Bernard Pettitt, PhD

Director, Sealy Center for Structural Biology

  • 12189 Citations
  • 62 h-Index
1978 …2021

Research output per year

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Research Output

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Article
2005

On the mechanism of hydrophobic association of nanoscopic solutes

Choudhury, N. & Pettitt, B. M., Mar 16 2005, In : Journal of the American Chemical Society. 127, 10, p. 3556-3567 12 p.

Research output: Contribution to journalArticle

248 Scopus citations

Protein folding, stability, and solvation structure in osmolyte solutions

Rösgen, J., Pettitt, B. M. & Bolen, D. W., Nov 2005, In : Biophysical Journal. 89, 5, p. 2988-2997 10 p.

Research output: Contribution to journalArticle

116 Scopus citations

Simple bond length dependence: A correspondence between reactive fluid theories

Dyer, K. M., Perkyns, J. S. & Pettitt, B. M., Jun 15 2005, In : Journal of Chemical Physics. 122, 23, 236101.

Research output: Contribution to journalArticle

5 Scopus citations
2004

A fast solver for the Ornstein-Zernike equations

Kelley, C. T. & Pettitt, B. M., Jul 1 2004, In : Journal of Computational Physics. 197, 2, p. 491-501 11 p.

Research output: Contribution to journalArticle

17 Scopus citations

A non-Watson-Crick motif of base-pairing on surfaces for untethered oligonucleotides

Wong, K. Y., Vainrub, A., Powdrill, T., Hogan, M. & Pettitt, B. M., Feb 15 2004, In : Molecular Simulation. 30, 2-3, p. 121-129 9 p.

Research output: Contribution to journalArticle

11 Scopus citations

Combined hopping-superexchange model of a hole transfer in DNA

Lakhno, V. D., Sultanov, V. B. & Pettitt, B. M., Dec 11 2004, In : Chemical Physics Letters. 400, 1-3, p. 47-53 7 p.

Research output: Contribution to journalArticle

21 Scopus citations

How independent are the appearances of n-mers in different genomes?

Fofanov, Y., Luo, Y., Katili, C., Wang, J., Belosludtsev, Y., Powdrill, T., Belapurkar, C., Fofanov, V., Li, T. B., Chumakov, S. & Pettitt, B. M., Oct 12 2004, In : Bioinformatics. 20, 15, p. 2421-2428 8 p.

Research output: Contribution to journalArticle

43 Scopus citations

Orientation of DNA on a Surface from Simulation

Wong, K. Y. & Pettitt, B. M., Apr 5 2004, In : Biopolymers. 73, 5, p. 570-578 9 p.

Research output: Contribution to journalArticle

54 Scopus citations

Statistical Thermodynamic Approach to the Chemical Activities in Two-Component Solutions

Rösgen, J., Pettitt, B. M., Perkyns, J. & Bolen, D. W., Feb 12 2004, In : Journal of Physical Chemistry B. 108, 6, p. 2048-2055 8 p.

Research output: Contribution to journalArticle

28 Scopus citations

Theoretical Aspects of Genomic Variation Screening Using DNA Microarrays

Vainrub, A. & Pettitt, B. M., Apr 5 2004, In : Biopolymers. 73, 5, p. 614-620 7 p.

Research output: Contribution to journalArticle

19 Scopus citations

Uncovering the basis for nonideal behavior of biological molecules

Rösgen, J., Pettitt, B. M. & Bolen, D. W., Nov 16 2004, In : Biochemistry. 43, 45, p. 14472-14484 13 p.

Research output: Contribution to journalArticle

50 Scopus citations
2003

Sensitive quantitative nucleic acid detection using oligonucleotide microarrays

Vainrub, A. & Pettitt, B. M., Jul 2 2003, In : Journal of the American Chemical Society. 125, 26, p. 7798-7799 2 p.

Research output: Contribution to journalArticle

64 Scopus citations

Simulation of the bis-(penicillamine) enkephalin in ammonium chloride solution: A comparison with sodium chloride

Marlow, G. E. & Pettitt, B. M., Feb 1 2003, In : Biopolymers. 68, 2, p. 192-209 18 p.

Research output: Contribution to journalArticle

6 Scopus citations

Surface electrostatic effects in oligonucleotide microarrays: Control and optimization of binding thermodynamics

Vainrub, A. & Pettitt, B. M., Feb 1 2003, In : Biopolymers. 68, 2, p. 265-270 6 p.

Research output: Contribution to journalArticle

103 Scopus citations
2002

Computationally useful bridge diagram series. II. Diagrams in h-bonds

Perkyns, J. S., Dyer, K. M. & Pettitt, B. M., Jun 1 2002, In : Journal of Chemical Physics. 116, 21, p. 9404-9412 9 p.

Research output: Contribution to journalArticle

22 Scopus citations

Computationally useful bridge diagram series. III. Lennard-Jones mixtures

Dyer, K., Perkyns, J. & Pettitt, B. M., Jun 1 2002, In : Journal of Chemical Physics. 116, 21, p. 9413-9421 9 p.

