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Montgomery Pettitt

Research Profile

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Publications

TOP 3
Svetla Stoilova-McPhie; Steven Ludtke; Gillian C Lynch; B Montgomery Pettitt
Domain organization of membrane-bound factor VIII.
Andrew Harrison; Jef Hooyberghs; David P Kreil; Rastislav Levicky; Peter Noble; Albrecht Ott; B Montgomery Pettitt; Hans Binder; Arnaud Buhot; Conrad J Burden; Enrico Carlon; Lara J Gamble; Cynthia Gibas; Avraham Halperin; Diethard Tautz; Alexander E Pozhitkov
Physico-chemical foundations underpinning microarray and next-generation sequencing experiments.
Christopher G Myers; B Montgomery Pettitt
Communication: Origin of the contributions to DNA structure in phages.

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All Publications

2013: Svetla Stoilova-McPhie; Steven Ludtke; Gillian C Lynch; B Montgomery Pettitt
Domain organization of membrane-bound factor VIII.
Biopolymers 2013;99(7):448-59.
2013: Andrew Harrison; Jef Hooyberghs; David P Kreil; Rastislav Levicky; Peter Noble; Albrecht Ott; B Montgomery Pettitt; Hans Binder; Arnaud Buhot; Conrad J Burden; Enrico Carlon; Lara J Gamble; Cynthia Gibas; Avraham Halperin; Diethard Tautz; Alexander E Pozhitkov
Physico-chemical foundations underpinning microarray and next-generation sequencing experiments.
Nucleic acids research 2013;41(5):2779-96.
2013: Christopher G Myers; B Montgomery Pettitt
Communication: Origin of the contributions to DNA structure in phages.
The Journal of chemical physics 2013;138(7):071103.
2012: Jonathan M Fogg; Sarah A Harris; B Montgomery Pettitt; Graham L Randall; De Witt L Sumners; Lynn Zechiedrich
Bullied no more: when and how DNA shoves proteins around.
Quarterly reviews of biophysics 2012;45(3):257-99.
2011: Arnold Vainrub; B Montgomery Pettitt
Accurate prediction of binding thermodynamics for DNA on surfaces.
The journal of physical chemistry. B 2011;115(45):13300-3.
2011: Chuanying Chen; B Montgomery Pettitt
The binding process of a nonspecific enzyme with DNA.
Biophysical journal 2011;101(5):1139-47.
2011: Bin Lin; B Montgomery Pettitt
Electrostatic solvation free energy of amino acid side chain analogs: implications for the validity of electrostatic linear response in water.
Journal of computational chemistry 2011;32(5):878-85.
2011: Bin Lin; B Montgomery Pettitt
Note: On the universality of proximal radial distribution functions of proteins.
The Journal of chemical physics 2011;134(10):106101.
2011: Hironori Kokubo; Char Y Hu; B Montgomery Pettitt
Peptide conformational preferences in osmolyte solutions: transfer free energies of decaalanine.
Journal of the American Chemical Society 2011;133(6):1849-58.
2011: Jesse J Howard; Gillian C Lynch; B Montgomery Pettitt
Ion and solvent density distributions around canonical B-DNA from integral equations.
The journal of physical chemistry. B 2011;115(3):547-56.
2010: Jesse J Howard; John S Perkyns; B Montgomery Pettitt
The behavior of ions near a charged wall-dependence on ion size, concentration, and surface charge.
The journal of physical chemistry. B 2010;114(18):6074-83.
2010: Char Y Hu; Hironori Kokubo; Gillian C Lynch; D Wayne Bolen; B Montgomery Pettitt
Backbone additivity in the transfer model of protein solvation.
Protein science : a publication of the Protein Society 2010;19(5):1011-22.
2010: Char Y Hu; Gillian C Lynch; Hironori Kokubo; B Montgomery Pettitt
Trimethylamine N-oxide influence on the backbone of proteins: an oligoglycine model.
Proteins 2010;78(3):695-704.
2010: John S Perkyns; Gillian C Lynch; Jesse J Howard; B Montgomery Pettitt
Protein solvation from theory and simulation: Exact treatment of Coulomb interactions in three-dimensional theories.
The Journal of chemical physics 2010;132(6):064106.
