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1
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Stan G, Brooks BR, Lorimer GH, Thirumalai D.
Identifying natural substrates for chaperonins using a sequence-based approach.
Protein Sci 14(1): 193-201, 2005.
[Text Abstract on PubMed]
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2
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Wu X, Brooks BR.
Isotropic periodic sum: a method for the calculation of long-range interactions.
J Chem Phys 122(4): 44107, 2005.
[Text Abstract on PubMed]
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3
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Zheng W, Brooks BR, Doniach S, Thirumalai D.
Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved.
Structure 13(4): 565-77, 2005.
[Text Abstract on PubMed]
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4
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Zheng W, Brooks BR.
Normal-modes-based prediction of protein conformational changes guided by distance constraints.
Biophys J 88(5): 3109-17, 2005.
[Text Abstract on PubMed]
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5
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Chu JW, Brooks BR, Trout BL.
Oxidation of methionine residues in aqueous solutions: free methionine and methionine in granulocyte colony-stimulating factor.
J Am Chem Soc 126(50): 16601-7, 2004.
[Text Abstract on PubMed]
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6
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Chu JW, Yin J, Brooks BR, Wang DI, Ricci MS, Brems DN, Trout BL.
A comprehensive picture of non-site specific oxidation of methionine residues by peroxides in protein pharmaceuticals.
J Pharm Sci 93(12): 3096-102, 2004.
[Text Abstract on PubMed]
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7
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Wu X, Brooks BR.
Beta-hairpin folding mechanism of a nine-residue peptide revealed from molecular dynamics simulations in explicit water.
Biophys J 86(4): 1946-58, 2004.
[Text Abstract on PubMed]
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8
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Petrella RJ, Andricioaei I, Brooks BR, Karplus M.
An improved method for nonbonded list generation: rapid determination of near-neighbor pairs.
J Comput Chem 24(2): 222-31, 2003.
[Text Abstract on PubMed]
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9
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Stan G, Thirumalai D, Lorimer GH, Brooks BR.
Annealing function of GroEL: structural and bioinformatic analysis.
Biophys Chem 100(1-3): 453-67, 2003.
[Text Abstract on PubMed]
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10
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Wu X, Milne JL, Borgnia MJ, Rostapshov AV, Subramaniam S, Brooks BR.
A core-weighted fitting method for docking atomic structures into low-resolution maps: application to cryo-electron microscopy.
J Struct Biol 141(1): 63-76, 2003.
[Text Abstract on PubMed]
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11
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Dolan EA, Venable RM, Pastor RW, Brooks BR.
Simulations of membranes and other interfacial systems using P2(1) and Pc periodic boundary conditions.
Biophys J 82(5): 2317-25, 2002.
[Text Abstract on PubMed]
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12
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Lipsitz RS, Sharma Y, Brooks BR, Tjandra N.
Hydrogen bonding in high-resolution protein structures: a new method to assess NMR protein geometry.
J Am Chem Soc 124(35): 10621-6, 2002.
[Text Abstract on PubMed]
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13
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Milne JL, Shi D, Rosenthal PB, Sunshine JS, Domingo GJ, Wu X, Brooks BR, Perham RN, Henderson R, Subramaniam S.
Molecular architecture and mechanism of an icosahedral pyruvate dehydrogenase complex: a multifunctional catalytic machine.
EMBO J 21(21): 5587-98, 2002.
[Text Abstract on PubMed]
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14
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Wu X, Wang S, Brooks BR.
Direct observation of the folding and unfolding of a beta-hairpin in explicit water through computer simulation.
J Am Chem Soc 124(19): 5282-3, 2002.
[Text Abstract on PubMed]
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15
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Speelman B, Brooks BR, Post CB.
Molecular dynamics simulations of human rhinovirus and an antiviral compound.
Biophys J 80(1): 121-9, 2001.
[Text Abstract on PubMed]
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16
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Lee YS, Hodoscek M, Brooks BR, Kador PF.
Catalytic mechanism of aldose reductase studied by the combined potentials of quantum mechanics and molecular mechanics.
Biophys Chem 70(3): 203-16, 1998.
[Text Abstract on PubMed]
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17
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Bhattacharyya D, Brooks BR, Callahan L.
Positioning of positively charged residues in the V3 loop correlates with HIV type 1 syncytium-inducing phenotype.
AIDS Res Hum Retroviruses 12(2): 83-90, 1996.
[Text Abstract on PubMed]
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18
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Osawa Y, Darbyshire JF, Steinbach PJ, Brooks BR.