Research output: Contribution to journalArticle

13 Scopus citations
122 Scopus citations

Fine-tuning function: Correlation of hinge domain interactions with functional distinctions between LacI and PurR

Swint-Kruse, L., Larson, C., Montgomery Pettitt, B. & Matthews, K. S., Apr 3 2002, In : Protein Science. 11, 4, p. 778-794 17 p.

Research output: Contribution to journalArticle

29 Scopus citations

Numerical simulation of the sedimentation of a tripole-like body in an incompressible viscous fluid

Juárez, L. H., Glowinski, R. & Pettitt, B. M., Aug 2002, In : Applied Mathematics Letters. 15, 6, p. 743-747 5 p.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations

Reconstruction of the genetic regulatory dynamics of the rat spinal cord development: Local Invariants approach

Fofanov, Y. & Pettitt, B. M., Oct 2002, In : Journal of Biomedical Informatics. 35, 5-6, p. 343-351 9 p.

Research output: Contribution to journalArticle

4 Scopus citations

Solvation and hydration of proteins and nucleic acids: A theoretical view of simulation and experiment

Makarov, V., Pettitt, B. M. & Feig, M., Jul 6 2002, In : Accounts of Chemical Research. 35, 6, p. 376-384 9 p.

Research output: Contribution to journalArticle

272 Scopus citations
2001

A reexamination of virial coefficients of the Lennard-Jones fluid

Dyer, K. M., Perkyns, J. S. & Pettitt, B. M., Jan 1 2001, In : Theoretical Chemistry Accounts. 105, 3, p. 244-251 8 p.

Research output: Contribution to journalArticle

14 Scopus citations

A study of DNA tethered to a surface by an all-atom molecular dynamics simulation

Wong, K. Y. & Pettitt, B. M., Jul 1 2001, In : Theoretical Chemistry Accounts. 106, 3, p. 233-235 3 p.

Research output: Contribution to journalArticle

42 Scopus citations

Conformations of an adenine bulge in a DNA octamer and its influence on DNA structure from molecular dynamics simulations

Feig, M., Zacharias, M. & Montgomery Pettitt, B., Jan 1 2001, In : Biophysical Journal. 81, 1, p. 352-370 19 p.

Research output: Contribution to journalArticle

Open Access
28 Scopus citations

Simulations of the bis-penicillamine enkephalin in sodium chloride solution: A parameter study

Marlow, G. E. & Montgomery Pettitt, B., Aug 23 2001, In : Biopolymers - Peptide Science Section. 60, 2, p. 134-152 19 p.

Research output: Contribution to journalArticle

9 Scopus citations

Structural basis for the activity of pp60c-src protein tyrosine kinase inhibitors

Prabhu, N. V., Siddiqui, S. A., McMurray, J. S. & Montgomery Pettitt, B., Aug 11 2001, In : Biopolymers. 59, 3, p. 167-179 13 p.

Research output: Contribution to journalArticle

3 Scopus citations
2000

A new boundary condition for computer simulations of interfacial systems

Wong, K. Y. & Pettitt, B. M., Aug 18 2000, In : Chemical Physics Letters. 326, 3-4, p. 193-198 6 p.

Research output: Contribution to journalArticle

14 Scopus citations

Residence times of water molecules in the hydration sites of myoglobin

Makarov, V. A., Andrews, B. K., Smith, P. E. & Pettitt, B. M., Dec 2000, In : Biophysical Journal. 79, 6, p. 2966-2974 9 p.

Research output: Contribution to journalArticle

Open Access
214 Scopus citations

Semi-grand canonical molecular dynamics simulation of bovine pancreatic trypsin inhibitor

Lynch, G. C. & Pettitt, B. M., Aug 15 2000, In : Chemical Physics. 258, 2-3, p. 405-413 9 p.

Research output: Contribution to journalArticle

10 Scopus citations

Thermodynamics of association to a molecule immobilized in an electric double layer

Vainrub, A. & Pettitt, B. M., Jun 9 2000, In : Chemical Physics Letters. 323, 1-2, p. 160-166 7 p.

Research output: Contribution to journalArticle

59 Scopus citations
1999

Comparison of the potentials of mean force for alanine tetrapeptide between integral equation theory and simulation

Prabhu, N. V., Perkyns, J. S., Blatt, H. D., Smith, P. E. & Pettitt, B. M., Apr 5 1999, In : Biophysical Chemistry. 78, 1-2, p. 113-126 14 p.

Research output: Contribution to journalArticle

11 Scopus citations

Hydration effects on the electrostatic potential around tuftsin

Valdeavella, C. V., Blatt, H. D., Yang, L. & Pettitt, B. M., Jul 1 1999, In : Biopolymers. 50, 2, p. 133-143 11 p.

Research output: Contribution to journalArticle

1 Scopus citations

Kirkwood-Buff Thermodynamics Derived from Grand Canonical Molecular Dynamics and DRISM Calculations

Lynch, G. C., Perkyns, J. S. & Pettitt, B. M., May 1 1999, In : Journal of Computational Physics. 151, 1, p. 135-145 11 p.