2009: Jun Feng; Ka-Yiu Wong; Kippi Dyer; B Montgomery Pettitt
Transport properties of water at functionalized molecular interfaces.
The Journal of chemical physics 2009;131(12):125102.
2009: Graham L Randall; Lynn Zechiedrich; B Montgomery Pettitt
In the absence of writhe, DNA relieves torsional stress with localized, sequence-dependent structural failure to preserve B-form.
Nucleic acids research 2009;37(16):5568-77.
2009: Jun Feng; Ka-Yiu Wong; Gillian C Lynch; Xiaolian Gao; B Montgomery Pettitt
Salt effects on surface-tethered peptides in solution.
The journal of physical chemistry. B 2009;113(28):9472-8.
2009: Chuanying Chen; Kurt Krause; B Montgomery Pettitt
Advantage of being a dimer for Serratia marcescens endonuclease.
The journal of physical chemistry. B 2009;113(2):511-21.
2008: Kippi M Dyer; John S Perkyns; George Stell; B Montgomery Pettitt
A molecular site-site integral equation that yields the dielectric constant.
The Journal of chemical physics 2008;129(10):104512.
2008: Peter G Vekilov; Oleg Galkin; B Montgomery Pettitt; Niharendu Choudhury; Ronald L Nagel
Determination of the transition-state entropy for aggregation suggests how the growth of sickle cell hemoglobin polymers can be slowed.
Journal of molecular biology 2008;377(3):882-8.
2007: Jun Feng; Ka-Yiu Wong; Gillian C Lynch; Xiaolian Gao; B Montgomery Pettitt
Peptide conformations for a microarray surface-tethered epitope of the tumor suppressor p53.
The journal of physical chemistry. B 2007;111(49):13797-806.
2007: Kippi M Dyer; John S Perkyns; B Montgomery Pettitt
A site-renormalized molecular fluid theory.
The Journal of chemical physics 2007;127(19):194506.
2007: Hironori Kokubo; Jörg Rösgen; David Bolen; B Montgomery Pettitt
Molecular basis of the apparent near ideality of urea solutions.
Biophysical journal 2007;93(10):3392-407.
2007: Hironori Kokubo; B Montgomery Pettitt
Preferential solvation in urea solutions at different concentrations: properties from simulation studies.
The journal of physical chemistry. B 2007;111(19):5233-42.
2007: Tiffany E Weksberg; Gillian C Lynch; Kurt L Krause; B Montgomery Pettitt
Molecular dynamics simulations of Trichomonas vaginalis ferredoxin show a loop-cap transition.
Biophysical journal 2007;92(10):3337-45.
2007: Niharendu Choudhury; B Montgomery Pettitt
The dewetting transition and the hydrophobic effect.
Journal of the American Chemical Society 2007;129(15):4847-52.
2007: Jörg Rösgen; B Montgomery Pettitt; David Bolen
An analysis of the molecular origin of osmolyte-dependent protein stability.
Protein science : a publication of the Protein Society 2007;16(4):733-43.
2007: Chuanying Chen; Brian W Beck; Kurt Krause; Tiffany E Weksberg; B Montgomery Pettitt
Effects of dimerization of Serratia marcescens endonuclease on water dynamics.
Biopolymers 2007;85(3):241-52.
2007: Kippi M Dyer; B Montgomery Pettitt; George Stell
Systematic investigation of theories of transport in the Lennard-Jones fluid.
The Journal of chemical physics 2007;126(3):034502.
2006: Niharendu Choudhury; B Montgomery Pettitt
Enthalpy-entropy contributions to the potential of mean force of nanoscopic hydrophobic solutes.
The journal of physical chemistry. B 2006;110(16):8459-63.
2006: Chuanying Chen; Brian W Beck; Kurt Krause; B Montgomery Pettitt
Solvent participation in Serratia marcescens endonuclease complexes.
Proteins 2006;62(4):982-95.
2005: Kippi M Dyer; John S Perkyns; B Montgomery Pettitt
Effective density terms in proper integral equations.
The Journal of chemical physics 2005;123(20):204512.
2005: Jörg Rösgen; B Montgomery Pettitt; David Bolen
Protein folding, stability, and solvation structure in osmolyte solutions.
