidMaps: protein-protein interaction pattern discovery platform for the structural analysis of virus capsids using Google Maps. Journal of Structural Biology. 190: 47-55. PMID 25697908 DOI: 10.1016/J.Jsb.2015.02.003 |
0.358 |
|
| 2015 |
Laricheva EN, Goh GB, Dickson A, Brooks CL. pH-dependent transient conformational states control optical properties in cyan fluorescent protein. Journal of the American Chemical Society. 137: 2892-900. PMID 25647152 DOI: 10.1021/Ja509233R |
0.586 |
|
| 2015 |
Zeng X, Mukhopadhyay S, Brooks CL. Residue-level resolution of alphavirus envelope protein interactions in pH-dependent fusion. Proceedings of the National Academy of Sciences of the United States of America. 112: 2034-9. PMID 25646410 DOI: 10.1073/Pnas.1414190112 |
0.347 |
|
| 2015 |
Cheng S, Zhang Y, Brooks CL. PCalign: a method to quantify physicochemical similarity of protein-protein interfaces. Bmc Bioinformatics. 16: 33. PMID 25638036 DOI: 10.1186/S12859-015-0471-X |
0.386 |
|
| 2015 |
Frank AT, Law SM, Ahlstrom LS, Brooks CL. Predicting Protein Backbone Chemical Shifts From Cα Coordinates: Extracting High Resolution Experimental Observables from Low Resolution Models. Journal of Chemical Theory and Computation. 11: 325-331. PMID 25620895 DOI: 10.1021/Ct5009125 |
0.818 |
|
| 2015 |
Ahlstrom LS, Law SM, Dickson A, Brooks CL. Multiscale modeling of a conditionally disordered pH-sensing chaperone. Journal of Molecular Biology. 427: 1670-80. PMID 25584862 DOI: 10.1016/J.Jmb.2015.01.002 |
0.79 |
|
| 2015 |
Li Y, Wei S, Wu J, Jasensky J, Xi C, Li H, Xu Y, Wang Q, Marsh ENG, Brooks CL, Chen Z. Effects of peptide immobilization sites on the structure and activity of surface tethered antimicrobial peptides Journal of Physical Chemistry C. 119: 7146-7155. DOI: 10.1021/Jp5125487 |
0.3 |
|
| 2015 |
Ding B, Panahi A, Ho JJ, Laaser JE, Brooks CL, Zanni MT, Chen Z. Probing site-specific structural information of peptides at model membrane interface in situ Journal of the American Chemical Society. 137: 10190-10198. DOI: 10.1021/jacs.5b04024 |
0.555 |
|
| 2015 |
Wang Q, Wei S, Wu J, Zou X, Sieggreen O, Liu Y, Xi C, Brooks CL, Chen Z. Interfacial Behaviors of Antimicrobial Peptide Cecropin P1 Immobilized on Different Self-Assembled Monolayers Journal of Physical Chemistry C. 119: 22542-22551. DOI: 10.1021/Acs.Jpcc.5B06882 |
0.302 |
|
| 2015 |
Panahi A, Brooks CL. Membrane Environment Modulates the pKa Values of Transmembrane Helices Journal of Physical Chemistry B. 119: 4601-4607. DOI: 10.1021/acs.jpcb.5b00289 |
0.524 |
|
| 2015 |
Wei S, Brooks CL. Stability and orientation of cecropin P1 on maleimide self-assembled monolayer (SAM) surfaces and suggested functional mutations Chinese Chemical Letters. 26: 485-490. DOI: 10.1016/J.Cclet.2015.03.020 |
0.35 |
|
| 2015 |
Armacost KA, Goh GB, Brooks CL. Biasing Potential Replica Exchange Multi-Site λ-Dynamics for Efficient Free Energy Calculations of Protein-Ligand Interactions Biophysical Journal. 108: 356a. DOI: 10.1016/J.Bpj.2014.11.1951 |
0.404 |
|
| 2015 |
Ahlstrom LS, Law SM, Dickson A, Brooks CL. A Multiscale Model for pH-Dependent Folding and Binding of a Conditionally Disordered Chaperone Biophysical Journal. 108: 347a. DOI: 10.1016/J.Bpj.2014.11.1900 |
0.8 |
|
| 2015 |
Dickson A, Ahlstrom LS, Brooks CL. Coupled folding and binding with 2D Window-Exchange Umbrella Sampling Journal of Computational Chemistry. DOI: 10.1002/jcc.24004 |
0.479 |
|
| 2014 |
Dickson A, Mustoe AM, Salmon L, Brooks CL. Efficient in silico exploration of RNA interhelical conformations using Euler angles and WExplore. Nucleic Acids Research. 42: 12126-37. PMID 25294827 DOI: 10.1093/Nar/Gku799 |
0.593 |
|
| 2014 |
Law SM, Ahlstrom LS, Panahi A, Brooks CL. Hamiltonian Mapping Revisited: Calibrating Minimalist Models to Capture Molecular Recognition by Intrinsically Disordered Proteins. The Journal of Physical Chemistry Letters. 5: 3441-3444. PMID 25289116 DOI: 10.1021/Jz501811K |
0.807 |
|
| 2014 |
Wang Z, Han X, He N, Chen Z, Brooks CL. Environmental effect on surface immobilized biological molecules. The Journal of Physical Chemistry. B. 118: 12176-85. PMID 25265065 DOI: 10.1021/Jp508550D |
0.332 |
|
| 2014 |
Frank AT, Law SM, Brooks CL. A simple and fast approach for predicting (1)H and (13)C chemical shifts: toward chemical shift-guided simulations of RNA. The Journal of Physical Chemistry. B. 118: 12168-75. PMID 25255209 DOI: 10.1021/Jp508342X |
0.791 |
|
| 2014 |
Mustoe AM, Brooks CL, Al-Hashimi HM. Topological constraints are major determinants of tRNA tertiary structure and dynamics and provide basis for tertiary folding cooperativity. Nucleic Acids Research. 42: 11792-804. PMID 25217593 DOI: 10.1093/Nar/Gku807 |
0.371 |
|
| 2014 |
Nobrega RP, Arora K, Kathuria SV, Graceffa R, Barrea RA, Guo L, Chakravarthy S, Bilsel O, Irving TC, Brooks CL, Matthews CR. Modulation of frustration in folding by sequence permutation. Proceedings of the National Academy of Sciences of the United States of America. 111: 10562-7. PMID 25002512 DOI: 10.1073/Pnas.1324230111 |
0.353 |
|
| 2014 |
Law SM, Gagnon JK, Mapp AK, Brooks CL. Prepaying the entropic cost for allosteric regulation in KIX. Proceedings of the National Academy of Sciences of the United States of America. 111: 12067-72. PMID 25002472 DOI: 10.1073/Pnas.1405831111 |
0.799 |
|
| 2014 |
Law SM, Frank AT, Brooks CL. PCASSO: a fast and efficient Cα-based method for accurately assigning protein secondary structure elements. Journal of Computational Chemistry. 35: 1757-61. PMID 24995959 DOI: 10.1002/Jcc.23683 |
0.802 |
|
| 2014 |
Goh GB, Laricheva EN, Brooks CL. Uncovering pH-dependent transient states of proteins with buried ionizable residues. Journal of the American Chemical Society. 136: 8496-9. PMID 24842060 DOI: 10.1021/Ja5012564 |
0.357 |
|
| 2014 |
Arthur EJ, King JT, Kubarych KJ, Brooks CL. Heterogeneous preferential solvation of water and trifluoroethanol in homologous lysozymes. The Journal of Physical Chemistry. B. 118: 8118-27. PMID 24823618 DOI: 10.1021/Jp501132Z |
0.4 |
|
| 2014 |
Zeng X, Chugh J, Casiano-Negroni A, Al-Hashimi HM, Brooks CL. Flipping of the ribosomal A-site adenines provides a basis for tRNA selection. Journal of Molecular Biology. 426: 3201-13. PMID 24813122 DOI: 10.1016/J.Jmb.2014.04.029 |
0.327 |
|
| 2014 |
Wang Z, Han X, He N, Chen Z, Brooks CL. Molecular structures of C- and N-terminus cysteine modified cecropin P1 chemically immobilized onto maleimide-terminated self-assembled monolayers investigated by molecular dynamics simulation. The Journal of Physical Chemistry. B. 118: 5670-80. PMID 24802888 DOI: 10.1021/Jp5023482 |
0.373 |
|
| 2014 |
Mustoe AM, Brooks CL, Al-Hashimi HM. Hierarchy of RNA functional dynamics. Annual Review of Biochemistry. 83: 441-66. PMID 24606137 DOI: 10.1146/Annurev-Biochem-060713-035524 |
0.339 |
|
| 2014 |
Han X, Liu Y, Wu FG, Jansensky J, Kim T, Wang Z, Brooks CL, Wu J, Xi C, Mello CM, Chen Z. Different interfacial behaviors of peptides chemically immobilized on surfaces with different linker lengths and via different termini. The Journal of Physical Chemistry. B. 118: 2904-12. PMID 24555411 DOI: 10.1021/Jp4122003 |
0.327 |
|
| 2014 |
Mustoe AM, Al-Hashimi HM, Brooks CL. Coarse grained models reveal essential contributions of topological constraints to the conformational free energy of RNA bulges. The Journal of Physical Chemistry. B. 118: 2615-27. PMID 24547945 DOI: 10.1021/Jp411478X |
0.357 |
|
| 2014 |
May ER, Arora K, Brooks CL. pH-induced stability switching of the bacteriophage HK97 maturation pathway. Journal of the American Chemical Society. 136: 3097-107. PMID 24495192 DOI: 10.1021/Ja410860N |
0.664 |
|
| 2014 |
Dickson A, Brooks CL. WExplore: hierarchical exploration of high-dimensional spaces using the weighted ensemble algorithm. The Journal of Physical Chemistry. B. 118: 3532-42. PMID 24490961 DOI: 10.1021/Jp411479C |
0.591 |
|
| 2014 |
Vashisth H, Skiniotis G, Brooks CL. Collective variable approaches for single molecule flexible fitting and enhanced sampling. Chemical Reviews. 114: 3353-65. PMID 24446720 DOI: 10.1021/Cr4005988 |
0.441 |
|
| 2014 |
Goh GB, Hulbert BS, Zhou H, Brooks CL. Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism. Proteins. 82: 1319-31. PMID 24375620 DOI: 10.1002/Prot.24499 |
0.437 |
|
| 2014 |
Taylor KA, Feig M, Brooks CL, Fagnant PM, Lowey S, Trybus KM. Role of the essential light chain in the activation of smooth muscle myosin by regulatory light chain phosphorylation. Journal of Structural Biology. 185: 375-82. PMID 24361582 DOI: 10.1016/J.Bpj.2013.11.4006 |
0.643 |
|
| 2014 |
King JT, Arthur EJ, Brooks CL, Kubarych KJ. Crowding induced collective hydration of biological macromolecules over extended distances. Journal of the American Chemical Society. 136: 188-94. PMID 24341684 DOI: 10.1021/Ja407858C |
0.374 |
|
| 2014 |
King JT, Arthur EJ, Osborne DG, Brooks CL, Kubarych KJ. Biomolecular hydration dynamics probed with 2D-IR spectroscopy: From dilute solution to a macromolecular crowd Chinese Chemical Letters. DOI: 10.1016/J.Cclet.2015.03.005 |
