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B. Montgomery Pettitt - Publications

Affiliations: 
Pharmacology and Toxicology University of Texas Medical Branch, Galveston, TX 
Area:
Biochemistry, Chemical Physics/Physical Chemistry, Computer Science
Website:
http://www.utmb.edu/phtox/Facultyinfo.asp?intFacID=74

170 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
2022 Workman RJ, Gorle S, Pettitt BM. Effects of Conformational Constraint on Peptide Solubility Limits. The Journal of Physical Chemistry. B. PMID 36450134 DOI: 10.1021/acs.jpcb.2c06458  0.759
2021 Workman RJ, Pettitt BM. Thermodynamic Compensation in Peptides Following Liquid-Liquid Phase Separation. The Journal of Physical Chemistry. B. PMID 34110175 DOI: 10.1021/acs.jpcb.1c02093  0.758
2020 Pettitt BM, Schwartz BJ, Sterpone F, Túri L, Willard AP. Tribute to Peter J. Rossky. The Journal of Physical Chemistry. B. 124: 10591-10593. PMID 33233898 DOI: 10.1021/acs.jpcb.0c09810  0.626
2020 Yu B, Pettitt BM, Iwahara J. Dynamics of Ionic Interactions at Protein-Nucleic Acid Interfaces. Accounts of Chemical Research. PMID 32845610 DOI: 10.1021/Acs.Accounts.0C00212  0.313
2020 Lai CL, Chen C, Ou SC, Prentiss M, Pettitt BM. Interactions between identical DNA double helices. Physical Review. E. 101: 032414. PMID 32289903 DOI: 10.1103/Physreve.101.032414  0.328
2020 Bores C, Pettitt BM. Structure and the role of filling rate on model dsDNA packed in a phage capsid. Physical Review. E. 101: 012406. PMID 32069548 DOI: 10.1103/Physreve.101.012406  0.325
2020 Seckfort D, Lynch GC, Pettitt BM. The lac repressor hinge helix in context: The effect of the DNA binding domain and symmetry. Biochimica Et Biophysica Acta. General Subjects. 129538. PMID 31958546 DOI: 10.1016/J.Bbagen.2020.129538  0.305
2019 Yu B, Pettitt BM, Iwahara J. Experimental Evidence of Solvent-Separated Ion Pairs as Metastable States in Electrostatic Interactions of Biological Macromolecules. The Journal of Physical Chemistry Letters. PMID 31809050 DOI: 10.1021/Acs.Jpclett.9B03084  0.349
2019 Ou SC, Pettitt BM. Correction to "Free Energy Calculations Based on Coupling Proximal Distribution Functions and Thermodynamic Cycles". Journal of Chemical Theory and Computation. PMID 31539243 DOI: 10.1021/Acs.Jctc.9B00927  0.303
2019 Ou S, Pettitt BM. Free Energy Calculations Based on Coupling Proximal Distribution Functions and Thermodynamic Cycles. Journal of Chemical Theory and Computation. PMID 30768893 DOI: 10.1021/Acs.Jctc.8B01157  0.356
2019 Seckfort D, Pettitt BM. Price of disorder in the lac repressor hinge helix Biopolymers. 110. PMID 30485404 DOI: 10.1002/Bip.23239  0.301
2018 Drake JA, Pettitt BM. Thermodynamics of Conformational Transitions in a Disordered Protein Backbone Model. Biophysical Journal. 114: 2799-2810. PMID 29925017 DOI: 10.1016/J.Bpj.2018.04.027  0.349
2017 Asthagiri D, Karandur D, Tomar DS, Pettitt BM. Intramolecular Interactions Overcome Hydration to Drive the Collapse Transition of Gly15. The Journal of Physical Chemistry. B. PMID 28774177 DOI: 10.1021/Acs.Jpcb.7B05469  0.313
2017 Myers CG, Pettitt BM. Phage-like packing structures with mean field sequence dependence. Journal of Computational Chemistry. PMID 28349552 DOI: 10.1002/Jcc.24727  0.316
2016 Ou S, Drake JA, Pettitt BM. Nonpolar Solvation Free Energy from Proximal Distribution Functions. The Journal of Physical Chemistry. B. PMID 27992228 DOI: 10.1021/Acs.Jpcb.6B09528  0.391
2016 Drake JA, Harris RC, Pettitt BM. Solvation Thermodynamics of Oligoglycine with Respect to Chain Length and Flexibility. Biophysical Journal. 111: 756-67. PMID 27558719 DOI: 10.1016/J.Bpj.2016.07.013  0.351
2016 Dyer KM, Perkyns JS, Pettitt BM. Dielectric behavior for saline solutions from renormalized diagrammatically proper interaction site model theory. Journal of Physics. Condensed Matter : An Institute of Physics Journal. 28: 414006. PMID 27546725 DOI: 10.1088/0953-8984/28/41/414006  0.772
2016 Harris RC, Pettitt BM. Reconciling the understanding of 'hydrophobicity' with physics-based models of proteins. Journal of Physics. Condensed Matter : An Institute of Physics Journal. 28: 083003. PMID 26836518 DOI: 10.1088/0953-8984/28/8/083003  0.373
2015 Tomar DS, Weber V, Pettitt BM, Asthagiri D. Importance of Hydrophilic Hydration and Intramolecular Interactions in the Thermodynamics of Helix-Coil Transition and Helix-Helix Assembly in a Deca-Alanine Peptide. The Journal of Physical Chemistry. B. PMID 26649757 DOI: 10.1021/Acs.Jpcb.5B09881  0.317
