Welcome to the Gray Lab
About Us Research Publications People Facilities Positions Courses Links Wiki

Journal Publications: (Additional listings at Google Scholar)
  1. Drew, K., Renfrew, P. D., Craven, T., Butterfoss, G. L., Chou, F.-C., Lyskov, S., Bullock, B. N., Watkins, A., Labonte, J. W., Pacella, M., Kilambi, K. P., Leaver-Fay, A., Kuhlman, B., Gray, J. J., Bradley, P., Kirshenbaum, K., Arora, P. S., Das, R., & Bonneau, R. "Adding Diverse Noncanonical Backbones to Rosetta: Enabling Peptidomimetic Design," accepted for publication in PLoS One (2013).

  2. Xu, J., Tack, D., Hughes, R. A., Ellington, A. D., & Gray, J. J. "Structure-based Non-canonical Amino Acid Design to Covalently Crosslink an Antibody-Antigen Complex," accepted for publication in J. Struct. Biol. (2013) (Invited for special issue on "Designing Protein Function.") Online

  3. Lyskov, S.*, Chou F.-C.*, Conchúir, S. Ó., Der, B. S., Drew, K., Kuroda, D., Xu, J., Renfrew, P. D., Sripakdeevong, P., Borgo, B., Havranek, J. J., Kuhlman, B., Kortemme, T., Bonneau, R., Gray, J. J.†, Das, R.† "Serverification of Molecular Modeling Applications: the Rosetta Online Server that Includes Everyone (ROSIE)," accepted for publication in PLoS One (2013). (*These authors contributed equally to this work; †co-corresponding authors) Invited special collection.

  4. Leaver-Fay, A., O'Meara, M., J., Tyka, M., Jacak, R., Song, Y., Kellogg, E. H., Thompson, J., Davis, I. W., Pache, R. A., Lyskov, S., Gray, J. J., Kortemme, T., Richardson, J. S., Havranek, J. J., Snoeyink, J., Baker, D. & Kuhlman, B., "Scientific Benchmarks for Guiding Macromolecular Energy Function Improvement," Meth. Enz. 523, 109-143 (2013). Online

  5. Tarasevich, B. J., Perez-Salas, U. Masica, D. L., Philo, J., Kienzle, P., Srueger, S., Majkrzak, C. F., Gray, J. J., and Shaw, W. J., "Neutron Reflectometry Studies of the Adsorbed Structure of the Amelogenin, LRAP," J. Phys. Chem. B 117(11), 3098-3109 (2013). Online

  6. B. Chaikind, K. P. Kilambi, J. J. Gray and M. Ostermeier, "Targeted DNA Methylation Using an Artificially Bisected M.HhaI Fused to Zinc Fingers," PLoS One 7(9), e44852 (2012). Online

  7. K. P. Kilambi and J. J. Gray, "Rapid Calculation of Protein pKa Values using Rosetta," Biophys. J. 103(3), 587-595 (2012). Online

  8. Y. Ye, M. R. Stahley, J. Xu, J. I. Friedman, Y. Sun, J. N. McKnight, J. J. Gray, G. D. Bowman and J. T. Stivers, "Enzymatic Excision of Uracil Residues in Nucleosomes Depends on the Local DNA Structure and Dynamics," Biochemistry 51(30), 6028-6038 (2012). Online

  9. A. E. Miklos, C. Kluwe, B. S. Der, S. Pai, A. Sircar, R. A. Hughes, M. Berrondo, J. Xu, V. Codrea, P. E. Buckley, A. M. Calm, H. S. Welsh, C. R. Warner, M. A. Zacharko, J. P. Carney, J. J. Gray, G. Georgiou, B. Kuhlman, A. D. Ellington, "Structure-Based Design of Supercharged, Highly Thermoresistant Antibodies," Chemistry & Biology 19(4), 449-455 (2012). Online

  10. S. B. Schrier, M. K. Sayeg, & J. J. Gray, "Prediction of Calcite Morphology from Computational and Experimental Studies of Mutations of a De Novo Designed Peptide," Langmuir 27(18), 11520-11527 (2011). Online

  11. S. J. Fleishman, T. A. Whitehead, E. M. Strauch and about 95 others including K. P. Kilambi, A. Sircar, and J. J. Gray, "Community-wide assessment of protein-interface modeling suggests improvements to design methodology," J. Mol. Biol. 414(2), 289-302 (2011). Online

  12. S. Chaudhury, M. Berrondo, B. D. Weitzner, P. Muthu, H. Bergman, & J. J. Gray, "Benchmarking and analysis of protein docking performance in RosettaDock 3.2," PLoS One 6(8): e22477 (2011). Online