0.339 |
|
| 2014 |
Panahi A, Brooks CL. Exploring pKa Values for Buried Residues in Membrane Bilayers using Constant pH Molecular Dynamics Simulations Biophysical Journal. 106: 640a. DOI: 10.1016/J.Bpj.2013.11.3542 |
0.655 |
|
| 2014 |
Mustoe AM, Al-Hashimi HM, Brooks CL. Linking RNA Secondary Structure to the Free Energy of Tertiary Structure Folding through Coarse-Grained Models Biophysical Journal. 106: 284a. DOI: 10.1016/J.Bpj.2013.11.1661 |
0.366 |
|
| 2014 |
Arora K, Brooks CL. ATP Acts as Switch for Toggling Calreticulin Between its Lectin and Chaperone Function Biophysical Journal. 106: 247a. DOI: 10.1016/J.Bpj.2013.11.1445 |
0.369 |
|
| 2013 |
Dickson A, Brooks CL. Quantifying chaperone-mediated transitions in the proteostasis network of E. coli. Plos Computational Biology. 9: e1003324. PMID 24244134 DOI: 10.1371/Journal.Pcbi.1003324 |
0.597 |
|
| 2013 |
Vashisth H, Storaska AJ, Neubig RR, Brooks CL. Conformational dynamics of a regulator of G-protein signaling protein reveals a mechanism of allosteric inhibition by a small molecule. Acs Chemical Biology. 8: 2778-84. PMID 24093330 DOI: 10.1021/Cb400568G |
0.406 |
|
| 2013 |
Suddala KC, Rinaldi AJ, Feng J, Mustoe AM, Eichhorn CD, Liberman JA, Wedekind JE, Al-Hashimi HM, Brooks CL, Walter NG. Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure. Nucleic Acids Research. 41: 10462-75. PMID 24003028 DOI: 10.1093/Nar/Gkt798 |
0.351 |
|
| 2013 |
Laricheva EN, Arora K, Knight JL, Brooks CL. Deconstructing activation events in rhodopsin. Journal of the American Chemical Society. 135: 10906-9. PMID 23841875 DOI: 10.1021/Ja4042687 |
0.301 |
|
| 2013 |
Ahlstrom LS, Dickson A, Brooks CL. Binding and folding of the small bacterial chaperone HdeA. The Journal of Physical Chemistry. B. 117: 13219-25. PMID 23738772 DOI: 10.1021/Jp403264S |
0.618 |
|
| 2013 |
Goh GB, Knight JL, Brooks CL. Towards Accurate Prediction of Protonation Equilibrium of Nucleic Acids. The Journal of Physical Chemistry Letters. 4: 760-766. PMID 23526474 DOI: 10.1021/Jz400078D |
0.331 |
|
| 2013 |
Goh GB, Knight JL, Brooks CL. pH-dependent dynamics of complex RNA macromolecules. Journal of Chemical Theory and Computation. 9: 935-943. PMID 23525495 DOI: 10.1021/Ct300942Z |
0.376 |
|
| 2013 |
Vashisth H, Skiniotis G, Brooks CL. Enhanced sampling and overfitting analyses in structural refinement of nucleic acids into electron microscopy maps. The Journal of Physical Chemistry. B. 117: 3738-46. PMID 23506287 DOI: 10.1021/Jp3126297 |
0.377 |
|
| 2013 |
Nikolova EN, Goh GB, Brooks CL, Al-Hashimi HM. Characterizing the protonation state of cytosine in transient G·C Hoogsteen base pairs in duplex DNA. Journal of the American Chemical Society. 135: 6766-9. PMID 23506098 DOI: 10.1021/Ja400994E |
0.302 |
|
| 2013 |
Foit L, George JS, Zhang BW, Brooks CL, Bardwell JC. Chaperone activation by unfolding. Proceedings of the National Academy of Sciences of the United States of America. 110: E1254-62. PMID 23487787 DOI: 10.1073/Pnas.1222458110 |
0.345 |
|
| 2013 |
Dickson A, Brooks CL. Native states of fast-folding proteins are kinetic traps. Journal of the American Chemical Society. 135: 4729-34. PMID 23458553 DOI: 10.1021/Ja311077U |
0.603 |
|
| 2013 |
Law SM, Zhang BW, Brooks CL. pH-sensitive residues in the p19 RNA silencing suppressor protein from carnation Italian ringspot virus affect siRNA binding stability. Protein Science : a Publication of the Protein Society. 22: 595-604. PMID 23450521 DOI: 10.1002/Pro.2243 |
0.789 |
|
| 2013 |
Arora K, Brooks CL. Multiple intermediates, diverse conformations, and cooperative conformational changes underlie the catalytic hydride transfer reaction of dihydrofolate reductase. Topics in Current Chemistry. 337: 165-87. PMID 23420416 DOI: 10.1007/128_2012_408 |
0.335 |
|
| 2013 |
Cheng S, Brooks CL. Viral capsid proteins are segregated in structural fold space. Plos Computational Biology. 9: e1002905. PMID 23408879 DOI: 10.1371/Journal.Pcbi.1002905 |
0.382 |
|
| 2013 |
Wang N, Majmudar CY, Pomerantz WC, Gagnon JK, Sadowsky JD, Meagher JL, Johnson TK, Stuckey JA, Brooks CL, Wells JA, Mapp AK. Ordering a dynamic protein via a small-molecule stabilizer. Journal of the American Chemical Society. 135: 3363-6. PMID 23384013 DOI: 10.1021/Ja3122334 |
0.399 |
|
| 2013 |
Knight JL, Yesselman JD, Brooks CL. Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes. Journal of Computational Chemistry. 34: 893-903. PMID 23292859 DOI: 10.1002/Jcc.23199 |
0.356 |
|
| 2013 |
Foit L, Zhang B, George J, Brunetti L, Brooks C, Bardwell J. Acid-Induced Activation of the Periplasmic Chaperone HdeA Biophysical Journal. 104: 569a-570a. DOI: 10.1016/J.Bpj.2012.11.3163 |
0.323 |
|
| 2013 |
Vashisth H, Brooks CL. Enhanced Sampling Assisted Flexible Fitting of Atomic Structures into Electron Microscopy Maps Biophysical Journal. 104: 35a. DOI: 10.1016/J.Bpj.2012.11.232 |
0.431 |
|
| 2013 |
Foit L, Zhang B, George J, Brunetti L, Brooks C, Bardwell JC. Structural Studies on the Activation and Substrate Binding of a Conditionally Disordered Acid-Activated Chaperone Biophysical Journal. 104: 5a. DOI: 10.1016/J.Bpj.2012.11.050 |
0.375 |
|
| 2012 |
Dickson A, Brooks CL. Quantifying hub-like behavior in protein folding networks. Journal of Chemical Theory and Computation. 8: 3044-3052. PMID 24027492 DOI: 10.1021/Ct300537S |
0.589 |
|
| 2012 |
Mannige RV, Brooks CL, Shakhnovich EI. A universal trend among proteomes indicates an oily last common ancestor. Plos Computational Biology. 8: e1002839. PMID 23300421 DOI: 10.1371/Journal.Pcbi.1002839 |
0.514 |
|
| 2012 |
Vashisth H, Brooks CL. Conformational Sampling of Maltose-transporter Components in Cartesian Collective Variables is Governed by the Low-frequency Normal Modes. The Journal of Physical Chemistry Letters. 3: 3379-3384. PMID 23185650 DOI: 10.1021/Jz301650Q |
0.356 |
|
| 2012 |
Vashisth H, Skiniotis G, Brooks CL. Using enhanced sampling and structural restraints to refine atomic structures into low-resolution electron microscopy maps. Structure (London, England : 1993). 20: 1453-62. PMID 22958641 DOI: 10.1016/J.Str.2012.08.007 |
0.388 |
|
| 2012 |
King JT, Arthur EJ, Brooks CL, Kubarych KJ. Site-specific hydration dynamics of globular proteins and the role of constrained water in solvent exchange with amphiphilic cosolvents. The Journal of Physical Chemistry. B. 116: 5604-11. PMID 22530969 DOI: 10.1021/Jp300835K |
0.384 |
|
| 2012 |
May ER, Brooks CL. On the morphology of viral capsids: elastic properties and buckling transitions. The Journal of Physical Chemistry. B. 116: 8604-9. PMID 22409201 DOI: 10.1021/Jp300005G |
0.646 |
|
| 2012 |
Goh GB, Knight JL, Brooks CL. Constant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit Solvent. Journal of Chemical Theory and Computation. 8: 36-46. PMID 22337595 DOI: 10.1021/Ct2006314 |
0.361 |
|
| 2012 |
May ER, Feng J, Brooks CL. Exploring the symmetry and mechanism of virus capsid maturation via an ensemble of pathways. Biophysical Journal. 102: 606-12. PMID 22325284 DOI: 10.1016/J.Bpj.2011.12.016 |
0.644 |
|
| 2012 |
Roos WH, Gertsman I, May ER, Brooks CL, Johnson JE, Wuite GJ. Mechanics of bacteriophage maturation. Proceedings of the National Academy of Sciences of the United States of America. 109: 2342-7. PMID 22308333 DOI: 10.1073/Pnas.1109590109 |
0.647 |
|
| 2012 |
Yesselman JD, Price DJ, Knight JL, Brooks CL. MATCH: an atom-typing toolset for molecular mechanics force fields. Journal of Computational Chemistry. 33: 189-202. PMID 22042689 DOI: 10.1002/Jcc.21963 |
0.332 |
|
| 2012 |
Eichhorn CD, Feng J, Suddala KC, Walter NG, Brooks CL, Al-Hashimi HM. Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch. Nucleic Acids Research. 40: 1345-55. PMID 22009676 DOI: 10.1093/Nar/Gkr833 |
0.403 |
|
| 2012 |
Mustoe AM, Bailor MH, Teixeira RM, Brooks CL, Al-Hashimi HM. New insights into the fundamental role of topological constraints as a determinant of two-way junction conformation. Nucleic Acids Research. 40: 892-904. PMID 21937512 DOI: 10.1093/Nar/Gkr751 |
0.362 |
|
| 2012 |
Jacobsen DM, Bao ZQ, Brooks CL, Young MA. Dual Role of Magnesium Ions in Active pCDK2/Cyclin: Essential Activator of Kinase Activity and Partial Inhibitor of Product Release Biophysical Journal. 102: 271a. DOI: 10.1016/J.Bpj.2011.11.1495 |
0.321 |
|
| 2011 |
Knight JL, Brooks CL. Multi-Site λ-dynamics for simulated Structure-Activity Relationship studies. Journal of Chemical Theory and Computation. 7: 2728-2739. PMID 22125476 DOI: 10.1021/Ct200444F |
0.395 |
|
| 2011 |
Zhang BW, Brunetti L, Brooks CL. Probing pH-dependent dissociation of HdeA dimers. Journal of the American Chemical Society. 133: 19393-8. PMID 22026371 DOI: 10.1021/Ja2060066 |
0.338 |
|
| 2011 |
Arthur EJ, Yesselman JD, Brooks CL. Predicting extreme pKa shifts in staphylococcal nuclease mutants with constant pH molecular dynamics. Proteins. 79: 3276-86. PMID 22002886 DOI: 10.1002/Prot.23195 |
0.414 |
|
| 2011 |