2015 Chen C, Esadze A, Zandarashvili L, Nguyen D, Pettitt BM, Iwahara J. Dynamic Equilibria of Short-Range Electrostatic Interactions at Molecular Interfaces of Protein-DNA Complexes. The Journal of Physical Chemistry Letters. 6: 2733-2737. PMID 26207171 DOI: 10.1021/Acs.Jpclett.5B01134  0.363
2015 Karandur D, Harris RC, Pettitt BM. Protein collapse driven against solvation free energy without H-bonds. Protein Science : a Publication of the Protein Society. PMID 26174309 DOI: 10.1002/Pro.2749  0.325
2015 Zhang C, Lai CL, Pettitt BM. Computation of virial coefficients from integral equations. The Journal of Chemical Physics. 142: 214110. PMID 26049482 DOI: 10.1063/1.4921790  0.318
2015 Drake JA, Pettitt BM. Force field-dependent solution properties of glycine oligomers. Journal of Computational Chemistry. 36: 1275-85. PMID 25952623 DOI: 10.1002/Jcc.23934  0.351
2015 Wang Q, Myers CG, Pettitt BM. Twist-induced defects of the P-SSP7 genome revealed by modeling the cryo-EM density. The Journal of Physical Chemistry. B. 119: 4937-43. PMID 25793549 DOI: 10.1021/Acs.Jpcb.5B00865  0.308
2015 Dyer KM, Perkyns JS, Pettitt BM. Solubility Limits in Lennard-Jones Mixtures: Effects of Disparate Molecule Geometries. The Journal of Physical Chemistry. B. 119: 9450-9. PMID 25621892 DOI: 10.1021/Jp512992N  0.748
2014 Harris RC, Drake JA, Pettitt BM. Multibody correlations in the hydrophobic solvation of glycine peptides. The Journal of Chemical Physics. 141: 22D525. PMID 25494796 DOI: 10.1063/1.4901886  0.345
2014 Harris RC, Pettitt BM. Effects of geometry and chemistry on hydrophobic solvation. Proceedings of the National Academy of Sciences of the United States of America. 111: 14681-6. PMID 25258413 DOI: 10.1073/Pnas.1406080111  0.35
2014 Karandur D, Wong KY, Pettitt BM. Solubility and aggregation of Gly(5) in water. The Journal of Physical Chemistry. B. 118: 9565-72. PMID 25019618 DOI: 10.1021/Jp503358N  0.356
2014 Tomar DS, Weber V, Pettitt BM, Asthagiri D. Conditional solvation thermodynamics of isoleucine in model peptides and the limitations of the group-transfer model. The Journal of Physical Chemistry. B. 118: 4080-7. PMID 24650057 DOI: 10.1021/Jp500727U  0.351
2014 Truchon JF, Pettitt BM, Labute P. A Cavity Corrected 3D-RISM Functional for Accurate Solvation Free Energies. Journal of Chemical Theory and Computation. 10: 934-941. PMID 24634616 DOI: 10.1021/Ct4009359  0.362
2014 Wang Q, Pettitt BM. Modeling DNA thermodynamics under torsional stress. Biophysical Journal. 106: 1182-93. PMID 24606942 DOI: 10.1016/J.Bpj.2014.01.022  0.33
2014 Karandur D, Wong K, Pettitt BM. Protein Folding and Collapse: Thermodynamics of Aggregation of Gly5 vs Concentration in Solution Biophysical Journal. 106: 483a. DOI: 10.1016/J.Bpj.2013.11.2730  0.352
2013 Dyer KM, Pettitt BM. Proximal distributions from angular correlations: a measure of the onset of coarse-graining. The Journal of Chemical Physics. 139: 214111. PMID 24320368 DOI: 10.1063/1.4832895  0.745
2013 Myers CG, Pettitt BM. Communication: Origin of the contributions to DNA structure in phages. The Journal of Chemical Physics. 138: 071103. PMID 23444988 DOI: 10.1063/1.4791708  0.33
2011 Howard JJ, Pettitt BM. Integral equations in the study of polar and ionic interaction site fluids. Journal of Statistical Physics. 145: 441-466. PMID 22383857 DOI: 10.1007/S10955-011-0260-5  0.356
2011 Chen C, Pettitt BM. The binding process of a nonspecific enzyme with DNA. Biophysical Journal. 101: 1139-47. PMID 21889451 DOI: 10.1016/J.Bpj.2011.07.016  0.336
2011 Ambia-Garrido J, Vainrub A, Pettitt BM. Free energy considerations for nucleic acids with dangling ends near a surface: a coarse grained approach. Journal of Physics: Condensed Matter. 23: 325101-325101. PMID 21743128 DOI: 10.1088/0953-8984/23/32/325101  0.313
2011 Kokubo H, Hu CY, Pettitt BM. Peptide conformational preferences in osmolyte solutions: transfer free energies of decaalanine. Journal of the American Chemical Society. 133: 1849-58. PMID 21250690 DOI: 10.1021/Ja1078128  0.384
2011 Howard JJ, Lynch GC, Pettitt BM. Ion and solvent density distributions around canonical B-DNA from integral equations. The Journal of Physical Chemistry. B. 115: 547-56. PMID 21190358 DOI: 10.1021/Jp107383S  0.402
2011 Lin B, Pettitt BM. Electrostatic solvation free energy of amino acid side chain analogs: implications for the validity of electrostatic linear response in water. Journal of Computational Chemistry. 32: 878-85. PMID 20941733 DOI: 10.1002/Jcc.21668  0.342