Biophysical journal 2005;89(5):2988-97.
2005: Kippi M Dyer; John S Perkyns; B Montgomery Pettitt
Simple bond length dependence: a correspondence between reactive fluid theories.
The Journal of chemical physics 2005;122(23):236101.
2005: Niharendu Choudhury; B Montgomery Pettitt
Dynamics of water trapped between hydrophobic solutes.
The journal of physical chemistry. B 2005;109(13):6422-9.
2005: Niharendu Choudhury; B Montgomery Pettitt
On the mechanism of hydrophobic association of nanoscopic solutes.
Journal of the American Chemical Society 2005;127(10):3556-67.
2004: Jörg Rösgen; B Montgomery Pettitt; David Bolen
Uncovering the basis for nonideal behavior of biological molecules.
Biochemistry 2004;43(45):14472-84.
2004: Yuriy Fofanov; Yi Luo; Charles Katili; Jim Wang; Yuri Belosludtsev; Thomas F Powdrill; Chetan Belapurkar; Viacheslav Fofanov; Tong-Bin Li; Sergey Chumakov; B Montgomery Pettitt
How independent are the appearances of n-mers in different genomes?
Bioinformatics (Oxford, England) 2004;20(15):2421-8.
2004: Arnold Vainrub; B Montgomery Pettitt
Theoretical aspects of genomic variation screening using DNA microarrays.
Biopolymers 2004;73(5):614-20.
2004: Ka-Yiu Wong; B Montgomery Pettitt
Orientation of DNA on a surface from simulation.
Biopolymers 2004;73(5):570-8.
2003: Arnold Vainrub; B Montgomery Pettitt
Sensitive quantitative nucleic acid detection using oligonucleotide microarrays.
Journal of the American Chemical Society 2003;125(26):7798-9.
2003: Arnold Vainrub; B Montgomery Pettitt
Surface electrostatic effects in oligonucleotide microarrays: control and optimization of binding thermodynamics.
Biopolymers 2003;68(2):265-70.
2003: Gail E Marlow; B Montgomery Pettitt
Simulation of the bis-(penicillamine) enkephalin in ammonium chloride solution: a comparison with sodium chloride.
Biopolymers 2003;68(2):192-209.
2002: Yuriy Fofanov; B Montgomery Pettitt
Reconstruction of the genetic regulatory dynamics of the rat spinal cord development: local invariants approach.
Journal of biomedical informatics 2002;35(5-6):343-51.
2002: Arnold Vainrub; B Montgomery Pettitt
Coulomb blockage of hybridization in two-dimensional DNA arrays.
Physical review. E, Statistical, nonlinear, and soft matter physics 2002;66(4 Pt 1):041905.
2002: Vladimir Makarov; B Montgomery Pettitt; Michael Feig
Solvation and hydration of proteins and nucleic acids: a theoretical view of simulation and experiment.
Accounts of chemical research 2002;35(6):376-84.
2002: Liskin Swint-Kruse; Christopher Larson; B Montgomery Pettitt; Kathleen S Matthews
Fine-tuning function: correlation of hinge domain interactions with functional distinctions between LacI and PurR.
Protein science : a publication of the Protein Society 2002;11(4):778-94.
2001: NV Prabhu; S A Siddiqui; J S McMurray; B Montgomery Pettitt
Structural basis for the activity of pp60(c-src) protein tyrosine kinase inhibitors.
Biopolymers 2001;59(3):167-79.
2001: Michael Feig; M Zacharias; B Montgomery Pettitt
Conformations of an adenine bulge in a DNA octamer and its influence on DNA structure from molecular dynamics simulations.
Biophysical journal 2001;81(1):352-70.
2001: G E Marlow; B Montgomery Pettitt
Simulations of the bis-penicillamine enkephalin in sodium chloride solution: a parameter study.
Biopolymers 2001;60(2):134-52.
2000: Vladimir Makarov; BK Andrews; PE Smith; B Montgomery Pettitt
Residence times of water molecules in the hydration sites of myoglobin.
Biophysical journal 2000;79(6):2966-74.
1999: NV Prabhu; John S Perkyns; B Montgomery Pettitt
Modeling of alpha-MSH conformations with implicit solvent.