Knight JL, Brooks CL. Applying efficient implicit nongeometric constraints in alchemical free energy simulations Journal of Computational Chemistry. 32: 3423-3432. PMID 21919014 DOI: 10.1002/Jcc.21921 |
0.391 |
|
| 2011 |
Knight JL, Brooks CL. Surveying implicit solvent models for estimating small molecule absolute hydration free energies . 32: 2909-2923. PMID 21735452 DOI: 10.1002/Jcc.21876 |
0.365 |
|
| 2011 |
Rahaman O, Estrada TP, Doren DJ, Taufer M, Brooks CL, Armen RS. Evaluation of several two-step scoring functions based on linear interaction energy, effective ligand size, and empirical pair potentials for prediction of protein-ligand binding geometry and free energy. Journal of Chemical Information and Modeling. 51: 2047-65. PMID 21644546 DOI: 10.1021/Ci1003009 |
0.348 |
|
| 2011 |
May ER, Aggarwal A, Klug WS, Brooks CL. Viral capsid equilibrium dynamics reveals nonuniform elastic properties. Biophysical Journal. 100: L59-61. PMID 21641297 DOI: 10.1016/J.Bpj.2011.04.026 |
0.637 |
|
| 2011 |
May ER, Brooks CL. Determination of viral capsid elastic properties from equilibrium thermal fluctuations. Physical Review Letters. 106: 188101. PMID 21635128 DOI: 10.1103/Physrevlett.106.188101 |
0.657 |
|
| 2011 |
Bailor MH, Mustoe AM, Brooks CL, Al-Hashimi HM. Topological constraints: using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation. Current Opinion in Structural Biology. 21: 296-305. PMID 21497083 DOI: 10.1016/J.Sbi.2011.03.009 |
0.325 |
|
| 2011 |
Feng J, Walter NG, Brooks CL. Cooperative and directional folding of the preQ1 riboswitch aptamer domain. Journal of the American Chemical Society. 133: 4196-9. PMID 21375305 DOI: 10.1021/Ja110411M |
0.334 |
|
| 2011 |
Arora K, Brooks CL. Exploring the functional landscape of biomolecular machines via elastic network normal mode analysis Molecular Machines in Biology: Workshop of the Cell. 59-77. DOI: 10.1017/CBO9781139003704.006 |
0.344 |
|
| 2011 |
Mustoe AM, Al-Hashimi HM, Brooks CL. A Coarse Grain RNA Model for Exploration of RNA Conformational Space Biophysical Journal. 100: 238a. DOI: 10.1016/J.Bpj.2010.12.1518 |
0.392 |
|
| 2011 |
Yesselman JD, Al-Hashimi HM, Brooks CL. Exploring RNA Drug Binding Using Consistent Charge Models Biophysical Journal. 100: 159a. DOI: 10.1016/J.Bpj.2010.12.1085 |
0.35 |
|
| 2010 |
Hirschi JS, Arora K, Brooks CL, Schramm VL. Conformational dynamics in human purine nucleoside phosphorylase with reactants and transition-state analogues. The Journal of Physical Chemistry. B. 114: 16263-72. PMID 20936808 DOI: 10.1021/Jp108056S |
0.313 |
|
| 2010 |
May ER, Armen RS, Mannan AM, Brooks CL. The flexible C-terminal arm of the Lassa arenavirus Z-protein mediates interactions with multiple binding partners Proteins: Structure, Function and Bioinformatics. 78: 2251-2264. PMID 20544962 DOI: 10.1002/Prot.22738 |
0.692 |
|
| 2010 |
Michino M, Chen J, Stevens RC, Brooks CL. FoldGPCR: structure prediction protocol for the transmembrane domain of G protein-coupled receptors from class A. Proteins. 78: 2189-201. PMID 20544957 DOI: 10.1002/Prot.22731 |
0.554 |
|
| 2010 |
Zimmermann J, Romesberg FE, Brooks CL, Thorpe IF. Molecular description of flexibility in an antibody combining site. The Journal of Physical Chemistry. B. 114: 7359-70. PMID 20455589 DOI: 10.1021/Jp906421V |
0.424 |
|
| 2010 |
Yoshimoto K, Arora K, Brooks CL. Hexameric helicase deconstructed: interplay of conformational changes and substrate coupling. Biophysical Journal. 98: 1449-57. PMID 20409463 DOI: 10.1016/J.Bpj.2009.12.4315 |
0.324 |
|
| 2010 |
Armen RS, Schiller SM, Brooks CL. Steric and thermodynamic limits of design for the incorporation of large unnatural amino acids in aminoacyl-tRNA synthetase enzymes Proteins: Structure, Function and Bioinformatics. 78: 1926-1938. PMID 20310065 DOI: 10.1002/Prot.22706 |
0.324 |
|
| 2010 |
Hills RD, Kathuria SV, Wallace LA, Day IJ, Brooks CL, Matthews CR. Topological frustration in beta alpha-repeat proteins: sequence diversity modulates the conserved folding mechanisms of alpha/beta/alpha sandwich proteins. Journal of Molecular Biology. 398: 332-50. PMID 20226790 DOI: 10.1016/J.Jmb.2010.03.001 |
0.343 |
|
| 2009 |
Armen RS, Chen J, Brooks CL. An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics. Journal of Chemical Theory and Computation. 5: 2909-2923. PMID 20160879 DOI: 10.1021/Ct900262T |
0.564 |
|
| 2009 |
Knight JL, Brooks CL. Validating CHARMM parameters and exploring charge distribution rules in structure-based drug design. Journal of Chemical Theory and Computation. 5: 1680-1691. PMID 20046995 DOI: 10.1021/Ct900079T |
0.317 |
|
| 2009 |
Zhong L, Matthews JF, Hansen PI, Crowley MF, Cleary JM, Walker RC, Nimlos MR, Brooks CL, Adney WS, Himmel ME, Brady JW. Computational simulations of the Trichoderma reesei cellobiohydrolase I acting on microcrystalline cellulose Ibeta: the enzyme-substrate complex. Carbohydrate Research. 344: 1984-92. PMID 19699474 DOI: 10.1016/J.Carres.2009.07.005 |
0.342 |
|
| 2009 |
Michino M, Brooks CL. Predicting structurally conserved contacts for homologous proteins using sequence conservation filters. Proteins. 77: 448-53. PMID 19475704 DOI: 10.1002/Prot.22456 |
0.317 |
|
| 2009 |
Michino M, Abola E, Brooks CL, Dixon JS, Moult J, Stevens RC. Community-wide assessment of GPCR structure modelling and ligand docking: GPCR Dock 2008. Nature Reviews. Drug Discovery. 8: 455-63. PMID 19461661 DOI: 10.1038/Nrd2877 |
0.327 |
|
| 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 |
0.785 |
|
| 2009 |
Knight JL, Brooks CL. λ-dynamics free energy simulation methods Journal of Computational Chemistry. 30: 1692-1700. PMID 19421993 DOI: 10.1002/Jcc.21295 |
0.439 |
|
| 2009 |
Hills RD, Brooks CL. Insights from coarse-grained Gō models for protein folding and dynamics. International Journal of Molecular Sciences. 10: 889-905. PMID 19399227 DOI: 10.3390/Ijms10030889 |
0.436 |
|
| 2009 |
Taufer M, Armen R, Chen J, Teller P, Brooks C. Computational multiscale modeling in protein - Ligand docking Ieee Engineering in Medicine and Biology Magazine. 28: 58-69. PMID 19349252 DOI: 10.1109/Memb.2009.931789 |
0.506 |
|
| 2009 |
Carrillo-Tripp M, Shepherd CM, Borelli IA, Venkataraman S, Lander G, Natarajan P, Johnson JE, Brooks CL, Reddy VS. VIPERdb2: an enhanced and web API enabled relational database for structural virology. Nucleic Acids Research. 37: D436-42. PMID 18981051 DOI: 10.1093/Nar/Gkn840 |
0.352 |
|
| 2009 |
Armen RS, Chen J, Brooks CL. An evaluation of explicit receptor flexibility in molecular docking using molecular dynamics and torsion angle molecular dynamics Journal of Chemical Theory and Computation. 5: 2909-2923. DOI: 10.1021/ct900262t |
0.462 |
|
| 2009 |
Head-Gordon T, Head-Gordon M, Frisch MJ, Brooks C, Pople J. A theoretical study of alanine dipeptide and analogs International Journal of Quantum Chemistry. 36: 311-322. DOI: 10.1002/Qua.560360725 |
0.581 |
|
| 2008 |
Nguyen HD, Brooks CL. Generalized structural polymorphism in self-assembled viral particles. Nano Letters. 8: 4574-81. PMID 19367856 DOI: 10.1021/Nl802828V |
0.348 |
|
| 2008 |
Hills RD, Brooks CL. Coevolution of function and the folding landscape: correlation with density of native contacts. Biophysical Journal. 95: L57-9. PMID 18708465 DOI: 10.1529/Biophysj.108.143388 |
0.425 |
|
| 2008 |
Hills RD, Brooks CL. Subdomain competition, cooperativity, and topological frustration in the folding of CheY. Journal of Molecular Biology. 382: 485-95. PMID 18644380 DOI: 10.1016/J.Jmb.2008.07.007 |
0.388 |
|
| 2008 |
Mannige RV, Brooks CL. Tilable nature of virus capsids and the role of topological constraints in natural capsid design. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 77: 051902. PMID 18643097 DOI: 10.1103/Physreve.77.051902 |
0.315 |
|
| 2008 |
Carrillo-Tripp M, Brooks CL, Reddy VS. A novel method to map and compare protein-protein interactions in spherical viral capsids. Proteins. 73: 644-55. PMID 18491385 DOI: 10.1002/Prot.22088 |
0.342 |
|
| 2008 |
Lee J, Chen J, Brooks CL, Im W. Application of solid-state NMR restraint potentials in membrane protein modeling. Journal of Magnetic Resonance (San Diego, Calif. : 1997). 193: 68-76. PMID 18462966 DOI: 10.1016/J.Jmr.2008.04.023 |
0.699 |
|
| 2008 |
Szurmant H, Bu L, Brooks CL, Hoch JA. An essential sensor histidine kinase controlled by transmembrane helix interactions with its auxiliary proteins. Proceedings of the National Academy of Sciences of the United States of America. 105: 5891-6. PMID 18408157 DOI: 10.1073/Pnas.0800247105 |
0.321 |
|
| 2008 |
Bu L, Brooks CL. De novo prediction of the structures of M. tuberculosis membrane proteins. Journal of the American Chemical Society. 130: 5384-5. PMID 18386898 DOI: 10.1021/Ja710213P |
0.346 |
|
| 2008 |
Chen J, Brooks CL, Khandogin J. Recent advances in implicit solvent-based methods for biomolecular simulations. Current Opinion in Structural Biology. 18: 140-8. PMID 18304802 DOI: 10.1016/J.Sbi.2008.01.003 |
0.633 |
|
| 2008 |
Chen J, Brooks CL. Implicit modeling of nonpolar solvation for simulating protein folding and conformational transitions. Physical Chemistry Chemical Physics : Pccp. 10: 471-81. PMID 18183310 DOI: 10.1039/B714141F |
