- Chaudhury, S. & Gray, J. J.
“Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles,”
accepted for publication in J. Mol. Biol. (2008). Available as
Article in Press.
- S. Lyskov & J. J. Gray,
"The RosettaDock server for local protein-protein docking,"
accepted for publication in Nucleic Acids Research Server Issue (2008).
Available in Advance Access |
PDF
- K. Pickin, S. Chaudhury, B. Dancy, J. J. Gray & P. Cole,
"Analysis of protein kinase autophosphorylation using expressed protein ligation and computational modeling,"
J. Am. Chem. Soc. 130(17), 5667-5669 (2008).
Online |
PDF
- M. Berrondo, M. Ostermeier & J. J. Gray,
"Structure prediction of domain insertion proteins from
structures of the individual domains,"
Structure 16(4), 513-527 (2008).
Online |
PDF
- K. Makrodimitris, D. L. Masica, E. T. Kim & J. J. Gray,
"Structure prediction of protein-solid surface interactions reveals a molecular recognition motif of statherin for hydroxyapatite,"
J. Am. Chem. Soc. 129(44), 13713-13722 (2007).
Online |
PDF
- M.D. Daily, T.J. Upadhyaya & J. J. Gray,
"Contact rearrangements form coupled networks from local motions in allosteric proteins,"
Proteins 71(1), 455-466 (2008).
Online |
PDF |
Supplementary material
- S. Chaudhury,* A. Sircar,* A. Sivasubramanian, M. Berrondo & J. J. Gray,
"Incorporating biochemical information and backbone flexibility in RosettaDock for CAPRI rounds 6-12,"
Proteins 69(4), 793-800 (2007).
Online |
PDF
(*These authors contributed equally to this work.)
- Sivasubramanian, A., Maynard, J. A. & Gray, J.J.
"Modeling the structure of mAb 14B7 bound to the anthrax protective antigen,"
Proteins 70(1), 218-230 (2008).
Online |
PDF
- Meitzler, J., Gray, J.J. & Hendrickson, T. L., "Truncation of the caspase-related
subunit (Gpi8p) of Saccharomyces cerevisiae GPI transamidase: Dimerization revealed,"
Arch. Biochem. Biophys. 462(1), 83-93 (2007).
Online |
PDF
- Daily, M.D. & Gray, J.J., "Local motions in a benchmark of allosteric proteins,"
Proteins 67(2), 385-399 (2007).
Online |
PDF |
Supplementary material
- Gray, J.J., "Biomolecular Modeling in a Process Dyanmics and Control Course,"
Chemical Engineering Education 40(4), 297-306 (Fall 2006).
PDF
- Gray, J.J., "High-resolution protein-protein docking,"
Curr. Op. Struct. Biol. 16(2), 183-193 (2006).
Online |
PDF
- A. Sivasubramanian, G. Chao, H.M. Pressler, K.D. Witrup, and J.J. Gray,
"Structural model of the mAb 806-EGFR complex using computational docking
followed by computational and experimental mutagenesis,"
Structure 14(3), 401-414 (2006).
Online |
PDF
- M.D. Daily, D. Masica, A. Sivasubramanian, S. Somarouthu, and J.J. Gray,
"CAPRI rounds 3-5 reveal promising successes and future challenges for RosettaDock,"
Proteins 60(2), 181-186 (2005).
Online |
PDF
- P. Singh, A.M. Mhaka, S.B. Christensen, J.J. Gray, S.R. Denmeade, and J.T. Isaacs,
"Applying linear interaction energy method for rational design of non-competitive
allosteric inhibitors of the SERCA ATPase,"
J. Med. Chem. 48(8), 3005-3014 (2005).
Online |
PDF
- Gray, J.J., "The Interaction of Proteins with Solid Surfaces,"
Curr. Op. Struct. Biol. 14(1), 110-115 (2004).
Online |
PDF
- Gray, J.J., S.E. Moughan, T. Kortemme, O. Schueler-Furman, K.M.S. Misura, A.V. Morozov, D. Baker, "Protein-Protein Docking Predictions for the CAPRI Experiment,"
Proteins 52(1), 118-122 (2003).
Online |
PDF
- Gray, J.J., S.E. Moughan, C. Wang, O. Schueler-Furman, B. Kuhlman, C.A. Rohl, D. Baker,
"Protein-Protein Docking with Simultaneous Optimization of Rigid-Body Displacement and Side-Chain Conformations,"
J. Mol. Biol. 331(1), 281-299 (2003).
Online |
PDF
- Gray, J.J., D.H. Klein, B.A. Korgel, R.T. Bonnecaze,
"Microstructure formation and kinetics in the random sequential adsorption of polydisperse tethered nanoparticles modeled as hard disks,"
Langmuir 17(8), 2317-2328 (2001).
Online |
PDF
- Gray, J.J., R.T. Bonnecaze,
"Adsorption of colloidal particles by Brownian dynamics simulation: kinetics and surface structures,"
J. Chem. Phys. 114(3), (2001). 1366-1381
Online |
PDF
- Gray, J.J., R. T. Bonnecaze,
"Adsorption of charge-bidisperse mixtures of colloidal particles,"
Langmuir 17(25), 7935-7947 (2001).
Online |
PDF
- Gray, J.J., D.H. Klein, R.T. Bonnecaze, B.A. Korgel,
"Non-equilibrium phase behavior during the random sequential adsorption of tethered hard disks,"
Phys. Rev. Lett. 85(21), 4430-4433 (2000).
Online |
PDF
- Gray, J.J., B. Chiang, R.T. Bonnecaze,
"Origin of anomalous multibody interactions,"
Nature 402, 750 (1999, brief communication).
Online |
PDF
- Gray, J.J., R.T. Bonnecaze,
"Rheology and dynamics of sheared arrays of colloidal particles,"
J. Rheology 42(5
(1998). 1121-1151
Online |
PDF
- Lee, G.M., J.J. Gray, and B.O. Palsson,
"Effect of trisodium citrate treatment on hybridoma cell viability,"
Biotechnology Techniques 5(4), 295-298 (1991).
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