Research output: Contribution to journalArticle

12 Scopus citations

Large scale distributed data repository: Design of a molecular dynamics trajectory database

Feig, M., Abdullah, M., Johnsson, L. & Pettitt, B. M., Nov 1999, In : Future Generation Computer Systems. 16, 1, p. 101-110 10 p.

Research output: Contribution to journalArticle

15 Scopus citations

Modeling high-resolution hydration patterns in correlation with DNA sequence and conformation

Feig, M. & Pettitt, B. M., Mar 5 1999, In : Journal of Molecular Biology. 286, 4, p. 1075-1095 21 p.

Research output: Contribution to journalArticle

102 Scopus citations

Modeling of α-MSH conformations with implicit solvent

Prabhu, N. V., Perkyns, J. S. & Pettitt, B. M., Nov 4 1999, In : Journal of Peptide Research. 54, 5, p. 394-407 14 p.

Research output: Contribution to journalArticle

24 Scopus citations

Sodium and chlorine ions as part of the DNA solvation shell

Feig, M. & Pettitt, B. M., Oct 1999, In : Biophysical journal. 77, 4, p. 1769-1781 13 p.

Research output: Contribution to journalArticle

Open Access
181 Scopus citations

Structure and dynamics of α-MSH using DRISM integral equation theory and stochastic dynamics

Prabhu, N. V., Perkyns, J. S., Pettitt, B. M. & Hruby, V. J., Sep 1 1999, In : Biopolymers. 50, 3, p. 255-272 18 p.

Research output: Contribution to journalArticle

17 Scopus citations
1998

A molecular simulation picture of DNA hydration around A- And B-DNA

Feig, M. & Montgomery Pettitt, B., Jan 1 1998, In : Biopolymers. 48, 4, p. 199-209 11 p.

Research output: Contribution to journalArticle

83 Scopus citations

Characterizing global substates of myoglobin

Andrews, B. K., Romo, T., Clarage, J. B., Pettitt, B. M. & Phillips, G. N., May 15 1998, In : Structure. 6, 5, p. 587-594 8 p.

Research output: Contribution to journalArticle

Open Access
38 Scopus citations

Comparison of simulated and experimentally determined dynamics for a variant of the Lacl DNA-binding domain, Nlac-P

Swint-Kruse, L., Matthews, K. S., Smith, P. E. & Pettitt, B. M., Jan 1998, In : Biophysical journal. 74, 1, p. 413-421 9 p.

Research output: Contribution to journalArticle

Open Access
15 Scopus citations

Crystallographic water sites from a theoretical perspective

Feig, M. & Pettitt, B. M., Nov 15 1998, In : Structure. 6, 11, p. 1351-1354 4 p.

Research output: Contribution to journalArticle

Open Access
32 Scopus citations

Diffusion of solvent around biomolecular solutes: A molecular dynamics simulation study

Makarov, V. A., Feig, M., Andrews, B. K. & Pettitt, B. M., Jul 1998, In : Biophysical Journal. 75, 1, p. 150-158 9 p.

Research output: Contribution to journalArticle

Open Access
134 Scopus citations

NMR and quenched molecular dynamics studies of superpotent linear and cyclic α-melanotropins

Al-Obeidi, F., O'Connor, S. D., Job, C., Hruby, V. J. & Pettitt, B. M., Jun 8 1998, In : Journal of Peptide Research. 51, 6, p. 420-431 12 p.

Research output: Contribution to journalArticle

37 Scopus citations

Protein hydration density: Theory, simulations and crystallography

Pettitt, B. M., Makarov, V. A. & Andrews, B. K., Apr 1998, In : Current Opinion in Structural Biology. 8, 2, p. 218-221 4 p.

Research output: Contribution to journalArticle

50 Scopus citations

Reconstructing the protein-water interface

Makarov, V. A., Andrews, B. K. & Pettitt, B. M., Dec 1 1998, In : Biopolymers. 45, 7, p. 469-478 10 p.

Research output: Contribution to journalArticle

59 Scopus citations

Structural equilibrium of DNA represented with different force fields

Feig, M. & Pettitt, B. M., Jul 1998, In : Biophysical Journal. 75, 1, p. 134-149 16 p.

Research output: Contribution to journalArticle

Open Access
116 Scopus citations
1997

A simple two-dimensional representation for the common secondary structural elements of polypeptides and proteins

Smith, P. E., Blatt, H. D. & Pettitt, B. M., Jan 1 1997, In : Proteins: Structure, Function and Genetics. 27, 2, p. 227-233 7 p.

Research output: Contribution to journalArticle

Computationally useful bridge diagram series for the structure and thermodynamics of Lennard-Jones fluids

Perkyns, J. & Pettitt, B. M., Apr 1997, In : Theoretical Chemistry Accounts. 96, 1, p. 61-70 10 p.

Research output: Contribution to journalArticle

15 Scopus citations

Environmentally dependent conformational preferences of peptides

Smith, P. E., Blatt, H. D. & Pettitt, B. M., Oct 7 1997, In : Journal of the American Chemical Society. 119, 37, p. 8714-8715 2 p.

Research output: Contribution to journalArticle

1 Scopus citations