  13. E. Baugh, S. Lyskov, B. D. Weitzner, & J. J. Gray, "Real-time PyMOL visualization for Rosetta and PyRosetta," PLoS One, 6(8): e21931 (2011). Online

  14. M. Berrondo & J. J. Gray, "Computed structures of point deletion mutants and their enzymatic activities," Proteins 79(10), 2844-2860 (2011). Online (featured cover art)

  15. D. L. Masica, J. J. Gray† & W. Shaw†, "Partial high-resolution structure of phosphorylated and non-phosphorylated leucine-rich amelogenin protein adsorbed to hydroxyapatite," J. Phys. Chem. C 115(28), 13775-13785 (2011). (†co-corresponding authors) Online

  16. A. Sircar, K. A. Sanni, J. Shi, & J. J. Gray, "Analysis and Modeling of the Variable Region of Camelid Single Domain Antibodies," J. Immunology, 186(11), 6357-6367 (2011). Online | Supplementary Material

  17. M. D. McKee, Y. Nakano, D. L. Masica, J. J. Gray, I. Lemire, R. Heft, P. Crine, & J. L. Millan, "Enzyme Replacement Therapy Prevents Dental Defects in a Model of Hypophosphatasia," J. Dental Res. 90(4), 470-476 (2011). Online (featured cover art)

  18. A. Leaver-Fay, M. Tyka, S. M. Lewis, O. F. Lange, J. Thompson, R. Jacak, K. Kaufman, P. D. Renfrew, C. A. Smith, W. Sheffler, I. W. Davis, S. Cooper, A. Treuille, D. J. Mandell, F. Fichter, Y.-E. A. Ban., S. J. Fleishman, J. E. Corn., D. E. Kim, S. Lyskov, M. Berrondo, S. Mentzer, Z. Popovic, J. J. Havranek, J. Karanicolas, R. Das, J. Meiler, T. Kortemme, J. J. Gray, B. Kuhlman, D. Baker, P. Bradley, "Rosetta3: An object-oriented software suite for the simulation and design of macromolecules," Meth. Enz. 487, 545-574 (2011). Online

  19. W. E. Bocik, A. Sircar, J. J. Gray† & J. R. Tolman†, "Mechanism of polyubiquitin chain recognition by the human ubiquitin conjugating enzyme Ube2g2," J. Biol. Chem. 286(5), 3981-3991 (2011). (†co-corresponding authors) Online

  20. D. L. Masica, J. Ashworth, M. Ndao, G. Drobny & J. J. Gray, "Structure determination method for biomineral-associated protein using combined solid-state NMR and computational structure prediction," Structure, 18(12), 1678-1687 (2010). Online

  21. B. Keshet, J. J. Gray & T. A. Good, "Structurally distinct toxicity inhibitors bind at common loci on beta-amyloid fibril," Prot. Sci., 19(12), 2291-2304 (2010). Online

  22. D. L. Masica, S. B. Schrier, E. Specht & J. J. Gray, "De novo design of peptide-calcite biomineralization systems," J. Am. Chem. Soc., 132(35), 12252-12262 (2010). Online

  23. A. Sircar, S. Chaudhury, K. P. Kilambi, M. Berrondo & J. J. Gray, "A generalized approach to sampling backbone conformations with RosettaDock for CAPRI rounds 13-19," Proteins 78(15), 3115-3123 (2010). Online

  24. M. Berrondo, J. J. Gray & R. Schleif, "Computational predictions of the mutant behavior of AraC," J. Mol. Biol., 398(3), 462-470 (2010). Online

  25. S. Chaudhury, S. Lyskov & J. J. Gray, "PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta," Bioinformatics, 26(5), 689-691 (2010). Online

  26. A. Sircar & J. J. Gray, "SnugDock: Paratope structural optimization during antibody-antigen docking compensates for errors in antibody homology models," PLoS Comput. Biol. 6(1): e1000644 (2010). Online

  27. W. N. Addison, D. L. Masica, J. J. Gray & M. D. McKee, "Phosphorylation-dependent inhibition of mineralization by osteopontin ASARM peptides is regulated by PHEX cleavage," J. Bone & Mineral Research 25(4), 695-705 (2010). Online

  28. S. Chaudhury & J. J. Gray, "Identification of structural mechanisms of HIV-1 protease specificity using computational peptide docking and implications for drug resistance," Structure 17(12), 1636-1648 (2009). Online