2010 Ambia-Garrido J, Vainrub A, Pettitt BM. A model for Structure and Thermodynamics of ssDNA and dsDNA Near a Surface: a Coarse Grained Approach. Computer Physics Communications. 181: 2001-2007. PMID 20957064 DOI: 10.1016/J.Cpc.2010.08.029  0.356
2010 Hu CY, Kokubo H, Lynch GC, Bolen DW, Pettitt BM. Backbone additivity in the transfer model of protein solvation. Protein Science : a Publication of the Protein Society. 19: 1011-22. PMID 20306490 DOI: 10.1002/Pro.378  0.352
2010 Perkyns JS, Lynch GC, Howard JJ, Pettitt BM. Protein solvation from theory and simulation: Exact treatment of Coulomb interactions in three-dimensional theories. The Journal of Chemical Physics. 132: 064106. PMID 20151732 DOI: 10.1063/1.3299277  0.44
2010 Hu CY, Lynch GC, Kokubo H, Pettitt BM. Trimethylamine N-oxide influence on the backbone of proteins: an oligoglycine model. Proteins. 78: 695-704. PMID 19790265 DOI: 10.1002/Prot.22598  0.351
2010 Chen C, Pettitt BM. Free Energy Landscape of Nonspecific Protein-DNA Encounter Biophysical Journal. 98: 75a. DOI: 10.1016/J.Bpj.2009.12.424  0.322
2009 Dyer KM, Perkyns JS, Stell G, Pettitt BM. Site-renormalised molecular fluid theory: on the utility of a two-site model of water. Molecular Physics. 107: 423-431. PMID 19920881 DOI: 10.1080/00268970902845313  0.753
2009 Feng J, Wong KY, Dyer K, Pettitt BM. Transport properties of water at functionalized molecular interfaces. The Journal of Chemical Physics. 131: 125102. PMID 19791920 DOI: 10.1063/1.3224122  0.743
2009 Randall GL, Zechiedrich L, Pettitt BM. In the absence of writhe, DNA relieves torsional stress with localized, sequence-dependent structural failure to preserve B-form. Nucleic Acids Research. 37: 5568-77. PMID 19586933 DOI: 10.1093/Nar/Gkp556  0.3
2009 Feng J, Wong KY, Lynch GC, Gao X, Pettitt BM. Salt effects on surface-tethered peptides in solution. The Journal of Physical Chemistry. B. 113: 9472-8. PMID 19548651 DOI: 10.1021/Jp902537F  0.322
2009 Chen C, Krause K, Pettitt BM. Advantage of being a dimer for Serratia marcescens endonuclease. The Journal of Physical Chemistry. B. 113: 511-21. PMID 19053714 DOI: 10.1021/Jp8057838  0.364
2009 Kokubo H, Hu C, Pettitt BM. 1TP3-07 Peptide conformational preferences in different solutions analyzed by transfer free energy calculations(The 47th Annual Meeting of the Biophysical Society of Japan) Seibutsu Butsuri. 49: S35. DOI: 10.2142/Biophys.49.S35_2  0.309
2009 Pettitt BM, Gadre SR, Matcha RL. Theoretical compton profile anisotropics in molecules and solids. VIII. Vibrational, rotational, and temperature-dependent diatomic alkali halide anisotropics International Journal of Quantum Chemistry. 18: 697-706. DOI: 10.1002/Qua.560180871  0.707
2008 Dyer KM, Perkyns JS, Stell G, Pettitt BM. A molecular site-site integral equation that yields the dielectric constant. The Journal of Chemical Physics. 129: 104512. PMID 19044929 DOI: 10.1063/1.2976580  0.765
2008 Wong KY, Pettitt BM. The pathway of oligomeric DNA melting investigated by molecular dynamics simulations. Biophysical Journal. 95: 5618-26. PMID 18952784 DOI: 10.1529/Biophysj.108.141010  0.328
2007 Dyer K, Perkyns J, Pettitt B, Stell G. An angle dependent site-renormalized theory for the conformations of n-butane in a simple fluid. Condensed Matter Physics / Institute For Condensed Matter Physics of the National Academy of Sciences of Ukraine. 10: 331-342. PMID 20664717 DOI: 10.5488/Cmp.10.3.331  0.76
2007 Dyer KM, Perkyns JS, Pettitt BM. A site-renormalized molecular fluid theory. The Journal of Chemical Physics. 127: 194506. PMID 18035891 DOI: 10.1063/1.2785188  0.757
2007 Kokubo H, Rösgen J, Bolen DW, Pettitt BM. Molecular basis of the apparent near ideality of urea solutions. Biophysical Journal. 93: 3392-407. PMID 17693466 DOI: 10.1529/Biophysj.107.114181  0.365
2007 Kokubo H, Pettitt BM. Preferential solvation in urea solutions at different concentrations: properties from simulation studies. The Journal of Physical Chemistry. B. 111: 5233-42. PMID 17447807 DOI: 10.1021/Jp067659X  0.357
2007 Marucho M, Pettitt BM. Optimized theory for simple and molecular fluids Journal of Chemical Physics. 126. PMID 17411108 DOI: 10.1063/1.2711205  0.374
2007 Weksberg TE, Lynch GC, Krause KL, Pettitt BM. Molecular dynamics simulations of Trichomonas vaginalis ferredoxin show a loop-cap transition. Biophysical Journal. 92: 3337-45. PMID 17325017 DOI: 10.1529/Biophysj.106.088096  0.33
