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Charles L. Brooks, III - Publications

University of Michigan, Ann Arbor, Ann Arbor, MI 
computational biophysics

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

Year Citation  Score
2019 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  1
2019 Tweedy SE, Rodríguez Benítez A, Narayan ARH, Zimmerman PM, Brooks CL, Wymore T. Hydroxyl Radical-Coupled Electron-Transfer Mechanism of Flavin-Dependent Hydroxylases. The Journal of Physical Chemistry. B. PMID 31532200 DOI: 10.1021/acs.jpcb.9b08178  0.32
2019 Benítez AR, Tweedy S, Baker Dockrey SA, Lukowski AL, Wymore T, Khare D, Brooks CL, Palfey BA, Smith JL, Narayan ARH. Structural basis for selectivity in flavin-dependent monooxygenase-catalyzed oxidative dearomatization. Acs Catalysis. 9: 3633-3640. PMID 31346489 DOI: 10.1021/acscatal.8b04575  0.32
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  1
2019 Dockrey SAB, Suh CE, Benítez AR, Wymore T, Brooks CL, Narayan ARH. Positioning-Group-Enabled Biocatalytic Oxidative Dearomatization. Acs Central Science. 5: 1010-1016. PMID 31263760 DOI: 10.1021/acscentsci.9b00163  0.32
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  0.68
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  0.56
2018 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 JCA. Reply to 'Misreading chaperone-substrate complexes from random noise'. Nature Structural & Molecular Biology. PMID 30297780 DOI: 10.1038/s41594-018-0145-2  0.84
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  0.48
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  0.64
2018 Xiao M, Wei S, Li Y, Jasensky J, Chen J, Brooks CL, Chen Z. Molecular interactions between single layered MoS and biological molecules. Chemical Science. 9: 1769-1773. PMID 29675220 DOI: 10.1039/c7sc04884j  0.68
2017 Li Y, Ogorzalek TL, Wei S, Zhang X, Yang P, Jasensky J, Brooks CL, Marsh ENG, Chen Z. Effect of immobilization site on the orientation and activity of surface-tethered enzymes. Physical Chemistry Chemical Physics : Pccp. PMID 29235592 DOI: 10.1039/c7cp06063g  0.68
2017 Daher M, Mustoe AM, Morriss-Andrews A, Brooks Iii CL, Walter NG. Tuning RNA folding and function through rational design of junction topology. Nucleic Acids Research. 45: 9706-9715. PMID 28934478 DOI: 10.1093/nar/gkx614  0.84
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  0.88
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  1
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  0.84
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  0.6
2016 Bruno PA, Morriss-Andrews A, Henderson AR, Brooks CL, Mapp AK. A Synthetic Loop Replacement Peptide That Blocks Canonical NF-κB Signaling. Angewandte Chemie (International Ed. in English). PMID 27791341 DOI: 10.1002/anie.201607990  0.4
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  0.6
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  0.84
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  1
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  0.84
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  1
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  0.4
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  0.64
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  0.84
2015 Wijeyesakere SJ, Gagnon JK, Arora K, Brooks CL, Raghavan M. Regulation of calreticulin-major histocompatibility complex (MHC) class I interactions by ATP. Proceedings of the National Academy of Sciences of the United States of America. 112: E5608-17. PMID 26420867 DOI: 10.1073/pnas.1510132112  0.76
2015 Gunasekara SM, Hicks MN, Park J, Brooks CL, Serate J, Saunders CV, Grover SK, Goto JJ, Lee JW, Youn H. Directed Evolution of the Escherichia coli cAMP Receptor Protein at the cAMP Pocket. The Journal of Biological Chemistry. PMID 26378231 DOI: 10.1074/jbc.M115.678474  0.44
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  0.84
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  1
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  0.68
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  0.64
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  1
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  0.84
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  0.64
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  0.6
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  1
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  1
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  0.84
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  1
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  0.36
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  1
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  0.84
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  0.6
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  1
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  1
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  0.64
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  0.84
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  0.36
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  0.84
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  0.36
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  0.84
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  0.6
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  0.32
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  0.64
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.jsb.2013.12.008  1
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  0.32
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  0.84
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  0.6
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  0.84
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  0.64