0.616 |
|
| 2008 |
Bu L, Michino M, Wolf RM, Brooks CL. Improved model building and assessment of the Calcium-sensing receptor transmembrane domain. Proteins. 71: 215-26. PMID 17932932 DOI: 10.1002/Prot.21685 |
0.343 |
|
| 2008 |
Chen J, Brooks CL, Scheraga HA. Revisiting the carboxylic acid dimers in aqueous solution: interplay of hydrogen bonding, hydrophobic interactions, and entropy. The Journal of Physical Chemistry. B. 112: 242-9. PMID 17880128 DOI: 10.1021/Jp074355H |
0.573 |
|
| 2008 |
Olson MA, Feig M, Brooks CL. Prediction of protein loop conformations using multiscale modeling methods with physical energy scoring functions. Journal of Computational Chemistry. 29: 820-31. PMID 17876760 DOI: 10.1002/Jcc.20827 |
0.725 |
|
| 2008 |
Zhong L, Matthews JF, Crowley MF, Rignall T, Talón C, Cleary JM, Walker RC, Chukkapalli G, McCabe C, Nimlos MR, Brooks CL, Himmel ME, Brady JW. Interactions of the complete cellobiohydrolase I from Trichodera reesei with microcrystalline cellulose Iβ Cellulose. 15: 261-273. DOI: 10.1007/S10570-007-9186-0 |
0.375 |
|
| 2007 |
Arora K, Brooks CL. Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism. Proceedings of the National Academy of Sciences of the United States of America. 104: 18496-501. PMID 18000050 DOI: 10.1073/Pnas.0706443104 |
0.392 |
|
| 2007 |
Bostick DL, Brooks CL. Selectivity in K+ channels is due to topological control of the permeant ion's coordinated state. Proceedings of the National Academy of Sciences of the United States of America. 104: 9260-5. PMID 17519335 DOI: 10.1073/Pnas.0700554104 |
0.305 |
|
| 2007 |
Thorpe IF, Brooks CL. Molecular evolution of affinity and flexibility in the immune system. Proceedings of the National Academy of Sciences of the United States of America. 104: 8821-6. PMID 17488816 DOI: 10.1073/Pnas.0610064104 |
0.33 |
|
| 2007 |
Khavrutskii IV, Price DJ, Lee J, Brooks CL. Conformational change of the methionine 20 loop of Escherichia coli dihydrofolate reductase modulates pKa of the bound dihydrofolate. Protein Science : a Publication of the Protein Society. 16: 1087-100. PMID 17473015 DOI: 10.1110/Ps.062724307 |
0.774 |
|
| 2007 |
Bostick DL, Brooks CL. On the equivalence point for ammonium (de)protonation during its transport through the AmtB channel. Biophysical Journal. 92: L103-5. PMID 17434945 DOI: 10.1529/Biophysj.107.109165 |
0.308 |
|
| 2007 |
Chen J, Brooks CL. Can molecular dynamics simulations provide high-resolution refinement of protein structure? Proteins. 67: 922-30. PMID 17373704 DOI: 10.1002/Prot.21345 |
0.596 |
|
| 2007 |
Hills RD, Brooks CL. Hydrophobic cooperativity as a mechanism for amyloid nucleation. Journal of Molecular Biology. 368: 894-901. PMID 17368485 DOI: 10.1016/J.Jmb.2007.02.043 |
0.338 |
|
| 2007 |
Khandogin J, Raleigh DP, Brooks CL. Folding intermediate in the villin headpiece domain arises from disruption of a N-terminal hydrogen-bonded network. Journal of the American Chemical Society. 129: 3056-7. PMID 17311386 DOI: 10.1021/Ja0688880 |
0.381 |
|
| 2007 |
Nguyen HD, Reddy VS, Brooks CL. Deciphering the kinetic mechanism of spontaneous self-assembly of icosahedral capsids. Nano Letters. 7: 338-44. PMID 17297998 DOI: 10.1021/Nl062449H |
0.364 |
|
| 2007 |
Bostick DL, Brooks CL. Deprotonation by dehydration: the origin of ammonium sensing in the AmtB channel. Plos Computational Biology. 3: e22. PMID 17291160 DOI: 10.1371/Journal.Pcbi.0030022 |
0.34 |
|
| 2007 |
Chen J, Brooks CL. Critical importance of length-scale dependence in implicit modeling of hydrophobic interactions. Journal of the American Chemical Society. 129: 2444-5. PMID 17288425 DOI: 10.1021/Ja068383+ |
0.594 |
|
| 2007 |
Bu L, Im W, Brooks CL. Membrane assembly of simple helix homo-oligomers studied via molecular dynamics simulations. Biophysical Journal. 92: 854-63. PMID 17085501 DOI: 10.1529/Biophysj.106.095216 |
0.406 |
|
| 2007 |
Patel S, Brooks CL. Structure, thermodynamics, and liquid-vapor equilibrium of ethanol from molecular-dynamics simulations using nonadditive interactions. The Journal of Chemical Physics. 123: 164502. PMID 16268707 DOI: 10.1063/1.2009730 |
0.342 |
|
| 2007 |
Khandogin J, Brooks CL. Chapter 1 Molecular Simulations of pH-Mediated Biological Processes Annual Reports in Computational Chemistry. 3: 3-13. DOI: 10.1016/S1574-1400(07)03001-0 |
0.423 |
|
| 2006 |
Khandogin J, Chen J, Brooks CL. Exploring atomistic details of pH-dependent peptide folding. Proceedings of the National Academy of Sciences of the United States of America. 103: 18546-50. PMID 17116871 DOI: 10.1073/Pnas.0605216103 |
0.572 |
|
| 2006 |
Khavrutskii IV, Arora K, Brooks CL. Harmonic Fourier beads method for studying rare events on rugged energy surfaces. The Journal of Chemical Physics. 125: 174108. PMID 17100430 DOI: 10.1063/1.2363379 |
0.717 |
|
| 2006 |
Zimmermann J, Oakman EL, Thorpe IF, Shi X, Abbyad P, Brooks CL, Boxer SG, Romesberg FE. Antibody evolution constrains conformational heterogeneity by tailoring protein dynamics. Proceedings of the National Academy of Sciences of the United States of America. 103: 13722-7. PMID 16954202 DOI: 10.1073/Pnas.0603282103 |
0.394 |
|
| 2006 |
Tama F, Ren G, Brooks CL, Mitra AK. Model of the toxic complex of anthrax: responsive conformational changes in both the lethal factor and the protective antigen heptamer. Protein Science : a Publication of the Protein Society. 15: 2190-200. PMID 16943448 DOI: 10.1110/Ps.062293906 |
0.635 |
|
| 2006 |
Sherman MB, Guenther RH, Tama F, Sit TL, Brooks CL, Mikhailov AM, Orlova EV, Baker TS, Lommel SA. Removal of divalent cations induces structural transitions in red clover necrotic mosaic virus, revealing a potential mechanism for RNA release. Journal of Virology. 80: 10395-406. PMID 16920821 DOI: 10.1128/Jvi.01137-06 |
0.609 |
|
| 2006 |
Khandogin J, Brooks CL. Toward the accurate first-principles prediction of ionization equilibria in proteins. Biochemistry. 45: 9363-73. PMID 16878971 DOI: 10.1021/Bi060706R |
0.463 |
|
| 2006 |
Patel SA, Brooks CL. Revisiting the hexane-water interface via molecular dynamics simulations using nonadditive alkane-water potentials Journal of Chemical Physics. 124. PMID 16774363 DOI: 10.1063/1.2198538 |
0.364 |
|
| 2006 |
Khavrutskii IV, Byrd RH, Brooks CL. A line integral reaction path approximation for large systems via nonlinear constrained optimization: application to alanine dipeptide and the beta hairpin of protein G. The Journal of Chemical Physics. 124: 194903. PMID 16729840 DOI: 10.1063/1.2194544 |
0.73 |
|
| 2006 |
Tama F, Brooks CL. Symmetry, form, and shape: guiding principles for robustness in macromolecular machines. Annual Review of Biophysics and Biomolecular Structure. 35: 115-33. PMID 16689630 DOI: 10.1146/Annurev.Biophys.35.040405.102010 |
0.668 |
|
| 2006 |
Yadav MK, Leman LJ, Price DJ, Brooks CL, Stout CD, Ghadiri MR. Coiled coils at the edge of configurational heterogeneity. Structural analyses of parallel and antiparallel homotetrameric coiled coils reveal configurational sensitivity to a single solvent-exposed amino acid substitution. Biochemistry. 45: 4463-73. PMID 16584182 DOI: 10.1021/Bi060092Q |
0.374 |
|
| 2006 |
Chen J, Im W, Brooks CL. Balancing solvation and intramolecular interactions: toward a consistent generalized Born force field. Journal of the American Chemical Society. 128: 3728-36. PMID 16536547 DOI: 10.1021/Ja057216R |
0.603 |
|
| 2006 |
Konecny R, Trylska J, Tama F, Zhang D, Baker NA, Brooks CL, McCammon JA. Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids. Biopolymers. 82: 106-20. PMID 16278831 DOI: 10.1002/Bip.20409 |
0.673 |
|
| 2006 |
Patel S, Brooks CL. A nonadditive methanol force field: bulk liquid and liquid-vapor interfacial properties via molecular dynamics simulations using a fluctuating charge model. The Journal of Chemical Physics. 122: 024508. PMID 15638599 DOI: 10.1063/1.1827604 |
0.357 |
|
| 2006 |
Taufer M, An C, Kerstens A, Brooks CL. PredictorΗome: A "protein structure prediction supercomputer" based on global computing Ieee Transactions On Parallel and Distributed Systems. 17: 786-796. DOI: 10.1109/Tpds.2006.110 |
0.381 |
|
| 2006 |
Patel S, Brooks CL. Fluctuating charge force fields: recent developments and applications from small molecules to macromolecular biological systems Molecular Simulation. 32: 231-249. DOI: 10.1080/08927020600726708 |
0.338 |
|
| 2006 |
Mitra K, Schaffitzel C, Shaikh T, Tama F, Jenni S, Brooks CL, Ban N, Frank J. Erratum: Structure of the E. coli protein-conducting channel bound to a translating ribosome Nature. 443: 718-718. DOI: 10.1038/Nature05086 |
0.61 |
|
| 2005 |
Im W, Chen J, Brooks CL. Peptide and protein folding and conformational equilibria: theoretical treatment of electrostatics and hydrogen bonding with implicit solvent models. Advances in Protein Chemistry. 72: 173-98. PMID 16581377 DOI: 10.1016/S0065-3233(05)72007-6 |
0.553 |
|
| 2005 |