2007 Dyer KM, Pettitt BM, Stell G. Systematic investigation of theories of transport in the Lennard-Jones fluid. The Journal of Chemical Physics. 126: 034502. PMID 17249879 DOI: 10.1063/1.2424714  0.729
2007 Chen C, Beck BW, Krause K, Weksberg TE, Pettitt BM. Effects of dimerization of Serratia marcescens endonuclease on water dynamics. Biopolymers. 85: 241-52. PMID 17133507 DOI: 10.1002/Bip.20641  0.352
2007 Dyer K, Perkyns J, Pettitt B, Steli G. An angle dependent site-renormalized theory for the conformations of n-butane in a simple fluid Condensed Matter Physics. 10: 331-342.  0.727
2006 Chen C, Beck BW, Krause K, Pettitt BM. Solvent participation in Serratia marcescens endonuclease complexes. Proteins. 62: 982-95. PMID 16355414 DOI: 10.1002/Prot.20694  0.351
2005 Choudhury N, Pettitt BM. Dynamics of water trapped between hydrophobic solutes. The Journal of Physical Chemistry. B. 109: 6422-9. PMID 16851715 DOI: 10.1021/Jp045439I  0.376
2005 Dyer KM, Perkyns JS, Pettitt BM. Effective density terms in proper integral equations. The Journal of Chemical Physics. 123: 204512. PMID 16351286 DOI: 10.1063/1.2116987  0.758
2005 Rösgen J, Pettitt BM, Bolen DW. Protein folding, stability, and solvation structure in osmolyte solutions. Biophysical Journal. 89: 2988-97. PMID 16113118 DOI: 10.1529/Biophysj.105.067330  0.307
2005 Dyer KM, Perkyns JS, Pettitt BM. Simple bond length dependence: a correspondence between reactive fluid theories. The Journal of Chemical Physics. 122: 236101. PMID 16008496 DOI: 10.1063/1.1893829  0.747
2004 Wong KY, Pettitt BM. Orientation of DNA on a surface from simulation. Biopolymers. 73: 570-8. PMID 15048781 DOI: 10.1002/Bip.20004  0.304
2004 Wong KY, Vainrub A, Powdrill T, Hogan M, Pettitt BM. A non-Watson-Crick motif of base-pairing on surfaces for untethered oligonucleotides Molecular Simulation. 30: 121-129. DOI: 10.1080/0892702031000152181  0.324
2004 Rösgen J, Pettitt BM, Perkyns J, Bolen DW. Statistical Thermodynamic Approach to the Chemical Activities in Two-Component Solutions Journal of Physical Chemistry B. 108: 2048-2055. DOI: 10.1021/Jp036325U  0.313
2004 Lakhno VD, Sultanov VB, Pettitt BM. Combined hopping-superexchange model of a hole transfer in DNA Chemical Physics Letters. 400: 47-53. DOI: 10.1016/J.Cplett.2004.10.077  0.308
2003 Vainrub A, Pettitt BM. Surface electrostatic effects in oligonucleotide microarrays: control and optimization of binding thermodynamics. Biopolymers. 68: 265-70. PMID 12548628 DOI: 10.1002/Bip.10271  0.329
2003 Marlow GE, Pettitt BM. Simulation of the bis-(penicillamine) enkephalin in ammonium chloride solution: a comparison with sodium chloride. Biopolymers. 68: 192-209. PMID 12548623 DOI: 10.1002/Bip.10292  0.334
2002 Makarov V, Pettitt BM, Feig M. Solvation and hydration of proteins and nucleic acids: a theoretical view of simulation and experiment. Accounts of Chemical Research. 35: 376-84. PMID 12069622 DOI: 10.1021/Ar0100273  0.596
2002 Swint-Kruse L, Larson C, Pettitt BM, Matthews KS. Fine-tuning function: correlation of hinge domain interactions with functional distinctions between LacI and PurR. Protein Science : a Publication of the Protein Society. 11: 778-94. PMID 11910022 DOI: 10.1110/Ps.4050102  0.323
2002 Dyer K, Perkyns J, Pettitt BM. Computationally useful bridge diagram series. III. Lennard-Jones mixtures Journal of Chemical Physics. 116: 9413-9421. DOI: 10.1063/1.1473661  0.75
2002 Perkyns JS, Dyer KM, Pettitt BM. Computationally useful bridge diagram series. II. Diagrams in h-bonds Journal of Chemical Physics. 116: 9404-9412. DOI: 10.1063/1.1473660  0.746
2001 Feig M, Zacharias M, Pettitt BM. Conformations of an adenine bulge in a DNA octamer and its influence on DNA structure from molecular dynamics simulations. Biophysical Journal. 81: 352-70. PMID 11423420 DOI: 10.1016/S0006-3495(01)75705-0  0.585
2001 Dyer KM, Perkyns JS, Pettitt BM. A reexamination of virial coefficients of the Lennard-Jones fluid Theoretical Chemistry Accounts. 105: 244-251. DOI: 10.1007/S002140000205  0.743
2000 Makarov VA, Andrews BK, Smith PE, Pettitt BM. Residence times of water molecules in the hydration sites of myoglobin. Biophysical Journal. 79: 2966-74. PMID 11106604 DOI: 10.1016/S0006-3495(00)76533-7  0.496
2000 Vainrub A, Pettitt BM. Thermodynamics of association to a molecule immobilized in an electric double layer Chemical Physics Letters. 323: 160-166. DOI: 10.1016/S0009-2614(00)00512-1  0.331
