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Author

  • Bernard Pettitt
2011

The binding process of a nonspecific enzyme with DNA

Chen, C. & Pettitt, B. M., Sep 7 2011, In : Biophysical Journal. 101, 5, p. 1139-1147 9 p.

Research output: Contribution to journalArticle

22 Scopus citations
2015

Examining the Assumptions Underlying Continuum-Solvent Models

Harris, R. C. & Pettitt, B., Sep 1 2015, In : Journal of Chemical Theory and Computation. 11, 10, p. 4593-4600 8 p.

Research output: Contribution to journalArticle

14 Scopus citations
2011

Fast calculations of electrostatic solvation free energy from reconstructed solvent density using proximal radial distribution functions

Lin, B., Wong, K. Y., Hu, C., Kokubo, H. & Pettitt, B. M., Jul 7 2011, In : Journal of Physical Chemistry Letters. 2, 13, p. 1626-1632 7 p.

Research output: Contribution to journalArticle

16 Scopus citations
2015

Twist-induced defects of the P-SSP7 genome revealed by modeling the cryo-EM density

Wang, Q., Myers, C. G. & Pettitt, B. M., Apr 16 2015, In : Journal of Physical Chemistry B. 119, 15, p. 4937-4943 7 p.

Research output: Contribution to journalArticle

4 Scopus citations

Force field-dependent solution properties of glycine oligomers

Drake, J. A. & Pettitt, B. M., Jun 1 2015, In : Journal of Computational Chemistry. 36, 17, p. 1275-1285 11 p.

Research output: Contribution to journalArticle

20 Scopus citations
2013

Communication: Origin of the contributions to DNA structure in phages

Myers, C. G. & Pettitt, B. M., Feb 21 2013, In : Journal of Chemical Physics. 138, 7, 071103.

Research output: Contribution to journalArticle

5 Scopus citations
2014

A cavity corrected 3D-RISM functional for accurate solvation free energies

Truchon, J. F., Pettitt, B. M. & Labute, P., Mar 11 2014, In : Journal of Chemical Theory and Computation. 10, 3, p. 934-941 8 p.

Research output: Contribution to journalArticle

85 Scopus citations
2011

Free energy considerations for nucleic acids with dangling ends near a surface: Acoarse grained approach

Ambia-Garrido, J., Vainrub, A. & Montgomery Pettitt, B., Aug 17 2011, In : Journal of Physics Condensed Matter. 23, 32, 325101.

Research output: Contribution to journalArticle

5 Scopus citations
2015

Systematic identification of single amino acid variants in glioma stem-cell-derived chromosome 19 proteins

Lichti, C. F., Mostovenko, E., Wadsworth, P. A., Lynch, G. C., Pettitt, B. M., Sulman, E. P., Wang, Q., Lang, F. F., Rezeli, M., Marko-Varga, G., Végvári, Á. & Nilsson, C. L., Feb 6 2015, In : Journal of Proteome Research. 14, 2, p. 778-786 9 p.

Research output: Contribution to journalArticle

16 Scopus citations
2016
15 Scopus citations
2018

Peptide Solubility Limits: Backbone and Side-Chain Interactions

Sarma, R., Wong, K. Y., Lynch, G. C. & Pettitt, B. M., Apr 5 2018, In : Journal of Physical Chemistry B. 122, 13, p. 3528-3539 12 p.

Research output: Contribution to journalArticle

1 Scopus citations
2020

Physical Chemistry of the Protein Backbone: Enabling the Mechanisms of Intrinsic Protein Disorder

Drake, J. A., Drake, J. A. & Pettitt, B. M., Jun 4 2020, In : Journal of Physical Chemistry B. 124, 22, p. 4379-4390 12 p.

Research output: Contribution to journalArticle

2014

Effects of geometry and chemistry on hydrophobic salvation

Harris, R. C., Pettitt, B. M. & Debenedetti, P. G., Oct 14 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 41, p. 14681-14686 6 p.

Research output: Contribution to journalArticle

40 Scopus citations
2018
3 Scopus citations
2016

Solvation Thermodynamics of Oligoglycine with Respect to Chain Length and Flexibility

Drake, J. A., Harris, R. C. & Pettitt, B. M., Aug 23 2016, In : Biophysical journal. 111, 4, p. 756-767 12 p.

Research output: Contribution to journalArticle

8 Scopus citations
2019

Price of disorder in the lac repressor hinge helix

Seckfort, D. & Montgomery Pettitt, B., Jan 2019, In : Biopolymers. 110, 1, e23239.

Research output: Contribution to journalArticle

1 Scopus citations
2013

Comparison of the structural and dynamic effects of 5-methylcytosine and 5-chlorocytosine in a CpG dinucleotide sequence

Theruvathu, J. A., Yin, Y. W., Pettitt, B. M. & Sowers, L. C., Nov 26 2013, In : Biochemistry. 52, 47, p. 8590-8598 9 p.