Mitra K, Schaffitzel C, Shaikh T, Tama F, Jenni S, Brooks CL, Ban N, Frank J. Structure of the E. coli protein-conducting channel bound to a translating ribosome. Nature. 438: 318-24. PMID 16292303 DOI: 10.1038/Nature04133 |
0.634 |
|
| 2005 |
Natarajan P, Lander GC, Shepherd CM, Reddy VS, Brooks CL, Johnson JE. Exploring icosahedral virus structures with VIPER. Nature Reviews. Microbiology. 3: 809-17. PMID 16205712 DOI: 10.1038/Nrmicro1283 |
0.303 |
|
| 2005 |
Thorpe IF, Brooks CL. Conformational substates modulate hydride transfer in dihydrofolate reductase. Journal of the American Chemical Society. 127: 12997-3006. PMID 16159295 DOI: 10.1021/Ja053558L |
0.377 |
|
| 2005 |
Chen J, Im W, Brooks CL. Application of torsion angle molecular dynamics for efficient sampling of protein conformations. Journal of Computational Chemistry. 26: 1565-78. PMID 16145655 DOI: 10.1002/Jcc.20293 |
0.613 |
|
| 2005 |
Price DJ, Brooks CL. Detailed considerations for a balanced and broadly applicable force field: a study of substituted benzenes modeled with OPLS-AA. Journal of Computational Chemistry. 26: 1529-41. PMID 16108048 DOI: 10.1002/Jcc.20284 |
0.361 |
|
| 2005 |
Khandogin J, Brooks CL. Constant pH molecular dynamics with proton tautomerism. Biophysical Journal. 89: 141-57. PMID 15863480 DOI: 10.1529/Biophysj.105.061341 |
0.433 |
|
| 2005 |
Im W, Brooks CL. Interfacial folding and membrane insertion of designed peptides studied by molecular dynamics simulations. Proceedings of the National Academy of Sciences of the United States of America. 102: 6771-6. PMID 15860587 DOI: 10.1073/Pnas.0408135102 |
0.336 |
|
| 2005 |
Falke S, Tama F, Brooks CL, Gogol EP, Fisher MT. The 13 angstroms structure of a chaperonin GroEL-protein substrate complex by cryo-electron microscopy. Journal of Molecular Biology. 348: 219-30. PMID 15808865 DOI: 10.1016/J.Jmb.2005.02.027 |
0.654 |
|
| 2005 |
Guvench O, Brooks CL. Tryptophan side chain electrostatic interactions determine edge-to-face vs parallel-displaced tryptophan side chain geometries in the designed beta-hairpin "trpzip2". Journal of the American Chemical Society. 127: 4668-74. PMID 15796532 DOI: 10.1021/Ja043492E |
0.682 |
|
| 2005 |
Chen J, Won HS, Im W, Dyson HJ, Brooks CL. Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling. Journal of Biomolecular Nmr. 31: 59-64. PMID 15692739 DOI: 10.1007/S10858-004-6056-Z |
0.586 |
|
| 2005 |
Tama F, Feig M, Liu J, Brooks CL, Taylor KA. The requirement for mechanical coupling between head and S2 domains in smooth muscle myosin ATPase regulation and its implications for dimeric motor function. Journal of Molecular Biology. 345: 837-54. PMID 15588830 DOI: 10.1016/J.Jmb.2004.10.084 |
0.758 |
|
| 2005 |
Guvench O, Price DJ, Brooks CL. Receptor rigidity and ligand mobility in trypsin-ligand complexes. Proteins. 58: 407-17. PMID 15578663 DOI: 10.1002/Prot.20326 |
0.7 |
|
| 2005 |
Tama F, Brooks CL. Diversity and identity of mechanical properties of icosahedral viral capsids studied with elastic network normal mode analysis. Journal of Molecular Biology. 345: 299-314. PMID 15571723 DOI: 10.1016/J.Jmb.2004.10.054 |
0.627 |
|
| 2005 |
Thorpe IF, Brooks CL. The coupling of structural fluctuations to hydride transfer in dihydrofolate reductase. Proteins. 57: 444-57. PMID 15382243 DOI: 10.1002/Prot.20219 |
0.342 |
|
| 2005 |
Skolnick J, Kolinski A, Brooks CL, Godzik A, Rey A. A method for predicting protein structure from sequence. Current Biology : Cb. 3: 414-23. PMID 15335708 DOI: 10.1016/0960-9822(93)90348-R |
0.393 |
|
| 2005 |
Taufer M, Crowley M, Price DJ, Chien AA, Brooks CL. Study of a highly accurate and fast protein-ligand docking method based on molecular dynamics Concurrency Computation Practice and Experience. 17: 1627-1641. DOI: 10.1002/Cpe.949 |
0.406 |
|
| 2004 |
Chen J, Im W, Brooks CL. Refinement of NMR structures using implicit solvent and advanced sampling techniques. Journal of the American Chemical Society. 126: 16038-47. PMID 15584737 DOI: 10.1021/Ja047624F |
0.581 |
|
| 2004 |
Price DJ, Brooks CL. A modified TIP3P water potential for simulation with Ewald summation. The Journal of Chemical Physics. 121: 10096-103. PMID 15549884 DOI: 10.1063/1.1808117 |
0.384 |
|
| 2004 |
Tama F, Miyashita O, Brooks CL. Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM. Journal of Structural Biology. 147: 315-26. PMID 15450300 DOI: 10.1016/J.Jsb.2004.03.002 |
0.63 |
|
| 2004 |
Dominy BN, Minoux H, Brooks CL. An electrostatic basis for the stability of thermophilic proteins. Proteins. 57: 128-41. PMID 15326599 DOI: 10.1002/Prot.20190 |
0.729 |
|
| 2004 |
Lee MS, Salsbury FR, Brooks CL. Constant-pH molecular dynamics using continuous titration coordinates. Proteins. 56: 738-52. PMID 15281127 DOI: 10.1002/Prot.20128 |
0.688 |
|
| 2004 |
Trylska J, Konecny R, Tama F, Brooks CL, McCammon JA. Ribosome motions modulate electrostatic properties. Biopolymers. 74: 423-31. PMID 15274086 DOI: 10.1002/Bip.20093 |
0.676 |
|
| 2004 |
Feig M, Im W, Brooks CL. Implicit solvation based on generalized Born theory in different dielectric environments. The Journal of Chemical Physics. 120: 903-11. PMID 15267926 DOI: 10.1063/1.1631258 |
0.676 |
|
| 2004 |
Patel S, Mackerell AD, Brooks CL. CHARMM fluctuating charge force field for proteins: II protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model. Journal of Computational Chemistry. 25: 1504-14. PMID 15224394 DOI: 10.1002/Jcc.20077 |
0.612 |
|
| 2004 |
Chen J, Brooks CL, Wright PE. Model-free analysis of protein dynamics: assessment of accuracy and model selection protocols based on molecular dynamics simulation. Journal of Biomolecular Nmr. 29: 243-57. PMID 15213423 DOI: 10.1023/B:Jnmr.0000032504.70912.58 |
0.554 |
|
| 2004 |
Stoycheva AD, Brooks CL, Onuchic JN. Gatekeepers in the ribosomal protein s6: thermodynamics, kinetics, and folding pathways revealed by a minimalist protein model. Journal of Molecular Biology. 340: 571-85. PMID 15210355 DOI: 10.1016/J.Jmb.2004.04.073 |
0.578 |
|
| 2004 |
Mackerell AD, Feig M, Brooks CL. Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. Journal of Computational Chemistry. 25: 1400-15. PMID 15185334 DOI: 10.1002/Jcc.20065 |
0.771 |
|
| 2004 |
Ferrara P, Gohlke H, Price DJ, Klebe G, Brooks CL. Assessing scoring functions for protein-ligand interactions. Journal of Medicinal Chemistry. 47: 3032-47. PMID 15163185 DOI: 10.1021/Jm030489H |
0.35 |
|
| 2004 |
Feig M, Karanicolas J, Brooks CL. MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology. Journal of Molecular Graphics & Modelling. 22: 377-95. PMID 15099834 DOI: 10.1016/J.Jmgm.2003.12.005 |
0.796 |
|
| 2004 |
Feig M, Brooks CL. Recent advances in the development and application of implicit solvent models in biomolecule simulations. Current Opinion in Structural Biology. 14: 217-24. PMID 15093837 DOI: 10.1016/J.Sbi.2004.03.009 |
0.723 |
|
| 2004 |
Bursulaya BD, Totrov M, Abagyan R, Brooks CL. Comparative study of several algorithms for flexible ligand docking. Journal of Computer-Aided Molecular Design. 17: 755-63. PMID 15072435 DOI: 10.1023/B:Jcam.0000017496.76572.6F |
0.317 |
|
| 2004 |
Guvench O, Brooks CL. Efficient approximate all-atom solvent accessible surface area method parameterized for folded and denatured protein conformations. Journal of Computational Chemistry. 25: 1005-14. PMID 15067676 DOI: 10.1002/Jcc.20026 |
0.716 |
|
| 2004 |
Tama F, Miyashita O, Brooks CL. Flexible multi-scale fitting of atomic structures into low-resolution electron density maps with elastic network normal mode analysis. Journal of Molecular Biology. 337: 985-99. PMID 15033365 DOI: 10.1016/J.Jmb.2004.01.048 |
0.634 |
|
| 2004 |
Im W, Brooks CL. De novo folding of membrane proteins: an exploration of the structure and NMR properties of the fd coat protein. Journal of Molecular Biology. 337: 513-9. PMID 15019773 DOI: 10.1016/J.Jmb.2004.01.045 |
0.43 |
|
| 2004 |
Karanicolas J, Brooks CL. Integrating folding kinetics and protein function: biphasic kinetics and dual binding specificity in a WW domain. Proceedings of the National Academy of Sciences of the United States of America. 101: 3432-7. PMID 14981252 DOI: 10.1073/Pnas.0304825101 |
0.654 |
|
| 2004 |
MacKerell AD, Feig M, Brooks CL. Improved treatment of the protein backbone in empirical force fields. Journal of the American Chemical Society. 126: 698-9. PMID 14733527 DOI: 10.1021/Ja036959E |
0.691 |
|
| 2004 |
Feig M, Onufriev A, Lee MS, Im W, Case DA, Brooks CL. Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures. Journal of Computational Chemistry. 25: 265-84. PMID 14648625 DOI: 10.1002/Jcc.10378 |
0.725 |
|
| 2004 |
Patel S, Brooks CL. CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations. Journal of Computational Chemistry. 25: 1-15. PMID 14634989 DOI: 10.1002/Jcc.10355 |
0.383 |
|
| 2004 |
Karanicolas J, Brooks CL. An evolution of minimalist models for protein folding: From the behavior of protein-like polymers to protein function Drug Discovery Today: Biosilico. 2: 127-133. DOI: 10.1016/S1741-8364(04)02404-7 |
0.659 |
|
| 2003 |