The journal of peptide research : official journal of the American Peptide Society 1999;54(5):394-407.
1999: Michael Feig; B Montgomery Pettitt
Sodium and chlorine ions as part of the DNA solvation shell.
Biophysical journal 1999;77(4):1769-81.
1999: NV Prabhu; John S Perkyns; B Montgomery Pettitt; V J Hruby
Structure and dynamics of alpha-MSH using DRISM integral equation theory and stochastic dynamics.
Biopolymers 1999;50(3):255-72.
1999: C V Valdeavella; HD Blatt; L Yang; B Montgomery Pettitt
Hydration effects on the electrostatic potential around tuftsin.
Biopolymers 1999;50(2):133-43.
1999: NV Prabhu; John S Perkyns; HD Blatt; PE Smith; B Montgomery Pettitt
Comparison of the potentials of mean force for alanine tetrapeptide between integral equation theory and simulation.
Biophysical chemistry 1999;78(1-2):113-26.
1999: Michael Feig; B Montgomery Pettitt
Modeling high-resolution hydration patterns in correlation with DNA sequence and conformation.
Journal of molecular biology 1999;286(4):1075-95.
1998: Michael Feig; B Montgomery Pettitt
Crystallographic water sites from a theoretical perspective.
Structure (London, England : 1993) 1998;6(11):1351-4.
1998: Vladimir Makarov; Michael Feig; BK Andrews; B Montgomery Pettitt
Diffusion of solvent around biomolecular solutes: a molecular dynamics simulation study.
Biophysical journal 1998;75(1):150-8.
1998: Michael Feig; B Montgomery Pettitt
Structural equilibrium of DNA represented with different force fields.
Biophysical journal 1998;75(1):134-49.
1998: Vladimir Makarov; BK Andrews; B Montgomery Pettitt
Reconstructing the protein-water interface.
Biopolymers 1998;45(7):469-78.
1998: BK Andrews; T Romo; JB Clarage; B Montgomery Pettitt; George N Phillips
Characterizing global substates of myoglobin.
Structure (London, England : 1993) 1998;6(5):587-94.
1998: B Montgomery Pettitt; Vladimir Makarov; BK Andrews
Protein hydration density: theory, simulations and crystallography.
Current opinion in structural biology 1998;8(2):218-21.
1998: Michael Feig; B Montgomery Pettitt
A molecular simulation picture of DNA hydration around A- and B-DNA.
Biopolymers 1998;48(4):199-209.
1998: Liskin Swint-Kruse; Kathleen S Matthews; PE Smith; B Montgomery Pettitt
Comparison of simulated and experimentally determined dynamics for a variant of the Lacl DNA-binding domain, Nlac-P.
Biophysical journal 1998;74(1):413-21.
1997: PE Smith; HD Blatt; B Montgomery Pettitt
A simple two-dimensional representation for the common secondary structural elements of polypeptides and proteins.
Proteins 1997;27(2):227-34.
1996: L Yang; C V Valdeavella; H D Blatt; B Montgomery Pettitt
Salt effects on peptide conformers: a dielectric study of tuftsin.
Biophysical journal 1996;71(6):3022-9.
1995: S Weerasinghe; PE Smith; B Montgomery Pettitt
Structure and stability of a model pyrimidine-purine-purine DNA triple helix with a GC.T mismatch by simulation.
Biochemistry 1995;34(50):16269-78.
1995: C V Valdeavella; H D Blatt; B Montgomery Pettitt
Simulations of conformers of tuftsin and a cyclic tuftsin analog.
International journal of peptide and protein research 1995;46(5):372-80.
1995: L Yang; S Weerasinghe; PE Smith; B Montgomery Pettitt
Dielectric response of triplex DNA in ionic solution from simulations.
Biophysical journal 1995;69(4):1519-27.
1995: R Mitra; B Montgomery Pettitt; RD Blake
Conformational states governing the rates of spontaneous transition mutations.
Biopolymers 1995;36(2):169-79.
1995: Y K Cheng; B Montgomery Pettitt
Solvent effects on model d(CG.G)7 and d(TA.T)7 DNA triple helices.
Biopolymers 1995;35(5):457-73.