Research output: Contribution to journalArticle

7 Scopus citations
2020

Structure and the role of filling rate on model dsDNA packed in a phage capsid

Bores, C. & Pettitt, B. M., Jan 13 2020, In : Physical Review E. 101, 1, 012406.

Research output: Contribution to journalArticle

2012

Studying proteins and peptides at material surfaces

Feng, J., Lynch, G. C. & Pettitt, B. M., 2012, RSC Biomolecular Sciences. Royal Society of Chemistry, p. 293-320 28 p. (RSC Biomolecular Sciences; vol. 1).

Research output: Chapter in Book/Report/Conference proceedingChapter

Bullied no more: When and how DNA shoves proteins around

Fogg, J. M., Randall, G. L., Pettitt, B. M., Sumners, D. W. L., Harris, S. A. & Zechiedrich, L., Aug 1 2012, In : Quarterly Reviews of Biophysics. 45, 3, p. 257-299 43 p.

Research output: Contribution to journalReview article

39 Scopus citations
2020

Interactions between identical DNA double helices

Lai, C. L., Chen, C., Ou, S. C., Prentiss, M. & Pettitt, B. M., Mar 2020, In : Physical Review E. 101, 3, 032414.

Research output: Contribution to journalArticle

1 Scopus citations
2019

Free Energy Calculations Based on Coupling Proximal Distribution Functions and Thermodynamic Cycles

Ou, S. C. & Pettitt, B. M., Apr 9 2019, In : Journal of Chemical Theory and Computation. 15, 4, p. 2649-2658 10 p.

Research output: Contribution to journalArticle

1 Scopus citations
2013

Domain organization of membrane-bound factor VIII

Stoilova-Mcphie, S., Lynch, G. C., Ludtke, S. & Pettitt, B. M., Jul 2013, In : Biopolymers. 99, 7, p. 448-459 12 p.

Research output: Contribution to journalArticle

18 Scopus citations
2016

Solute-Solvent Energetics Based on Proximal Distribution Functions

Ou, S. C. & Pettitt, B. M., Aug 25 2016, In : Journal of Physical Chemistry B. 120, 33, p. 8230-8237 8 p.

Research output: Contribution to journalArticle

7 Scopus citations
2018

Visualizing Individual RuBisCO and Its Assembly into Carboxysomes in Marine Cyanobacteria by Cryo-Electron Tomography

Dai, W., Chen, M., Myers, C., Ludtke, S. J., Pettitt, B. M., King, J. A., Schmid, M. F. & Chiu, W., Oct 19 2018, In : Journal of Molecular Biology. 430, 21, p. 4156-4167 12 p.

Research output: Contribution to journalArticle

6 Scopus citations
2015

Solvation and cavity occupation in biomolecules

Lynch, G. C., Perkyns, J. S., Nguyen, B. L. & Pettitt, B. M., May 2015, In : Biochimica et Biophysica Acta - General Subjects. 1850, 5, p. 923-931 9 p.

Research output: Contribution to journalArticle

4 Scopus citations
2016

Importance of disentanglement and entanglement during DNA replication and segregation: Comment on: “Disentangling DNA molecules” by Alexander Vologodskii

Bates, D., Pettitt, B. M., Buck, G. R. & Zechiedrich, L., Sep 1 2016, In : Physics of Life Reviews. 18, p. 160-164 5 p.

Research output: Contribution to journalComment/debate

1 Scopus citations
2013

Physico-chemical foundations underpinning microarray and next-generation sequencing experiments

Harrison, A., Binder, H., Buhot, A., Burden, C. J., Carlon, E., Gibas, C., Gamble, L. J., Halperin, A., Hooyberghs, J., Kreil, D. P., Levicky, R., Noble, P. A., Ott, A., Pettitt, B. M., Tautz, D. & Pozhitkov, A. E., Mar 2013, In : Nucleic acids research. 41, 5, p. 2779-2796 18 p.

Research output: Contribution to journalReview article

43 Scopus citations
2016

Accelerating the weighted histogram analysis method by direct inversion in the iterative subspace

Zhang, C., Lai, C. L. & Pettitt, B., Sep 1 2016, In : Molecular Simulation. 42, 13, p. 1079-1089 11 p.

Research output: Contribution to journalArticle

8 Scopus citations
2011

Accurate prediction of binding thermodynamics for DNA on surfaces

Vainrub, A. & Pettitt, B. M., Nov 17 2011, In : Journal of Physical Chemistry B. 115, 45, p. 13300-13303 4 p.

Research output: Contribution to journalArticle

20 Scopus citations
2018

Thermodynamics of Conformational Transitions in a Disordered Protein Backbone Model

Drake, J. A. & Pettitt, B. M., Jun 19 2018, In : Biophysical journal. 114, 12, p. 2799-2810 12 p.