Ohkubo YZ, Brooks CL. Exploring Flory's isolated-pair hypothesis: statistical mechanics of helix-coil transitions in polyalanine and the C-peptide from RNase A. Proceedings of the National Academy of Sciences of the United States of America. 100: 13916-21. PMID 14615586 DOI: 10.1073/Pnas.2334257100 |
0.329 |
|
| 2003 |
Karanicolas J, Brooks CL. Improved Gō-like models demonstrate the robustness of protein folding mechanisms towards non-native interactions. Journal of Molecular Biology. 334: 309-25. PMID 14607121 DOI: 10.1016/J.Jmb.2003.09.047 |
0.674 |
|
| 2003 |
Im W, Feig M, Brooks CL. An implicit membrane generalized born theory for the study of structure, stability, and interactions of membrane proteins. Biophysical Journal. 85: 2900-18. PMID 14581194 DOI: 10.1016/S0006-3495(03)74712-2 |
0.681 |
|
| 2003 |
Karanicolas J, Brooks CL. The importance of explicit chain representation in protein folding models: an examination of Ising-like models. Proteins. 53: 740-7. PMID 14579364 DOI: 10.1002/Prot.10459 |
0.678 |
|
| 2003 |
Im W, Lee MS, Brooks CL. Generalized born model with a simple smoothing function. Journal of Computational Chemistry. 24: 1691-702. PMID 12964188 DOI: 10.1002/Jcc.10321 |
0.377 |
|
| 2003 |
Salsbury FR, Han WG, Noodleman L, Brooks CL. Temperature-dependent behavior of protein-chromophore interactions: a theoretical study of a blue fluorescent antibody. Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry. 4: 848-55. PMID 12961983 DOI: 10.1002/Cphc.200300694 |
0.641 |
|
| 2003 |
Wu G, Robertson DH, Brooks CL, Vieth M. Detailed analysis of grid-based molecular docking: A case study of CDOCKER-A CHARMm-based MD docking algorithm. Journal of Computational Chemistry. 24: 1549-62. PMID 12925999 DOI: 10.1002/Jcc.10306 |
0.414 |
|
| 2003 |
Tama F, Valle M, Frank J, Brooks CL. Dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy. Proceedings of the National Academy of Sciences of the United States of America. 100: 9319-23. PMID 12878726 DOI: 10.1073/Pnas.1632476100 |
0.65 |
|
| 2003 |
Rod TH, Brooks CL. How dihydrofolate reductase facilitates protonation of dihydrofolate. Journal of the American Chemical Society. 125: 8718-9. PMID 12862454 DOI: 10.1021/Ja035272R |
0.362 |
|
| 2003 |
Lee MS, Feig M, Salsbury FR, Brooks CL. New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations. Journal of Computational Chemistry. 24: 1348-56. PMID 12827676 DOI: 10.1002/Jcc.10272 |
0.791 |
|
| 2003 |
Karanicolas J, Brooks CL. The structural basis for biphasic kinetics in the folding of the WW domain from a formin-binding protein: lessons for protein design? Proceedings of the National Academy of Sciences of the United States of America. 100: 3954-9. PMID 12655041 DOI: 10.1073/Pnas.0731771100 |
0.655 |
|
| 2003 |
Brooks CL. Protein and peptide folding explored with molecular simulations. Accounts of Chemical Research. 35: 447-54. PMID 12069630 DOI: 10.1021/Ar0100172 |
0.458 |
|
| 2003 |
Stoycheva AD, Onuchic JN, Brooks CL. Effect of gatekeepers on the early folding kinetics of a model β-barrel protein Journal of Chemical Physics. 119: 5722-5729. DOI: 10.1063/1.1599281 |
0.562 |
|
| 2003 |
Feig M, MacKerell AD, Brooks CL. Force field influence on the observation of π-helical protein structures in molecular dynamics simulations Journal of Physical Chemistry B. 107: 2831-2836. DOI: 10.1021/Jp027293Y |
0.701 |
|
| 2003 |
Brooks C. Theory and simulation The control and timescale of structure and reactivity in biological systems: from peptide folding to cellular networks Current Opinion in Structural Biology. 13: 143-145. DOI: 10.1016/S0959-440X(03)00042-3 |
0.311 |
|
| 2003 |
Lee MS, Feig M, Salsbury FR, Brooks CL. Erratum: New Analytic Approximation to the Standard Molecular Volume Definition and Its Application to Generalized Born Calculations (Journal of Computational Chemistry (2003) 24:11 (1348-1356)) Journal of Computational Chemistry. 24. DOI: 10.1002/Jcc.10367 |
0.759 |
|
| 2002 |
Damodaran KV, Reddy VS, Johnson JE, Brooks CL. A general method to quantify quasi-equivalence in icosahedral viruses Journal of Molecular Biology. 324: 723-737. PMID 12460573 DOI: 10.1016/S0022-2836(02)01138-5 |
0.319 |
|
| 2002 |
Shea JE, Onuchic JN, Brooks CL. Probing the folding free energy landscape of the Src-SH3 protein domain. Proceedings of the National Academy of Sciences of the United States of America. 99: 16064-8. PMID 12446834 DOI: 10.1073/Pnas.242293099 |
0.684 |
|
| 2002 |
Brooks CL. Protein folding: with a little help... Nature. 420: 33-4. PMID 12422201 DOI: 10.1038/420033A |
0.399 |
|
| 2002 |
Karanicolas J, Brooks CL. The origins of asymmetry in the folding transition states of protein L and protein G. Protein Science : a Publication of the Protein Society. 11: 2351-61. PMID 12237457 DOI: 10.1110/Ps.0205402 |
0.662 |
|
| 2002 |
Feig M, Brooks CL. Evaluating CASP4 predictions with physical energy functions. Proteins. 49: 232-45. PMID 12211003 DOI: 10.1002/Prot.10217 |
0.676 |
|
| 2002 |
Tama F, Wriggers W, Brooks CL. Exploring global distortions of biological macromolecules and assemblies from low-resolution structural information and elastic network theory. Journal of Molecular Biology. 321: 297-305. PMID 12144786 DOI: 10.1016/S0022-2836(02)00627-7 |
0.631 |
|
| 2002 |
Price DJ, Brooks CL. Modern protein force fields behave comparably in molecular dynamics simulations. Journal of Computational Chemistry. 23: 1045-57. PMID 12116391 DOI: 10.1002/Jcc.10083 |
0.388 |
|
| 2002 |
Fiser A, Feig M, Brooks CL, Sali A. Evolution and physics in comparative protein structure modeling. Accounts of Chemical Research. 35: 413-21. PMID 12069626 DOI: 10.1021/Ar010061H |
0.743 |
|
| 2002 |
Tama F, Brooks CL. The mechanism and pathway of pH induced swelling in cowpea chlorotic mottle virus. Journal of Molecular Biology. 318: 733-47. PMID 12054819 DOI: 10.1016/S0022-2836(02)00135-3 |
0.646 |
|
| 2002 |
Dominy BN, Perl D, Schmid FX, Brooks CL. The effects of ionic strength on protein stability: the cold shock protein family. Journal of Molecular Biology. 319: 541-54. PMID 12051927 DOI: 10.1016/S0022-2836(02)00259-0 |
0.726 |
|
| 2002 |
Dominy BN, Brooks CL. Identifying native-like protein structures using physics-based potentials. Journal of Computational Chemistry. 23: 147-60. PMID 11913380 DOI: 10.1002/Jcc.10018 |
0.759 |
|
| 2002 |
Brooks CL. Viewing protein folding from many perspectives. Proceedings of the National Academy of Sciences of the United States of America. 99: 1099-100. PMID 11830648 DOI: 10.1073/Pnas.042708199 |
0.376 |
|
| 2002 |
Lee MS, Salsbury FR, Brooks CL. Novel generalized Born methods Journal of Chemical Physics. 116: 10606-10614. DOI: 10.1063/1.1480013 |
0.665 |
|
| 2001 |
Reddy VS, Natarajan P, Okerberg B, Li K, Damodaran KV, Morton RT, Brooks CL, Johnson JE. Virus Particle Explorer (VIPER), a website for virus capsid structures and their computational analyses. Journal of Virology. 75: 11943-7. PMID 11711584 DOI: 10.1128/Jvi.75.24.11943-11947.2001 |
0.311 |
|
| 2001 |
Roche O, Kiyama R, Brooks CL. Ligand-protein database: linking protein-ligand complex structures to binding data. Journal of Medicinal Chemistry. 44: 3592-8. PMID 11606123 DOI: 10.1021/Jm000467K |
0.329 |
|
| 2001 |
Salsbury FR, Crowley MF, Brooks CL. Modeling of the metallo-beta-lactamase from B. fragilis: structural and dynamic effects of inhibitor binding. Proteins. 44: 448-59. PMID 11484222 DOI: 10.1002/Prot.1110 |
0.676 |
|
| 2001 |
Brooks CL, Onuchic JN, Wales DJ. Statistical thermodynamics: Taking a walk on a landscape Science. 293: 612-613. PMID 11474087 DOI: 10.1126/Science.1062559 |
0.486 |
|
| 2001 |
Shea JE, Brooks CL. From folding theories to folding proteins: A review and assessment of simulation studies of protein folding and unfolding Annual Review of Physical Chemistry. 52: 499-535. PMID 11326073 DOI: 10.1146/Annurev.Physchem.52.1.499 |
0.613 |
|
| 2001 |
Damodaran KV, Banba aS, Brooks CL. Application of Multiple Topology λ-Dynamics to a Host−Guest System: β-Cyclodextrin with Substituted Benzenes Journal of Physical Chemistry B. 105: 9316-9322. DOI: 10.1021/Jp010361G |
0.37 |
|
| 2000 |
Feig M, Rotkiewicz P, Kolinski A, Skolnick J, Brooks CL. Accurate reconstruction of all-atom protein representations from side-chain-based low-resolution models. Proteins. 41: 86-97. PMID 10944396 DOI: 10.1002/1097-0134(20001001)41:1<86::Aid-Prot110>3.0.Co;2-Y |
0.68 |
|
| 2000 |
Guo Z, Brooks CL. Thermodynamics of protein folding: a statistical mechanical study of a small all-beta protein. Biopolymers. 42: 745-57. PMID 10904547 DOI: 10.1002/(Sici)1097-0282(199712)42:7<745::Aid-Bip1>3.0.Co;2-T |
0.386 |
|
| 2000 |
Shea JE, Onuchic JN, Brooks CL. Energetic frustration and the nature of the transition state in protein folding Journal of Chemical Physics. 113: 7663-7671. DOI: 10.1063/1.1313792 |
0.648 |
|
| 2000 |
Banba S, Brooks CL. Free energy screening of small ligands binding to an artificial protein cavity Journal of Chemical Physics. 113: 3423-3433. DOI: 10.1063/1.1287147 |
0.376 |
|
| 2000 |