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  0.64
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  0.84
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  0.56
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  0.32
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  1
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  0.6
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  0.76
2012 Wymore T, Brooks CL. From Molecular Phylogenetics to Quantum Chemistry: Discovering Enzyme Design Principles through Computation. Computational and Structural Biotechnology Journal. 2: e201209018. PMID 24688659 DOI: 10.5936/csbj.201209018  0.32
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  0.32
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  0.52
2012 Majmudar CY, Højfeldt JW, Arevang CJ, Pomerantz WC, Gagnon JK, Schultz PJ, Cesa LC, Doss CH, Rowe SP, Vásquez V, Tamayo-Castillo G, Cierpicki T, Brooks CL, Sherman DH, Mapp AK. Sekikaic acid and lobaric acid target a dynamic interface of the coactivator CBP/p300. Angewandte Chemie (International Ed. in English). 51: 11258-62. PMID 23042634 DOI: 10.1002/anie.201206815  0.76
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  0.64
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  0.56
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  0.56
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  0.84
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  0.84
2011 Wymore T, Chen BY, Nicholas HB, Ropelewski AJ, Brooks CL. A Mechanism for Evolving Novel Plant Sesquiterpene Synthase Function. Molecular Informatics. 30: 896-906. PMID 27468109 DOI: 10.1002/minf.201100087  0.32
2011 Goh GB, García-Moreno E B, Brooks CL. The high dielectric constant of staphylococcal nuclease is encoded in its structural architecture. Journal of the American Chemical Society. 133: 20072-5. PMID 22085022 DOI: 10.1021/ja2084866  0.64
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  0.56
2011 Bailor MH, Mustoe AM, Brooks CL, Al-Hashimi HM. 3D maps of RNA interhelical junctions. Nature Protocols. 6: 1536-45. PMID 21959236 DOI: 10.1038/nprot.2011.385  0.84
2011 Liu W, Brooks CL. Functional impact of manipulation on the relative orientation of human prolactin receptor domains. Biochemistry. 50: 5333-44. PMID 21591677 DOI: 10.1021/bi101931u  0.44
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/  0.84
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  0.56
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  0.6
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  1
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  0.88
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  1
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  0.72
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  0.6
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  0.6
2005 Trylska J, McCammon JA, Brooks Iii CL. Exploring assembly energetics of the 30S ribosomal subunit using an implicit solvent approach. Journal of the American Chemical Society. 127: 11125-33. PMID 16076220 DOI: 10.1021/ja052639e  0.52
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  1
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  1
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  1
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  1
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  0.92
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  1
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  1
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  1
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/  1
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  1
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  1
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  1
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  1
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  0.92
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  1
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  0.92
2002 Feig M, Brooks CL. Evaluating CASP4 predictions with physical energy functions. Proteins. 49: 232-45. PMID 12211003 DOI: 10.1002/prot.10217  1
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  1
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  1
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  1
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  0.92
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  0.92
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  1
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  0.92
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  1
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  1
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  0.96
1992 Tobias DJ, Sneddon SF, Brooks CL. Stability of a model beta-sheet in water. Journal of Molecular Biology. 227: 1244-52. PMID 1433296  0.96
1991 Tobias DJ, Brooks CL. Thermodynamics and mechanism of alpha helix initiation in alanine and valine peptides. Biochemistry. 30: 6059-70. PMID 2043644  0.96
1991 Tobias DJ, Mertz JE, Brooks CL. Nanosecond time scale folding dynamics of a pentapeptide in water. Biochemistry. 30: 6054-8. PMID 2043643  0.96
1991 Head-Gordon T, Brooks CL. Virtual rigid body dynamics. Biopolymers. 31: 77-100. PMID 2025686 DOI: 10.1002/bip.360310108  1
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  0.96
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  1
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  0.96
1986 Brooks CL, Karplus M. Theoretical approaches to solvation of biopolymers. Methods in Enzymology. 127: 369-400. PMID 3736426  1
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  1
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  1
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