1995: J B Clarage; T Romo; BK Andrews; B Montgomery Pettitt; George N Phillips
A sampling problem in molecular dynamics simulations of macromolecules.
Proceedings of the National Academy of Sciences of the United States of America 1995;92(8):3288-92.
1995: George N Phillips; B Montgomery Pettitt
Structure and dynamics of the water around myoglobin.
Protein science : a publication of the Protein Society 1995;4(2):149-58.
1994: John S Perkyns; B Montgomery Pettitt
Integral equation approaches to structure and thermodynamics of aqueous salt solutions.
Biophysical chemistry 1994;51(2-3):129-42; discussion 142-6.
1994: V Lounnas; B Montgomery Pettitt; George N Phillips
A global model of the protein-solvent interface.
Biophysical journal 1994;66(3 Pt 1):601-14.
1994: V Lounnas; B Montgomery Pettitt
Distribution function implied dynamics versus residence times and correlations: solvation shells of myoglobin.
Proteins 1994;18(2):148-60.
1994: V Lounnas; B Montgomery Pettitt
A connected-cluster of hydration around myoglobin: correlation between molecular dynamics simulations and experiment.
Proteins 1994;18(2):133-47.
1993: R Mitra; B Montgomery Pettitt; G L Ramé; RD Blake
The relationship between mutation rates for the (C-G)-->(T-A) transition and features of T-G mispair structures in different neighbor environments, determined by free energy molecular mechanics.
Nucleic acids research 1993;21(25):6028-37.
1993: M Guha-Biswas; M Holder; B Montgomery Pettitt
On the mechanism of HRV-14 antiviral compounds: "slow growth" as a conformational search procedure.
Journal of medicinal chemistry 1993;36(23):3489-95.
1993: D J Kessler; B Montgomery Pettitt; Y K Cheng; S R Smith; Krishna Jayaraman; H M Vu; ME Hogan
Triple helix formation at distant sites: hybrid oligonucleotides containing a polymeric linker.
Nucleic acids research 1993;21(20):4810-5.
1993: V Mohan; Y K Cheng; G E Marlow; B Montgomery Pettitt
Molecular recognition of Watson-Crick base-pair reversals in triple-helix formation: use of nonnatural oligonucleotide bases.
Biopolymers 1993;33(9):1317-25.
1992: PE Smith; B Montgomery Pettitt
Amino acid side-chain populations in aqueous and saline solution: bis-penicillamine enkephalin.
Biopolymers 1992;32(12):1623-9.
1992: S D O'Connor; PE Smith; FA al-Obeidi; B Montgomery Pettitt
Quenched molecular dynamics simulations of tuftsin and proposed cyclic analogues.
Journal of medicinal chemistry 1992;35(15):2870-81.
1992: Y K Cheng; B Montgomery Pettitt
Stabilities of double- and triple-strand helical nucleic acids.
Progress in biophysics and molecular biology 1992;58(3):225-57.
1991: B Montgomery Pettitt; T Matsunaga; FA al-Obeidi; C Gehrig; V J Hruby; M Karplus
Dynamical search for bis-penicillamine enkephalin conformations.
Biophysical journal 1991;60(6):1540-4.
1991: R H Durland; D J Kessler; S Gunnell; M Duvic; B Montgomery Pettitt; ME Hogan
Binding of triple helix forming oligonucleotides to sites in gene promoters.
Biochemistry 1991;30(38):9246-55.
1991: PE Smith; FA al-Obeidi; B Montgomery Pettitt
Aspects of the design of conformationally constrained peptides.
Methods in enzymology 1991;202():411-36.
1990: G L Ramé; W F Lau; B Montgomery Pettitt
Flexibility of tripeptides in solution: free energy molecular mechanics.
International journal of peptide and protein research 1990;35(4):315-27.
1990: Herman van Vlijmen; G L Ramé; B Montgomery Pettitt
A study of model energetics and conformational properties of polynucleotide triplexes.
Biopolymers 1990;30(5-6):517-32.
1989: W F Lau; B Montgomery Pettitt
Selective elimination of interactions: a method for assessing thermodynamic contributions to ligand binding with application to rhinovirus antivirals.
Journal of medicinal chemistry 1989;32(12):2542-7.