and BDB, Brooks CL. Comparative Study of the Folding Free Energy Landscape of a Three-Stranded β-Sheet Protein with Explicit and Implicit Solvent Models Journal of Physical Chemistry B. 104: 12378-12383. DOI: 10.1021/Jp0027602 |
0.422 |
|
| 2000 |
Vaart Avd, Bursulaya BD, Brooks CL, Merz KM. Are Many-Body Effects Important in Protein Folding? Journal of Physical Chemistry B. 104: 9554-9563. DOI: 10.1021/Jp001193F |
0.324 |
|
| 1999 |
Shea JE, Onuchic JN, Brooks CL. Exploring the origins of topological frustration: Design of a minimally frustrated model of fragment B of protein A Proceedings of the National Academy of Sciences of the United States of America. 96: 12512-12517. PMID 10535953 DOI: 10.1073/Pnas.96.22.12512 |
0.668 |
|
| 1999 |
Dominy BN, Brooks CL. Methodology for protein-ligand binding studies: application to a model for drug resistance, the HIV/FIV protease system. Proteins. 36: 318-31. PMID 10409825 DOI: 10.1002/(Sici)1097-0134(19990815)36:3<318::Aid-Prot6>3.0.Co;2-K |
0.722 |
|
| 1999 |
Mohanty D, Dominy BN, Kolinski A, Brooks CL, Skolnick J. Correlation between knowledge-based and detailed atomic potentials: Application to the unfolding of the GCN4 leucine zipper Proteins: Structure, Function and Genetics. 35: 447-452. PMID 10382672 DOI: 10.1002/(Sici)1097-0134(19990601)35:4<447::Aid-Prot8>3.0.Co;2-O |
0.76 |
|
| 1999 |
Dominy BN, Brooks CL. Development of a Generalized Born Model Parametrization for Proteins and Nucleic Acids Journal of Physical Chemistry B. 103: 3765-3773. DOI: 10.1021/Jp984440C |
0.743 |
|
| 1999 |
Bursulaya BD, Brooks CL. Folding Free Energy Surface of a Three-Stranded β-Sheet Protein Journal of the American Chemical Society. 121: 9947-9951. DOI: 10.1021/Ja991764L |
0.434 |
|
| 1998 |
Vieth M, Hirst JD, Brooks CL. Do active site conformations of small ligands correspond to low free-energy solution structures? Journal of Computer-Aided Molecular Design. 12: 563-72. PMID 9879504 DOI: 10.1023/A:1008055202136 |
0.365 |
|
| 1998 |
Brooks CL, Gruebele M, Onuchic JN, Wolynes PG. Chemical physics of protein folding. Proceedings of the National Academy of Sciences of the United States of America. 95: 11037-8. PMID 9736683 DOI: 10.1073/pnas.95.19.11037 |
0.448 |
|
| 1998 |
Brooks CL. Simulations of protein folding and unfolding. Current Opinion in Structural Biology. 8: 222-6. PMID 9631297 DOI: 10.1016/S0959-440X(98)80043-2 |
0.412 |
|
| 1998 |
Sheinerman FB, Brooks CL. Calculations on folding of segment B1 of streptococcal protein G. Journal of Molecular Biology. 278: 439-56. PMID 9571063 DOI: 10.1006/Jmbi.1998.1688 |
0.42 |
|
| 1998 |
Sheinerman FB, Brooks CL. Molecular picture of folding of a small alpha/beta protein. Proceedings of the National Academy of Sciences of the United States of America. 95: 1562-7. PMID 9465055 DOI: 10.1073/Pnas.95.4.1562 |
0.414 |
|
| 1998 |
Reddy VS, Giesing HA, Morton RT, Kumar A, Post CB, Brooks CL, Johnson JE. Energetics of quasiequivalence: computational analysis of protein-protein interactions in icosahedral viruses. Biophysical Journal. 74: 546-58. PMID 9449355 DOI: 10.1016/S0006-3495(98)77813-0 |
0.389 |
|
| 1998 |
Shea JE, Nochomovitz YD, Guo Z, Brooks CL. Exploring the space of protein folding Hamiltonians: The balance of forces in a minimalist β-barrel model Journal of Chemical Physics. 109: 2895-2903. DOI: 10.1063/1.476842 |
0.59 |
|
| 1998 |
Vieth M, Hirst JD, Dominy BN, Daigler H, Brooks CL. Assessing search strategies for flexible docking Journal of Computational Chemistry. 19: 1623-1631. DOI: 10.1002/(Sici)1096-987X(19981115)19:14<1623::Aid-Jcc8>3.0.Co;2-L |
0.706 |
|
| 1998 |
Vieth M, Hirst JD, Kolinski A, Brooks CL. Assessing energy functions for flexible docking Journal of Computational Chemistry. 19: 1612-1622. DOI: 10.1002/(Sici)1096-987X(19981115)19:14<1612::Aid-Jcc7>3.0.Co;2-M |
0.351 |
|
| 1997 |
Sheinerman FB, Brooks CL. A molecular dynamics simulation study of segment B1 of protein G. Proteins. 29: 193-202. PMID 9329084 DOI: 10.1002/(Sici)1097-0134(199710)29:2<193::Aid-Prot7>3.0.Co;2-E |
0.411 |
|
| 1997 |
Guo Z, Brooks CL, Boczko EM. Exploring the folding free energy surface of a three-helix bundle protein Proceedings of the National Academy of Sciences of the United States of America. 94: 10161-10166. PMID 9294180 DOI: 10.1073/Pnas.94.19.10161 |
0.398 |
|
| 1997 |
Shirley WA, Brooks CL. Curious structure in "canonical" alanine-based peptides. Proteins. 28: 59-71. PMID 9144791 DOI: 10.1002/(Sici)1097-0134(199705)28:1<59::Aid-Prot6>3.0.Co;2-E |
0.333 |
|
| 1997 |
Young WS, Brooks CL. A reexamination of the hydrophobic effect: Exploring the role of the solvent model in computing the methane–methane potential of mean force Journal of Chemical Physics. 106: 9265-9269. DOI: 10.1063/1.474027 |
0.34 |
|
| 1996 |
Hirst JD, Vieth M, Skolnick J, Brooks CL. Predicting leucine zipper structures from sequence. Protein Engineering. 9: 657-62. PMID 8875642 DOI: 10.1093/Protein/9.8.657 |
0.323 |
|
| 1996 |
Young WS, Brooks CL. A microscopic view of helix propagation: N and C-terminal helix growth in alanine helices. Journal of Molecular Biology. 259: 560-72. PMID 8676388 DOI: 10.1006/Jmbi.1996.0339 |
0.379 |
|
| 1996 |
Kong X, Brooks CL. λ‐dynamics: A new approach to free energy calculations Journal of Chemical Physics. 105: 2414-2423. DOI: 10.1063/1.472109 |
0.371 |
|
| 1996 |
Ösapay K, Young WS, Bashford D, Brooks CL, Case DA. Dielectric Continuum Models for Hydration Effects on Peptide Conformational Transitions The Journal of Physical Chemistry. 100: 2698-2705. DOI: 10.1021/Jp9527315 |
0.384 |
|
| 1996 |
Brooks CL. Helix−Coil Kinetics: Folding Time Scales for Helical Peptides from a Sequential Kinetic Model The Journal of Physical Chemistry. 100: 2546-2549. DOI: 10.1021/Jp952674F |
0.309 |
|
| 1996 |
Simonson aT, Brooks CL. Charge Screening And The Dielectric Constant Of Proteins : Insights From Molecular Dynamics Journal of the American Chemical Society. 118: 8452-8458. DOI: 10.1021/Ja960884F |
0.366 |
|
| 1995 |
Hirst JD, Brooks CL. Molecular dynamics simulations of isolated helices of myoglobin. Biochemistry. 34: 7614-21. PMID 7779807 DOI: 10.1021/Bi00023A007 |
0.384 |
|
| 1995 |
Vieth M, Kolinski A, Brooks CL, Skolnick J. Prediction of quaternary structure of coiled coils. Application to mutants of the GCN4 leucine zipper. Journal of Molecular Biology. 251: 448-67. PMID 7650742 DOI: 10.1006/Jmbi.1995.0447 |
0.378 |
|
| 1995 |
Brooks CL. Methodological advances in molecular dynamics simulations of biological systems. Current Opinion in Structural Biology. 5: 211-5. PMID 7648323 DOI: 10.1016/0959-440X(95)80078-6 |
0.393 |
|
| 1995 |
Boczko EM, Brooks CL. First-principles calculation of the folding free energy of a three-helix bundle protein Science. 269: 393-396. PMID 7618103 DOI: 10.1126/Science.7618103 |
0.433 |
|
| 1995 |
Young WS, Brooks CL. Dynamic load balancing algorithms for replicated data molecular dynamics Journal of Computational Chemistry. 16: 715-722. DOI: 10.1002/Jcc.540160607 |
0.319 |
|
| 1994 |
Vieth M, Kolinski A, Brooks CL, Skolnick J. Prediction of the folding pathways and structure of the GCN4 leucine zipper. Journal of Molecular Biology. 237: 361-7. PMID 8151697 DOI: 10.1006/Jmbi.1994.1239 |
0.399 |
|
| 1994 |
Hirst JD, Brooks CL. Helicity, circular dichroism and molecular dynamics of proteins. Journal of Molecular Biology. 243: 173-8. PMID 7932747 DOI: 10.1006/Jmbi.1994.1644 |
0.364 |
|
| 1994 |
Young WS, Brooks CL. Implementation of a data parallel, logical domain decomposition method for interparticle interactions in molecular dynamics of structured molecular fluids Journal of Computational Chemistry. 15: 44-53. DOI: 10.1002/Jcc.540150106 |
0.375 |
|
| 1993 |
Karpen ME, Tobias DJ, Brooks CL. Statistical clustering techniques for the analysis of long molecular dynamics trajectories: analysis of 2.2-ns trajectories of YPGDV. Biochemistry. 32: 412-20. PMID 8422350 DOI: 10.1021/Bi00053A005 |
0.619 |
|
| 1993 |
Boczko EM, Brooks CL. Constant-temperature free energy surfaces for physical and chemical processes The Journal of Physical Chemistry. 97: 4509-4513. DOI: 10.1021/J100119A043 |
0.358 |
|
| 1993 |
Brooks C, Case DA. Simulations of peptide conformational dynamics and thermodynamics Chemical Reviews. 93: 2487-2502. DOI: 10.1021/Cr00023A008 |
0.346 |
|
| 1993 |
Brooks CL. Molecular simulations of peptide and protein unfolding: in quest of a molten globule Current Opinion in Structural Biology. 3: 92-98. DOI: 10.1016/0959-440X(93)90207-2 |
0.433 |
|
| 1992 |
Tobias DJ, Sneddon SF, Brooks CL. Stability of a model beta-sheet in water. Journal of Molecular Biology. 227: 1244-52. PMID 1433296 DOI: 10.1016/0022-2836(92)90534-Q |
0.569 |
|
| 1992 |
Brooks CL. Characterization of "native" apomyoglobin by molecular dynamics simulation. Journal of Molecular Biology. 227: 375-380. PMID 1404358 DOI: 10.1016/0022-2836(92)90893-O |
0.371 |
|
| 1992 |