  29. Y.-C. Chien, D. L. Masica, J. J. Gray, S. Nguyen, H. Vali & M. D. McKee, "Modulation of calcium oxalate dehydrate growth by selective crystal-face binding of phosphorylated osteopontin and poly-aspartate peptide showing occlusion by sectoral (compositional) zoning," J. Biol. Chem. 284, 23491-23501 (2009). Online

  30. A. Sircar,* E. Kim* & J. J. Gray, "RosettaAntibody: Antibody Variable Region Homology Modeling Server," Nucleic Acids Research 37 (Web Server Issue), W474-W479 (2009). Online (*These authors contributed equally to this work)

  31. D. L. Masica & J. J. Gray, "Solution- and adsorbed-state structural ensembles predicted for the statherin-hydroxyapatite system," Biophys. J. 96(8), 3082-3091 (2009). Online

  32. M.D. Daily & J. J. Gray, "Allosteric communication occurs via networks of tertiary and quaternary motions in proteins," PLoS Comput. Biol. 5(2): e1000293 (2009). Online

  33. A. Sivasubramanian,* A. Sircar,* S. Chaudhury & J. J. Gray, "Toward high-resolution homology modeling of antibody Fv regions and application to antibody-antigen docking," Proteins 74(2), 497-514 (2009). Online | (*These authors contributed equally to this work)

  34. S. Chaudhury & J. J. Gray, "Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles," J. Mol. Biol. 381(4), 1068-1087 (2008). Online

  35. S. Lyskov & J. J. Gray, "The RosettaDock server for local protein-protein docking," Nucleic Acids Research 36 (Web Server Issue), W233-W238 (2008). Online

  36. 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

  37. 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

  38. 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

  39. 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 | Supplementary material

  40. 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 (*These authors contributed equally to this work.)

  41. A. Sivasubramanian, J. A. Maynard, & J. J. Gray, "Modeling the structure of mAb 14B7 bound to the anthrax protective antigen," Proteins 70(1), 218-230 (2008). Online

  42. J. Meitzler, J. J. Gray & T. L. Hendrickson, "Truncation of the caspase-related subunit (Gpi8p) of Saccharomyces cerevisiae GPI transamidase: Dimerization revealed," Arch. Biochem. Biophys. 462(1), 83-93 (2007). Online

  43. M. D. Daily & J. J. Gray, "Local motions in a benchmark of allosteric proteins," Proteins 67(2), 385-399 (2007). Online | Supplementary material

  44. Gray, J.J., "Biomolecular Modeling in a Process Dyanmics and Control Course," Chemical Engineering Education 40(4), 297-306 (Fall 2006). PDF

  45. Gray, J.J., "High-resolution protein-protein docking," Curr. Op. Struct. Biol. 16(2), 183-193 (2006). Online

  46. 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

  47. 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

  48. 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

  49. Gray, J.J., "The Interaction of Proteins with Solid Surfaces," Curr. Op. Struct. Biol. 14(1), 110-115 (2004). Online

  50. 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

  51. 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

  52. 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

  53. 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

  54. Gray, J.J., R. T. Bonnecaze, "Adsorption of charge-bidisperse mixtures of colloidal particles," Langmuir 17(25), 7935-7947 (2001). Online

  55. 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

  56. Gray, J.J., B. Chiang, R.T. Bonnecaze, "Origin of anomalous multibody interactions," Nature 402, 750 (1999, brief communication). Online

  57. Gray, J.J., R.T. Bonnecaze, "Rheology and dynamics of sheared arrays of colloidal particles," J. Rheology 42(5 (1998). 1121-1151 Online

  58. 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).

Books:
  1. Gray, J.J.; S. Chaudhury; S. Lyskov; J.W. Labonte The PyRosetta Interactive Platform for Protein Structure Prediction and Design: A Set of Educational Modules, 2nd ed. Baltimore: 2013. | CreateSpace | Kindle Edition | PyRosetta Tutorial Page

Ph.D. Theses From The Gray Lab:
  1. Systematic Analysis of Motions and Communication Networks in a Benchmark Set of Allosteric Proteins, Dr. Michael Daily, 2008
  2. Structure Determination and Design of Biomineral-Associated Proteins, Dr. David Masica, 2009
  3. Predicting the Structure and Function of Protein Mutants, Dr. Monica Berrondo, 2010
  4. Using Computational Protein Docking to Model the Structure and Specificity of Protein Interactions, Dr. Siddhartha Chaudhury, 2010
  5. Computational Antibody Structure Prediction and Antibody-Antigen Docking, Dr. Aroop Sircar, 2010

Biophysics B.S. Honors Paper From The Gray Lab:
  1. The Selection of Near-Native Decoys In Protein-Protein Docking by Score Combinations Using the Rosetta All-Atom Force Field, Justin Porter, 2012