Sealy Center for Structural Biology and Molecular Biophysics

Cover of Proteins:

Cover of Proteins: Struct. Funct. Bioinfo., Vol. 62, Iss. 4, Mar 1, 2006; by C. Chen et al.

Cover of J. Phys.:

 Condens. Matter, Vol. 18, Iss. 14, Apr 12, 2006; by G. L. Randall et al.

J. Phys.:

Condens. Matter, Vol. 18, Iss. 14, Apr 12, 2006; by G. L. Randall et al.

J. Phys Cover

Condens. Matter, Vol. 18, Iss. 14, Apr 12, 2006; by G. L. Randall et al.

Cover of Biopolymers,

Vol. 85, Iss. 3, Feb 15, 2007; by C. Chen et al.

Cover of J. Phys. Chem. B

Vol. 113, Iss. 2, Jan 15, 2009; by C. Chen et al.

Cover of J. Comput Chem.

Vol. 36, Iss. 17, 2015; by JA Drake et al.

Cover of Biopolymers 110(1), e23239 (2019)

Price of disorder in the lac repressor hinge helix. Seckfort D, Pettitt BM.

3D-rendering of DNA chip

K.-Y. Wong & B. M. Pettitt, Theor. Chem. Acc., 106, 233-235 (2001)

DNA chip image

rendered with POV-Ray by K.-Y. Wong.

N-ColE7-DNA binding energy landscape

C. Chen & B. M. Pettitt, Biophys. J, 101, 1139-1147 (2011).

Serratia marcescens endonuclease

rendered by B. W. Beck

The water is translucent

with ions (Na-purple, Cl-green) in full VDW rendering and the triplex DNA in licorice representation rendered by Chandler Wilkerson.

DNA chip image rendered

 with POV-Ray by K.-Y. Wong

Hydration sites around myoglobin.

A. Vladimir et al. Biophys. J., 79, 2966-2974 (2000)

Hydrogen-bond residence times

in urea solutions. H. Kokubo & B. M. Pettitt. J. Phys. Chem. B, 111, 5233-5242 (2007)

Solvation of peptide

by water, TMAO, and urea. H. Kokubo et al. J. Am. Chem. Soc., 133, 1849-1858 (2011)

Charge densities

around AT basepair calculated from Integral Equation theory. J. J. Howard et al. J. Phys. Chem. B, 115, 547-556 (2011)

Water densities between

graphene plates from integral equations.  J. J. Howard et al. J. Chem. Theory Comput., 4, 1928-1939 (2008)

Water densities around

DNA base-pairs by integral equations. J. J. Howard et al. J. Phys. Chem. B, 115, 547-556 (2011)

Water density around

a sodium ion near a wall by integral equations. J. J. Howard et al. J. Phys. Chem. B, 114, 6074-6083 (2010)

Conformations of peptide

tethered to a surface by molecular dynamic simulation.  J. Feng et al. J. Phys. Chem. B, 111, 13797-13806 (2007)

MD Simulation

of ssDNA on the chip. K.-Y. Wong et al. Mol. Simul. 30, 121-129 (2004)

Pathway of DNA

melting by MD simuation. K.-Y. Wong & B. M. Pettitt. Biophys. J., 95, 5618-5626 (2008)

Metastable conformation

of DNA during melting by MD simuation. K.-Y. Wong & B. M. Pettitt. Biophys. J., 95, 5618-5626 (2008)

DNA duplex

tethered to a surface. K.-Y. Wong & B. M. Pettitt, Biopolymers, 73, 570-578 (2004)

N-ColE7-DNA

model complexes. C. Chen & B. M. Pettitt, Biophys. J, 101, 1139-1147 (2011)

Water density in

the proximity of SMnase-DNA complex. C. Chen et al. J. Phys. Chem. B, 113, 511-521 (2009)

Magnesium cluster

at the active site of SMnase. C. Chen et al. J. Phys. Chem. B, 113, 511-521 (2009)

Active site of

Trichomonas vaginalis ferredoxin. T. E. Weksberg et al. Biophys. J., 92, 3337-3345 (2007)

Electrostatic field

around DNA juxtaposition. G. L. Randall et al. J. Phys.: Condens. Matter. 18, S173-S185 (2006)

Counterion concentrations

around DNA juxtaposition. G. L. Randall et al. J. Phys.: Condens. Matter. 18, S173-S185 (2006)

Electrostatic solvation

free energies of five representative conformations of deca-alanine.  B. Lin et al. J. Phys. Chem. Lett., 2, 1626-1632 (2011)

A coarse grained model

for the thermodynamics of nucleic acid hybridization near surface. J. Ambia-Garrido et al. J. Phys.: Condens. Matter, 23, 325101 (2011)

DNA torsional stress relief

as a funcion of winding (σ = -0.179) G. L. Randall et al. Nucl. Acids Res., 37, 5568-5577 (2009)

P22 Phage:

cryo-EM Vs. simulation. C. G. Myers & B .M. Pettitt. J. Chem. Phys., 138, 071103 (2013)

Phage P-SSP7:

Coarse-grained DNA models. Q. Wang, C. G. Myers & B .M. Pettitt. J Phys Chem B., 119(15), 4937-43 (2015)

Dihedral angle

free energy surfaces as a function of force field. Drake JA, Pettitt BM. J Comput Chem., 36(17), 1275-85 (2015)

Models for the capsid of phage phi29

Effects of Model Shape, Volume, and Softness of the Capsid for DNA Packaging of phi29. Bores C, Woodson M, Morais MC, Pettitt BM. J Phys Chem B. 24(46):10337-103441 (2020)