1999 Feig M, Pettitt BM. Sodium and chlorine ions as part of the DNA solvation shell. Biophysical Journal. 77: 1769-81. PMID 10512802 DOI: 10.1016/S0006-3495(99)77023-2  0.551
1999 Prabhu NV, Perkyns JS, Pettitt BM, Hruby VJ. Structure and dynamics of alpha-MSH using DRISM integral equation theory and stochastic dynamics. Biopolymers. 50: 255-72. PMID 10397788 DOI: 10.1002/(Sici)1097-0282(199909)50:3<255::Aid-Bip3>3.0.Co;2-V  0.385
1999 Prabhu NV, Perkyns JS, Blatt HD, Smith PE, Pettitt BM. Comparison of the potentials of mean force for alanine tetrapeptide between integral equation theory and simulation. Biophysical Chemistry. 78: 113-26. PMID 10343385 DOI: 10.1016/S0301-4622(99)00014-9  0.559
1999 Feig M, Pettitt BM. Modeling high-resolution hydration patterns in correlation with DNA sequence and conformation. Journal of Molecular Biology. 286: 1075-95. PMID 10047483 DOI: 10.1006/Jmbi.1998.2486  0.537
1999 Feig M, Abdullah M, Johnsson L, Pettitt BM. Large scale distributed data repository: Design of a molecular dynamics trajectory database Future Generation Computer Systems. 16: 101-110. DOI: 10.1016/S0167-739X(99)00039-4  0.529
1999 Lynch GC, Perkyns JS, Pettitt BM. Kirkwood-Buff Thermodynamics Derived from Grand Canonical Molecular Dynamics and DRISM Calculations Journal of Computational Physics. 151: 135-145. DOI: 10.1006/Jcph.1998.6183  0.424
1998 Feig M, Pettitt BM. A molecular simulation picture of DNA hydration around A- and B-DNA. Biopolymers. 48: 199-209. PMID 10699840 DOI: 10.1002/(Sici)1097-0282(1998)48:4<199::Aid-Bip2>3.0.Co;2-5  0.521
1998 Feig M, Pettitt BM. Crystallographic water sites from a theoretical perspective. Structure (London, England : 1993). 6: 1351-4. PMID 9817850 DOI: 10.1016/S0969-2126(98)00135-X  0.543
1998 Makarov VA, Feig M, Andrews BK, Pettitt BM. Diffusion of solvent around biomolecular solutes: a molecular dynamics simulation study. Biophysical Journal. 75: 150-8. PMID 9649375 DOI: 10.1016/S0006-3495(98)77502-2  0.575
1998 Feig M, Pettitt BM. Structural equilibrium of DNA represented with different force fields. Biophysical Journal. 75: 134-49. PMID 9649374 DOI: 10.1016/S0006-3495(98)77501-0  0.561
1998 Andrews BK, Romo T, Clarage JB, Pettitt BM, Phillips GN. Characterizing global substates of myoglobin. Structure (London, England : 1993). 6: 587-94. PMID 9634696 DOI: 10.1016/S0969-2126(98)00060-4  0.328
1998 Pettitt BM, Makarov VA, Andrews BK. Protein hydration density: theory, simulations and crystallography. Current Opinion in Structural Biology. 8: 218-21. PMID 9631296 DOI: 10.1016/S0959-440X(98)80042-0  0.352
1998 Swint-Kruse L, Matthews KS, Smith PE, Pettitt BM. Comparison of simulated and experimentally determined dynamics for a variant of the Lacl DNA-binding domain, Nlac-P. Biophysical Journal. 74: 413-21. PMID 9449341 DOI: 10.1016/S0006-3495(98)77798-7  0.494
1997 Smith PE, Blatt HD, Pettitt BM. A simple two-dimensional representation for the common secondary structural elements of polypeptides and proteins. Proteins. 27: 227-34. PMID 9061787 DOI: 10.1002/(Sici)1097-0134(19970201)27:2<227::Aid-Prot9>3.0.Co;2-C  0.465
1997 Lynch GC, Pettitt BM. Grand canonical ensemble molecular dynamics simulations: Reformulation of extended system dynamics approaches Journal of Chemical Physics. 107: 8594-8610. DOI: 10.1063/1.475012  0.374
1997 Feig M, Pettitt BM. Experiment vs force fields: DNA conformation from molecular dynamics simulations Journal of Physical Chemistry B. 101: X-7363. DOI: 10.1021/Jp971180A  0.512
1997 Smith PE, Blatt HD, Pettitt BM. On the Presence of Rotational Ewald Artifacts in the Equilibrium and Dynamical Properties of a Zwitterionic Tetrapeptide in Aqueous Solution The Journal of Physical Chemistry B. 101: 3886-3890. DOI: 10.1021/Jp9637643  0.444
1997 Smith PE, Blatt HD, Pettitt BM. Environmentally dependent conformational preferences of peptides Journal of the American Chemical Society. 119: 8714-8715. DOI: 10.1021/Ja963752V  0.33
1997 Perkyns J, Pettitt BM. Computationally useful bridge diagram series for the structure and thermodynamics of Lennard-Jones fluids Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta). 96: 61-70. DOI: 10.1007/S002140050205  0.381
1997 Micu AM, Bagheri B, Ilin AV, Scott R, Pettitt B. Numerical Considerations in the Computation of the Electrostatic Free Energy of Interaction within the Poisson–Boltzmann Theory Journal of Computational Physics. 136: 263-271. DOI: 10.1006/Jcph.1997.5707  0.383