McDonald JJ, Brooks CL. A theoretical approach to drug design. 3. Relative thermodynamics of inhibitor binding by E. coli dihydrofolate reductase to ethyl derivatives of trimethoprim substituted at the 3', 4', and 5' positions Journal of the American Chemical Society. 114: 2062-2072. DOI: 10.1021/Ja00032A020 |
0.311 |
|
| 1992 |
Tobias DJ, Brooks CL. Conformational equilibrium in the alanine dipeptide in the gas phase and aqueous solution: a comparison of theoretical results The Journal of Physical Chemistry. 96: 3864-3870. DOI: 10.1021/J100188A054 |
0.584 |
|
| 1991 |
Constantine KL, De Marco A, Madrid M, Brooks CL, Llinás M. The solution conformations of ferrichrome and deferriferrichrome determined by 1H-NMR spectroscopy and computational modeling. Biopolymers. 30: 239-56. PMID 2279065 DOI: 10.1002/Bip.360300303 |
0.388 |
|
| 1991 |
Tobias DJ, Brooks CL. Thermodynamics and mechanism of alpha helix initiation in alanine and valine peptides. Biochemistry. 30: 6059-70. PMID 2043644 DOI: 10.1021/Bi00238A033 |
0.587 |
|
| 1991 |
Tobias DJ, Mertz JE, Brooks CL. Nanosecond time scale folding dynamics of a pentapeptide in water. Biochemistry. 30: 6054-8. PMID 2043643 DOI: 10.1021/Bi00238A032 |
0.605 |
|
| 1991 |
Head-Gordon T, Brooks CL. Virtual rigid body dynamics. Biopolymers. 31: 77-100. PMID 2025686 DOI: 10.1002/Bip.360310108 |
0.6 |
|
| 1991 |
Brooks CL, Young WS, Tobias DJ. Molecular Simulations On Supercomputers The International Journal of Supercomputing Applications. 5: 98-112. DOI: 10.1177/109434209100500409 |
0.499 |
|
| 1991 |
Lazaridis T, Tobias DJ, Brooks CL, Paulaitis ME. Reaction paths and free energy profiles for conformational transitions: An internal coordinate approach The Journal of Chemical Physics. 95: 7612-7625. DOI: 10.1063/1.461335 |
0.717 |
|
| 1991 |
Head-Gordon T, Head-Gordon M, Frisch MJ, Brooks CL, Pople JA. Theoretical study of blocked glycine and alanine peptide analogs Journal of the American Chemical Society. 113: 5989-5997. DOI: 10.1021/Ja00016A010 |
0.495 |
|
| 1991 |
Mertz JE, Tobias DJ, Brooks CL, Singh UC. Vector and parallel algorithms for the molecular dynamics simulation of macromolecules on shared-memory computers Journal of Computational Chemistry. 12: 1270-1277. DOI: 10.1002/Jcc.540121016 |
0.558 |
|
| 1990 |
Fleischman SH, Brooks CL. Protein-drug interactions: characterization of inhibitor binding in complexes of DHFR with trimethoprim and related derivatives. Proteins. 7: 52-61. PMID 2330368 DOI: 10.1002/Prot.340070106 |
0.396 |
|
| 1990 |
Tobias DJ, Sneddon SF, Brooks CL. Reverse turns in blocked dipeptides are intrinsically unstable in water. Journal of Molecular Biology. 216: 783-96. PMID 2258940 DOI: 10.1016/0022-2836(90)90399-7 |
0.581 |
|
| 1990 |
Tobias DJ, Brooks CL. The thermodynamics of solvophobic effects: A molecular‐dynamics study of n‐butane in carbon tetrachloride and water The Journal of Chemical Physics. 92: 2582-2592. DOI: 10.1063/1.457951 |
0.59 |
|
| 1989 |
Brooks CL, Karplus M. Solvent effects on protein motion and protein effects on solvent motion. Dynamics of the active site region of lysozyme. Journal of Molecular Biology. 208: 159-81. PMID 2769750 DOI: 10.1016/0022-2836(89)90093-4 |
0.527 |
|
| 1989 |
Sneddon SF, Tobias DJ, Brooks CL. Thermodynamics of amide hydrogen bond formation in polar and apolar solvents. Journal of Molecular Biology. 209: 817-20. PMID 2585511 DOI: 10.1016/0022-2836(89)90609-8 |
0.563 |
|
| 1989 |
Head-Gordon T, Brooks CL. Evaluation of simple model descriptions of the diffusional association rate for enzyme-ligand systems The Journal of Physical Chemistry. 93: 490-494. DOI: 10.1021/J100338A094 |
0.486 |
|
| 1989 |
Tobias DJ, Brooks CL, Fleischman SH. Conformational flexibility in free energy simulations Chemical Physics Letters. 156: 256-260. DOI: 10.1016/S0009-2614(89)87130-1 |
0.594 |
|
| 1988 |
Sneddon SF, Morgan RS, Brooks CL. A new classification of the amino acid side chains based on doublet acceptor energy levels. Biophysical Journal. 53: 83-9. PMID 3342271 DOI: 10.1016/S0006-3495(88)83068-6 |
0.308 |
|
| 1988 |
Tobias DJ, Brooks CL. Molecular dynamics with internal coordinate constraints The Journal of Chemical Physics. 89: 5115-5127. DOI: 10.1063/1.455654 |
0.561 |
|
| 1988 |
Brooks CL. Thermodynamic calculations on biological molecules International Journal of Quantum Chemistry. 34: 221-234. DOI: 10.1002/Qua.560340720 |
0.361 |
|
| 1988 |
Sneddon SF, Brooks CL. The influence of geometrical fluctuations on electron tunneling barriers in proteins International Journal of Quantum Chemistry. 34: 23-32. DOI: 10.1002/Qua.560340705 |
0.336 |
|
| 1987 |
Foresman JB, Brooks CL. An abinitio study of hydrated chloride ion complexes: Evidence of polarization effects and nonadditivity Journal of Chemical Physics. 87: 5892-5894. DOI: 10.1063/1.453511 |
0.303 |
|
| 1987 |
Fleischman SH, Brooks CL. Thermodynamics of aqueous solvation: Solution properties of alcohols and alkanes The Journal of Chemical Physics. 87: 3029-3037. DOI: 10.1063/1.453039 |
0.368 |
|
| 1987 |
Brooks CL. The influence of long‐range force truncation on the thermodynamics of aqueous ionic solutions The Journal of Chemical Physics. 86: 5156-5162. DOI: 10.1063/1.452636 |
0.343 |
|
| 1987 |
Head-Gordon T, Brooks CL. The role of electrostatics in the binding of small ligands to enzymes The Journal of Physical Chemistry. 91: 3342-3349. DOI: 10.1021/J100296A047 |
0.503 |
|
| 1987 |
Tobias DJ, Brooks CL. Calculation of free energy surfaces using the methods of thermodynamic perturbation theory Chemical Physics Letters. 142: 472-476. DOI: 10.1016/0009-2614(87)80646-2 |
0.602 |
|
| 1986 |
Brooks CL, Karplus M. Theoretical approaches to solvation of biopolymers. Methods in Enzymology. 127: 369-400. PMID 3736426 DOI: 10.1016/0076-6879(86)27031-7 |
0.53 |
|
| 1986 |
Brooks C, Brunger A, Francl M. Role of active site residues and solvation in RNase A Annals of the New York Academy of Sciences. 295-298. DOI: 10.1111/J.1749-6632.1986.Tb48046.X |
0.503 |
|
| 1986 |
Brooks CL. Thermodynamics of ionic solvation: Monte Carlo simulations of aqueous chloride and bromide ions The Journal of Physical Chemistry. 90: 6680-6684. DOI: 10.1021/J100283A017 |
0.354 |
|
| 1985 |
Brünger AT, Brooks CL, Karplus M. Active site dynamics of ribonuclease. Proceedings of the National Academy of Sciences of the United States of America. 82: 8458-62. PMID 3866234 DOI: 10.1073/Pnas.82.24.8458 |
0.504 |
|
| 1985 |
Brooks CL, Brünger A, Karplus M. Active site dynamics in protein molecules: a stochastic boundary molecular-dynamics approach. Biopolymers. 24: 843-65. PMID 2410050 DOI: 10.1002/Bip.360240509 |
0.529 |
|
| 1985 |
Brooks CL, Pettitt BM, Karplus M. Structural and energetic effects of truncating long ranged interactions in ionic and polar fluids The Journal of Chemical Physics. 83: 5897-5908. DOI: 10.1063/1.449621 |
0.607 |
|
| 1984 |
Brooks CL, Adelman SA. Dynamics of liquid state Chemical reactions: Photolysis of molecular iodine in liquid xenon The Journal of Chemical Physics. 80: 5598-5609. DOI: 10.1063/1.446624 |
0.613 |
|
| 1984 |
Brünger A, Brooks CL, Karplus M. Stochastic boundary conditions for molecular dynamics simulations of ST2 water Chemical Physics Letters. 105: 495-500. DOI: 10.1016/0009-2614(84)80098-6 |
0.626 |
|
| 1983 |
Balk MW, Brooks CL, Adelman SA. Dynamics of liquid state chemical reactions: Photodissociation dynamics and geminate recombination of molecular iodine in liquid solution The Journal of Chemical Physics. 79: 804-815. DOI: 10.1063/1.445830 |
0.642 |
|
| 1983 |
Brooks CL, Balk MW, Adelman SA. Dynamics of liquid state chemical reactions: Vibrational energy relaxation of molecular iodine in liquid solution The Journal of Chemical Physics. 79: 784-803. DOI: 10.1063/1.445829 |
0.633 |
|
| 1983 |
Brooks CL, Karplus M. Deformable stochastic boundaries in molecular dynamics The Journal of Chemical Physics. 79: 6312-6325. DOI: 10.1063/1.445724 |
0.5 |
|
| 1982 |
Brooks CL, Adelman SA. Dynamics of liquid state chemical reactions: Modeling of R-dependent correlation functions The Journal of Chemical Physics. 77: 484-497. DOI: 10.1063/1.443632 |
0.643 |
|
| 1982 |
Brooks CL, Adelman SA. Dynamics of liquid state chemical reactions: R-dependent correlation functions for I.+I. in CCl4 The Journal of Chemical Physics. 76: 1007-1023. DOI: 10.1063/1.443093 |
0.641 |
|
| 1982 |
Adelman SA, Brooks CL. Generalized Langevin models and condensed-phase chemical reaction dynamics Journal of Physical Chemistry. 86: 1511-1524. DOI: 10.1021/J100206A011 |
0.606 |
|
| 1980 |
Brooks CL, Berkowitz M, Adelman SA. Generalized Langevin theory for many‐body problems in chemical dynamics: Gas‐surface collisions, vibrational energy relaxation in solids, and recombination reactions in liquids The Journal of Chemical Physics. 73: 4353-4364. DOI: 10.1063/1.440718 |
0.64 |
|
| 1980 |
Berkowitz M, Brooks CL, Adelman SA. Generalized Langevin theory for many-body problems in chemical dynamics: Modeling of solid and liquid state response functions The Journal of Chemical Physics. 72: 3889-3898. DOI: 10.1063/1.439670 |
0.722 |
|
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