Metabolism-based transformation of myoglobin to an oxidase by BrCCl3 and molecular modeling of the oxidase form.
J Biol Chem 268(4): 2953-9, 1993.
[Text Abstract on PubMed]
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19
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Steinbach PJ, Brooks BR.
Protein hydration elucidated by molecular dynamics simulation.
Proc Natl Acad Sci U S A 90(19): 9135-9, 1993.
[Text Abstract on PubMed]
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20
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Venable RM, Brooks BR, Carson FW.
Theoretical studies of relaxation of a monomeric subunit of HIV-1 protease in water using molecular dynamics.
Proteins 15(4): 374-84, 1993.
[Text Abstract on PubMed]
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21
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Chandrasekhar I, Clore GM, Szabo A, Gronenborn AM, Brooks BR.
A 500 ps molecular dynamics simulation study of interleukin-1 beta in water. Correlation with nuclear magnetic resonance spectroscopy and crystallography.
J Mol Biol 226(1): 239-50, 1992.
[Text Abstract on PubMed]
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22
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Venable RM, Widmalm G, Brooks BR, Egan W, Pastor RW.
Conformational states of a TT mismatch from molecular dynamics simulation of duplex d (CGCGATTCGCG).
Biopolymers 32(7): 783-94, 1992.
[Text Abstract on PubMed]
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23
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Han KH, Syi JL, Brooks BR, Ferretti JA.
Solution conformations of the B-loop fragments of human transforming growth factor alpha and epidermal growth factor by 1H nuclear magnetic resonance and restrained molecular dynamics.
Proc Natl Acad Sci U S A 87(7): 2818-22, 1990.
[Text Abstract on PubMed]
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24
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Loncharich RJ, Brooks BR.
Temperature dependence of dynamics of hydrated myoglobin. Comparison of force field calculations with neutron scattering data.
J Mol Biol 215(3): 439-55, 1990.
[Text Abstract on PubMed]
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25
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Raghunathan G, Seetharamulu P, Brooks BR, Guy HR.
Models of delta-hemolysin membrane channels and crystal structures.
Proteins 8(3): 213-25, 1990.
[Text Abstract on PubMed]
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26
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Weston A, Newman MJ, Mann DL, Brooks BR.
Molecular mechanics and antibody binding in the structural analysis of polycyclic aromatic hydrocarbon-diol-epoxide--DNA adducts.
Carcinogenesis 11(5): 859-64, 1990.
[Text Abstract on PubMed]
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27
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Loncharich RJ, Brooks BR.
The effects of truncating long-range forces on protein dynamics.
Proteins 6(1): 32-45, 1989.
[Text Abstract on PubMed]
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28
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Reid RH, Hooper CA, Brooks BR.
Computer simulations of a tumor surface octapeptide epitope.
Biopolymers 28(1): 525-30, 1989.
[Text Abstract on PubMed]
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29
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Brooks BR, Pastor RW, Carson FW.
Theoretically determined three-dimensional structure for the repeating tetrapeptide unit of the circumsporozoite coat protein of the malaria parasite Plasmodium falciparum.
Proc Natl Acad Sci U S A 84(13): 4470-4, 1987.
[Text Abstract on PubMed]
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30
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Sklenár V, Brooks BR, Zon G, Bax A.
Absorption mode two-dimensional NOE spectroscopy of exchangeable protons in oligonucleotides.
FEBS Lett 216(2): 249-52, 1987.
[Text Abstract on PubMed]
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31
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Smith-Gill SJ, Mainhart C, Lavoie TB, Feldmann RJ, Drohan W, Brooks BR.
A three-dimensional model of an anti-lysozyme antibody.
J Mol Biol 194(4): 713-24, 1987.
[Text Abstract on PubMed]
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32
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Post CB, Brooks BR, Karplus M, Dobson CM, Artymiuk PJ, Cheetham JC, Phillips DC.
Molecular dynamics simulations of native and substrate-bound lysozyme. A study of the average structures and atomic fluctuations.
J Mol Biol 190(3): 455-79, 1986.
[Text Abstract on PubMed]
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33
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Irikura KK, Tidor B, Brooks BR, Karplus M.
Transition from B to Z DNA: contribution of internal fluctuations to the configurational entropy difference.
Science 229(4713): 571-2, 1985.
[Text Abstract on PubMed]
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34
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Tidor B, Irikura KK, Brooks BR, Karplus M.
Dynamics of DNA oligomers.
J Biomol Struct Dyn 1(1): 231-52, 1983.
[Text Abstract on PubMed]
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