1996 Smith PE, Pettitt BM. Ewald artifacts in liquid state molecular dynamics simulations The Journal of Chemical Physics. 105: 4289-4293. DOI: 10.1063/1.472246  0.527
1996 Yang L, Pettitt BM. B to A Transition of DNA on the Nanosecond Time Scale The Journal of Physical Chemistry. 100: 2564-2566. DOI: 10.1021/Jp953080F  0.311
1995 Weerasinghe S, Smith PE, Pettitt BM. Structure and stability of a model pyrimidine-purine-purine DNA triple helix with a GC.T mismatch by simulation. Biochemistry. 34: 16269-78. PMID 8845351 DOI: 10.1021/Bi00050A006  0.437
1995 Yang L, Weerasinghe S, Smith PE, Pettitt BM. Dielectric response of triplex DNA in ionic solution from simulations. Biophysical Journal. 69: 1519-27. PMID 8534822 DOI: 10.1016/S0006-3495(95)80022-6  0.443
1995 Cheng YK, Pettitt BM. Solvent effects on model d(CG.G)7 and d(TA.T)7 DNA triple helices. Biopolymers. 35: 457-73. PMID 7766818 DOI: 10.1002/Bip.360350505  0.366
1995 Weerasinghe S, Smith PE, Mohan V, Cheng Y, Pettitt BM. Nanosecond Dynamics and Structure of a Model DNA Triple Helix in Saltwater Solution Journal of the American Chemical Society. 117: 2147-2158. DOI: 10.1021/Ja00113A004  0.482
1995 Smith PE, Pettitt BM. Efficient Ewald electrostatic calculations for large systems Computer Physics Communications. 91: 339-344. DOI: 10.1016/0010-4655(95)00058-N  0.467
1995 Chen Z, Pettitt B. Non-isotropic solution of an OZ equation: matrix methods for integral equations Computer Physics Communications. 85: 239-250. DOI: 10.1016/0010-4655(94)00146-S  0.332
1994 Lounnas V, Pettitt BM. Distribution function implied dynamics versus residence times and correlations: solvation shells of myoglobin. Proteins. 18: 148-60. PMID 8159664 DOI: 10.1002/Prot.340180207  0.383
1994 Lounnas V, Pettitt BM. A connected-cluster of hydration around myoglobin: correlation between molecular dynamics simulations and experiment. Proteins. 18: 133-47. PMID 8159663 DOI: 10.1002/Prot.340180206  0.376
1994 Weerasinghe S, Pettitt BM. Ideal chemical potential contribution in molecular dynamics simulations of the grand canonical ensemble Molecular Physics. 82: 897-912. DOI: 10.1080/00268979400100654  0.339
1994 Ji J, Pettitt B. Phase transitions of water at constant excess chemical potential An application of grand molecular dynamics Molecular Physics. 82: 67-83. DOI: 10.1080/00268979400100064  0.347
1994 Valdeavella CV, Perkyns JS, Pettitt BM. Investigations into the common ion effect The Journal of Chemical Physics. 101: 5093-5109. DOI: 10.1063/1.467365  0.304
1994 Smith PE, Pettitt BM. Modeling Solvent in Biomolecular Systems The Journal of Physical Chemistry. 98: 9700-9711. DOI: 10.1021/J100090A002  0.426
1994 Cannon WR, Pettitt BM, McCammon JA. Sulfate Anion in Water: Model Structural, Thermodynamic, and Dynamic Properties The Journal of Physical Chemistry. 98: 6225-6230. DOI: 10.1021/J100075A027  0.473
1994 McCammon J, Pettitt B, Scott L. Ordinary differential equations of molecular dynamics Computers & Mathematics With Applications. 28: 319-326. DOI: 10.1016/0898-1221(94)00199-5  0.376
1993 Mohan V, Cheng YK, Marlow GE, Pettitt BM. Molecular recognition of Watson-Crick base-pair reversals in triple-helix formation: use of nonnatural oligonucleotide bases. Biopolymers. 33: 1317-25. PMID 8400029 DOI: 10.1002/Bip.360330902  0.373
1993 Mohan V, Smith PE, Pettitt BM. Evidence for a new spine of hydration: solvation of DNA triple helixes Journal of the American Chemical Society. 115: 9297-9298. DOI: 10.1021/Ja00073A059  0.344
1993 Smith PE, Marlow GE, Pettitt BM. Peptides in ionic solutions: a simulation study of a bis(penicillamine) enkephalin in sodium acetate solution Journal of the American Chemical Society. 115: 7493-7498. DOI: 10.1021/Ja00069A057  0.484
1993 Mohan V, Smith PE, Pettitt BM. Molecular dynamics simulation of ions and water around triplex DNA The Journal of Physical Chemistry. 97: 12984-12990. DOI: 10.1021/J100151A055  0.484
1993 Smith PE, Pettitt BM, Karplus M. Stochastic dynamics simulations of the alanine dipeptide using a solvent-modified potential energy surface The Journal of Physical Chemistry. 97: 6907-6913. DOI: 10.1021/J100128A027  0.656
1993 Marlow GE, Perkyns JS, Pettitt BM. Salt effects in peptide solutions: theory and simulations Chemical Reviews. 93: 2503-2521. DOI: 10.1021/Cr00023A009  0.323
1992 O'Connor SD, Smith PE, al-Obeidi F, Pettitt BM. Quenched molecular dynamics simulations of tuftsin and proposed cyclic analogues. Journal of Medicinal Chemistry. 35: 2870-81. PMID 1495018 DOI: 10.1021/Jm00093A021  0.514