Research output: Contribution to journalArticle

5 Scopus citations
2015

Dynamic equilibria of short-range electrostatic interactions at molecular interfaces of protein-DNA complexes

Chen, C., Esadze, A., Zandarashvili, L., Nguyen, D., Pettitt, B. & Iwahara, J., Jul 16 2015, In : Journal of Physical Chemistry Letters. 6, 14, p. 2733-2737 5 p.

Research output: Contribution to journalArticle

29 Scopus citations
2016

Protein collapse driven against solvation free energy without H-bonds

Karandur, D., Harris, R. C. & Pettitt, B. M., Jan 1 2016, In : Protein Science. 25, 1, p. 103-110 8 p.

Research output: Contribution to journalArticle

11 Scopus citations
2011

Note: On the universality of proximal radial distribution functions of proteins

Lin, B. & Pettitt, B. M., Mar 14 2011, In : Journal of Chemical Physics. 134, 10, 106101.

Research output: Contribution to journalArticle

15 Scopus citations
2020

The lac repressor hinge helix in context: The effect of the DNA binding domain and symmetry

Seckfort, D., Lynch, G. & Pettitt, B. M., Apr 2020, In : Biochimica et Biophysica Acta - General Subjects. 1864, 4, 129538.

Research output: Contribution to journalArticle

2016

Erratum: Computation of virial coefficients from integral equations (Journal of Chemical Physics (2015) 142 (214110))

Zhang, C., Lai, C. L. & Pettitt, B., Jun 14 2016, In : Journal of Chemical Physics. 144, 22, 229901.

Research output: Contribution to journalComment/debate

2011
25 Scopus citations
2015

Controlling microarray DNA hybridization efficiency by probe-surface distance and external surface electrostatics

Qamhieh, K. & Pettitt, B., Mar 30 2015, 4th International Congress in Advances in Applied Physics and Materials Science, APMAS 2014. American Institute of Physics Inc., Vol. 1653. 020090

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations
2019
2016

Dielectric behavior for saline solutions from renormalized diagrammatically proper interaction site model theory

Dyer, K. M., Perkyns, J. S. & Pettitt, B. M., Aug 22 2016, In : Journal of Physics Condensed Matter. 28, 41, 414006.

Research output: Contribution to journalArticle

1 Scopus citations
2011

Peptide conformational preferences in osmolyte solutions: Transfer free energies of decaalanine

Kokubo, H., Hu, C. Y. & Pettitt, B. M., Feb 16 2011, In : Journal of the American Chemical Society. 133, 6, p. 1849-1858 10 p.

Research output: Contribution to journalArticle

98 Scopus citations
2014

Modeling DNA thermodynamics under torsional stress

Wang, Q. & Pettitt, B. M., Mar 4 2014, In : Biophysical journal. 106, 5, p. 1182-1193 12 p.

Research output: Contribution to journalArticle

7 Scopus citations
2016

Reconciling the understanding of 'hydrophobicity' with physics-based models of proteins

Harris, R. C. & Pettitt, B. M., Feb 2 2016, In : Journal of Physics Condensed Matter. 28, 8, 083003.

Research output: Contribution to journalReview article

12 Scopus citations
2015
2 Scopus citations
2014

Multibody correlations in the hydrophobic solvation of glycine peptides

Harris, R. C., Drake, J. A. & Pettitt, B. M., Dec 14 2014, In : Journal of Chemical Physics. 141, 22, 22D525.

Research output: Contribution to journalArticle

11 Scopus citations
2016

Changes in conformational dynamics of basic side chains upon protein-DNA association

Esadze, A., Chen, C., Zandarashvili, L., Roy, S., Pettitt, B. M. & Iwahara, J., Aug 19 2016, In : Nucleic acids research. 44, 14, p. 6961-6970 10 p.

Research output: Contribution to journalArticle

37 Scopus citations
2019
3 Scopus citations

Allosteric discrimination at the NADH/ADP regulatory site of glutamate dehydrogenase

Nassar, O. M., Wong, K. Y., Lynch, G. C., Smith, T. J. & Pettitt, B. M., Dec 1 2019, In : Protein Science. 28, 12, p. 2080-2088 9 p.

Research output: Contribution to journalArticle

Mobility of Histidine Side Chains Analyzed with 15 N NMR Relaxation and Cross-Correlation Data: Insight into Zinc-Finger-DNA Interactions

Kemme, C. A., Luu, R. H., Chen, C., Pletka, C. C., Pettitt, B. M. & Iwahara, J., May 2 2019, In : Journal of Physical Chemistry B. 123, 17, p. 3706-3710 5 p.

Research output: Contribution to journalArticle