1992 Smith PE, Pettitt BM. Amino acid side-chain populations in aqueous and saline solution: Bis- penicillamine enkephalin Biopolymers. 32: 1623-1629. PMID 1472647 DOI: 10.1002/Bip.360321205  0.43
1992 Perkyns J, Pettitt BM. A site–site theory for finite concentration saline solutions The Journal of Chemical Physics. 97: 7656-7666. DOI: 10.1063/1.463485  0.363
1992 Ji J, Çaǧin T, Pettitt BM. Dynamic simulations of water at constant chemical potential The Journal of Chemical Physics. 96: 1333-1342. DOI: 10.1063/1.462169  0.376
1992 Dang LX, Pettitt BM, Rossky PJ. On the correlation between like ion pairs in water The Journal of Chemical Physics. 96: 4046-4047. DOI: 10.1063/1.461859  0.649
1992 Lounnas V, Pettitt BM, Findsen L, Subramaniam S. A microscopic view of protein solvation The Journal of Physical Chemistry. 96: 7157-7159. DOI: 10.1021/J100197A004  0.353
1992 Mohan V, Davis ME, McCammon JA, Pettitt BM. Continuum model calculations of solvation free energies: accurate evaluation of electrostatic contributions The Journal of Physical Chemistry. 96: 6428-6431. DOI: 10.1021/j100194a060  0.393
1991 Pettitt BM, Matsunaga T, al-Obeidi F, Gehrig C, Hruby VJ, Karplus M. Dynamical search for bis-penicillamine enkephalin conformations. Biophysical Journal. 60: 1540-4. PMID 1777571 DOI: 10.1016/S0006-3495(91)82188-9  0.529
1991 Smith PE, al-Obeidi F, Pettitt BM. Aspects of the design of conformationally constrained peptides. Methods in Enzymology. 202: 411-36. PMID 1664477 DOI: 10.1016/0076-6879(91)02021-Z  0.403
1991 Çagin T, Pettitt BM. Grand Molecular Dynamics: A Method for Open Systems Molecular Simulation. 6: 5-26. DOI: 10.1080/08927029108022137  0.329
1991 Mazor M, Pettitt BM. Convergence of the Chemical Potential in Aqueous simulations Molecular Simulation. 6: 1-4. DOI: 10.1080/08927029108022136  0.413
1991 Çağin T, Pettitt BM. Molecular dynamics with a variable number of molecules Molecular Physics. 72: 169-175. DOI: 10.1080/00268979100100111  0.32
1991 Smith PE, Pettitt BM. Peptides in ionic solutions: A comparison of the Ewald and switching function techniques The Journal of Chemical Physics. 95: 8430-8441. DOI: 10.1063/1.461272  0.444
1991 Smith PE, Pettitt BM. Effects of salt on the structure and dynamics of the bis(penicillamine) enkephalin zwitterion: a simulation study Journal of the American Chemical Society. 113: 6029-6037. DOI: 10.1021/Ja00016A015  0.473
1991 Yu HA, Karplus M, Pettitt BM. Aqueous solvation of N-methylacetamide conformers: comparison of simulations and integral equation theories Journal of the American Chemical Society. 113: 2425-2434. DOI: 10.1021/Ja00007A012  0.588
1991 Smith PE, Dang LX, Pettitt BM. Simulation of the structure and dynamics of the bis(penicillamine) enkephalin zwitterion Journal of the American Chemical Society. 113: 67-73. DOI: 10.1021/Ja00001A013  0.468
1990 Ramé GL, Lau WF, Pettitt BM. Flexibility of tripeptides in solution: free energy molecular mechanics. International Journal of Peptide and Protein Research. 35: 315-27. PMID 2345054 DOI: 10.1111/J.1399-3011.1990.Tb00056.X  0.387
1990 Van Vlijmen HW, Ramé GL, Pettitt BM. A study of model energetics and conformational properties of polynucleotide triplexes. Biopolymers. 30: 517-32. PMID 2265226 DOI: 10.1002/bip.360300505  0.76
1990 Dang LX, Pettitt BM. A theoretical study of like ion pairs in solution The Journal of Physical Chemistry. 94: 4303-4308. DOI: 10.1021/J100373A078  0.301
1989 Çain T, Pettitt BM. Elastic constants of nickel: Variations with respect to temperature and pressure. Physical Review B. 39: 12484-12491. PMID 9948114 DOI: 10.1103/Physrevb.39.12484  0.312
1989 Lau WF, Pettitt BM. Selective elimination of interactions: a method for assessing thermodynamic contributions to ligand binding with application to rhinovirus antivirals. Journal of Medicinal Chemistry. 32: 2542-7. PMID 2555511 DOI: 10.1021/Jm00132A008  0.301
1989 Madura JD, Pettitt BM, McCammon JA. Methods for calculating geometries of transition states in solution Chemical Physics. 129: 185-191. DOI: 10.1016/0301-0104(89)80003-5  0.604
1988 Madura JD, Pettitt BM, Calef DF. Water under high pressure Molecular Physics. 64: 325-336. DOI: 10.1080/00268978800100253  0.54
1988 Chen Z, Karim OA, Pettitt BM. A theory of the interionic structure of graphite intercalation synthetic metals: Variations with respect to interactions and state The Journal of Chemical Physics. 89: 1042-1048. DOI: 10.1063/1.455255  0.322
1988 Dang LX, Pettitt BM. A theoretical study of the inclusion complexes of β‐quinol The Journal of Chemical Physics. 89: 968-974. DOI: 10.1063/1.455166  0.318
1988 Hruby VJ, Kao LF, Pettitt BM, Karplus M. The conformational properties of the delta opioid peptide [cyclic] [D-pen2,D-pen5]enkephalin in aqueous solution determined by NMR and energy minimization calculations Journal of the American Chemical Society. 110: 3351-3359. DOI: 10.1021/Ja00219A002  0.544
1988 Pettitt BM, Karplus M. Conformational free energy of hydration for the alanine dipeptide: thermodynamic analysis The Journal of Physical Chemistry. 92: 3994-3997. DOI: 10.1021/J100324A061  0.552
1988 Madura JD, Pettitt BM. Effects of truncating long-range interactions in aqueous ionic solution simulations Chemical Physics Letters. 150: 105-108. DOI: 10.1016/0009-2614(88)80404-4  0.632
1988 HRUBY VJ, KAO L, PETTITT BM, KARPLUS M. ChemInform Abstract: Conformational Properties of the Delta Opioid Peptide Cyclic(D-Pen2,D-Pen5)enkephalin in Aqueous Solution Determined by NMR and Energy Minimization Calculations. Cheminform. 19. DOI: 10.1002/chin.198838055  0.494
1987 Karplus M, Ichiye T, Pettitt BM. Configurational entropy of native proteins. Biophysical Journal. 52: 1083-5. PMID 3427197 DOI: 10.1016/S0006-3495(87)83303-9  0.496
1987 Dang LX, Pettitt BM. Simple intramolecular model potentials for water The Journal of Physical Chemistry. 91: 3349-3354. DOI: 10.1021/J100296A048  0.373
1987 Pettitt BM, Calef DF. On the structure of high-density water at constant temperature The Journal of Physical Chemistry. 91: 1541-1545. DOI: 10.1021/J100290A050  0.341
1987 Karim OA, Pettitt B. Two-dimensional fluids in a periodic external potential: Intercalation in graphite Chemical Physics Letters. 137: 72-77. DOI: 10.1016/0009-2614(87)80306-8  0.337
1987 Madura JD, Pettitt BM, McCammon JA. Geometric considerations in the calculation of relative free energies of activation Chemical Physics Letters. 141: 83-87. DOI: 10.1016/0009-2614(87)80096-9  0.623
1986 Pettitt BM, Rossky PJ. Alkali halides in water: Ion–solvent correlations and ion–ion potentials of mean force at infinite dilution The Journal of Chemical Physics. 84: 5836-5844. DOI: 10.1063/1.449894  0.68
1986 Pettitt BM, Karplus M, Rossky PJ. Integral equation model for aqueous solvation of polyatomic solutes: application to the determination of the free energy surface for the internal motion of biomolecules The Journal of Physical Chemistry. 90: 6335-6345. DOI: 10.1021/J100281A055  0.719
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  0.68
1985 Pettitt BM, Karplus M. The potential of mean force between polyatomic molecules in polar molecular solvents The Journal of Chemical Physics. 83: 781-789. DOI: 10.1063/1.449493  0.595
1985 Pettitt BM, Karplus M. Role of electrostatics in the structure, energy and dynamics of biomolecules: a model study of N-methylalanylacetamide Journal of the American Chemical Society. 107: 1166-1173. DOI: 10.1021/Ja00291A014  0.554
1985 PETTITT BM, KARPLUS M. ChemInform Abstract: ROLE OF ELECTROSTATICS IN THE STRUCTURE, ENERGY AND DYNAMICS OF BIOMOLECULES: A MODEL STUDY OF N-METHYLALANYLACETAMIDE Chemischer Informationsdienst. 16. DOI: 10.1002/chin.198529077  0.505
1983 Rossky PJ, Pettitt BM, Stell G. The coupling of long and short range correlations in ISM liquids Molecular Physics. 50: 1263-1271. DOI: 10.1080/00268978300103021  0.672
1983 Hirata F, Rossky PJ, Pettitt BM. The interionic potential of mean force in a molecular polar solvent from an extended RISM equation The Journal of Chemical Physics. 78: 4133-4144. DOI: 10.1063/1.445090  0.679
1983 Pettitt BM, Rossky PJ. The contribution of hydrogen bonding to the structure of liquid methanol The Journal of Chemical Physics. 78: 7296-7299. DOI: 10.1063/1.444719  0.685
1983 PETTITT BM, ROSSKY PJ. ChemInform Abstract: THE CONTRIBUTION OF HYDROGEN BONDING TO THE STRUCTURE OF LIQUID METHANOL Chemischer Informationsdienst. 14. DOI: 10.1002/chin.198337054  0.588
1982 Pettitt BM, Rossky PJ. Integral equation predictions of liquid state structure for waterlike intermolecular potentials The Journal of Chemical Physics. 77: 1451-1457. DOI: 10.1063/1.443972  0.683
1982 Hirata F, Pettitt BM, Rossky PJ. Application of an extended RISM equation to dipolar and quadrupolar fluids The Journal of Chemical Physics. 77: 509-520. DOI: 10.1063/1.443606  0.703
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