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Journal Publications: (Additional listings at Google Scholar, PubMed, or Scopus)

  1. Kuroda, D. & Gray, J. J. "Shape complementarity of hydrogen bond preferences in protein-protein interfaces: Implications for antibody modeling and protein-protein docking," Bioinformatics in press (2016).

  2. DeKosky, B. J.,* Lungu, O.I.,* Park, D., Johnson, E. L., Charab, W., Chrysostomou, C., Kuroda, D., Ellington, A. D., Ippolito, G. C., Gray, J. J., & Georgiou, G. "Large-Scale Sequence and Structural Comparisons of Human Naive and Antigen-Experienced Antibody Repertoires," Proc. Natl. Acad. Sci. U S A in press (2016). (*These authors contributed equally to this work)

  3. Lensink, M., Velankar, S., Kryshtafovych, A., Huang, S., Duhovny-Schneidman, D., Sali, A., ... Marze, N., Roy Burman, S., Kuroda, D., Gray, J. J., ... and Wodak, S. [82 authors total] "Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment," Proteins in press (2016).

  4. R. F. Alford, J. Koehler Leman, B. D. Weitzner, A. M. Duran, D. C. Tilley, A. Elazar & J. J. Gray "An integrated framework advancing membrane protein modeling and design," PLoS Comput. Biol. 11(9): e1004398 (2015). Online

  5. Pierre, B., Labonte, J. W., Xiong, T., Aoraha, E., Williams, A., Shah, V., Chau, E., Helal, K. Y., Gray, J. J. & Kim, J. R. "Molecular determinants for protein stabilization by insertional fusion to a thermophilic host protein," ChemBioChem 16(16), 2392-2402 (2015). Online

  6. I. Matlahov, T. Iline-Vul, M. Abayev, E. M.-Y. Lee, M. Nadav-Tsubery, K. Keinan-Adamsky, J. J. Gray & G. Goobes, "Interfacial mineral-peptide properties of a mineral binding peptide from osteonectin and bone-like apatite," Chem. Mater. 27(16), 5562-5569 (2015). Online

  7. Jiang, Q., Arnold, S., Heanue, T., Kilambi, K. P., Doan, B., Kapoor, A., Ling, A. Y., Sosa, M. X., Guy, M., Jiang, Q., Burzynski, G., West, K., Bessling, S., Griseri, P., Amiel, J., Fernandez, R. M., Verheij, J. B. G. M., Hofstra, R. M. W., Borrego, S., Lyonnet, S., Ceccherini, I., Gray, J. J., Pachnis, V., McCallion, A. S. & Chakravarti, A. "Functional Loss of Semaphorin 3C and/or Semaphorin 3D and Their Epistatic Interaction with Ret Are Critical to Hirschsprung Disease Liability," Am. J. Human Genetics 96(4), 581-596 (2015). Online

  8. Weitzner, B. D., Dunbrack, R. & J. J. Gray. "The origin of CDR H3 structural diversity," Structure 23(2), 302-311 (2015). Online

  9. J. Koehler Leman, M. B. Ulmschneider & J. J. Gray. "Computational Modeling of Membrane Proteins," Proteins 83(1), 1-24 (2015). Online

  10. Kilambi, K. P., Reddy, K. & J. J. Gray. "Protein-protein docking with dynamic residue protonation states," PLoS Computational Biology 10(12), e1004018 (2014). Online

  11. B. Weitzner,* D. Kuroda,* N. Marze, J. Xu, & J. J. Gray. "Blind Prediction Performance of RosettaAntibody 3.0: Grafting, Relaxation, Kinematic Loop Modeling, and CDR Optimization," Proteins 82(8), 1611-1623 (2014). Online (*These authors contributed equally to this work)

  12. Firnberg, E., Labonte, J. W., Gray, J. J. & Ostermeier, M. "A Comprehensive, High-Resolution Map of a Gene's Fitness Landscape," Mol. Biol. Evol. 31(6), 1581-1592 (2014). Online

  13. 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," J. Struct. Biol. 185(2), 215-222 (2014) Online

  14. Lensink, M. F., Moal, I. H., Bates, P.A., Kastritis, P. L., Melquiond, A.S.J., Karaca, E., Schmitz, C., van Dijk, M., Bonvin, A. M. J. J., Eisenstein, M., Jiménez-García, B., Grosdidier, S., Solernou, A., Pérez-Cano, L., Pallara, C., Fernández-Recio, J., Xu, J., Muthu, P., Kilambi, K. P., Gray, J. J., Grudinin, S., Derevyanko, G., Mitchell, J. C., Wieting, J., Kanamori, E., Tsuchiya, Y., Murakami, Y., Sarmiento, J., Standley, D. M., Shirota, M., Kinoshita, K., Nakamura, H., Chavent, M., Ritchie, D. W., Park, H., Ko, J., Lee, H., Seok, C., Shen, Y., Kozakov, D., Vajda, S., Kundrotas, P. J., Vakser, I. A., Pierce, B. G., Hwang, H., Vreven, T., Weng, Z., Buch, I., Farkash, E., Wolfson, H. J., Zacharias, M., Qin, S., Zhou, H.-X., Huang, S.-Y., Zou, X., Wojdyla, J. A., Kleanthous, C., and Wodak, S. J. "Blind Prediction of Interfacial Water Positions in CAPRI," Proteins 82(4), 620-632 (2014). Online

  15. Kilambi, K. P., Pacella, M. S., Xu, J., Labonte, J., Porter, J., Muthu, P., Drew, K., Kuroda, D., Schueler-Furman, O., Bonneau, R., & Gray, J. J., "Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20-27," Proteins 81(12), 2201-2209 (2013). Online

  16. Pacella, M. S., Koo, D. C. E., Thottungal, R. A., & Gray, J. J. "Using the RosettaSurface Algorithm to Predict Protein Structure at Mineral Surfaces," Meth. Enz. 532, 343-366 (2013). Online

  17. Moretti, R., Fleishman, S. J., Agius, R., Torchala, M., Bates, P.A., ... Pacella, M., Kilambi, K. P., Gray, J. J., ... Velankar, S., Janin, J., Wodak, S. J., and Baker, D. (about 70 total authors) "Community-wide Evaluation of Methods for Predicting the Effect of Mutations on Protein-Protein Interactions," Proteins 81(11), 1980-1987. Online

  18. 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," PLoS One 8(7): e67051 (2013). Online

  19. Der, B. S., Kluwe, C., Miklos, A. E., Jacak, R., Lyskov, S., Gray, J. J., Georgiou, G., Ellington, A. D. & Kuhlman, B. "Alternative computational protocols for supercharging protein surfaces for reversible unfolding and retention of stability," PLoS One 8(5): e64363 (2013). Online

  20. 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)," PLoS One 8(5): e63906 (2013). (*These authors contributed equally to this work; †co-corresponding authors) Online

  21. 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

  22. 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

  23. 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

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

  25. 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

  26. 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

  27. 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

  28. 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

  29. 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

  30. 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

  31. 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)

  32. 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

  33. 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

  34. 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)

  35. 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

  36. 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

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

  38. 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

  39. 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

  40. 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

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

  42. 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

  43. 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

  44. 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

  45. 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

  46. 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

  47. 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)

  48. 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

  49. 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

  50. 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)

  51. 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

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

  53. 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

  54. 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

  55. 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

  56. 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
  57. 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.)
  58. 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

  59. 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

  60. M. D. Daily & J. J. Gray, "Local motions in a benchmark of allosteric proteins," Proteins 67(2), 385-399 (2007). Online | Supplementary material
  61. Gray, J.J., "Biomolecular Modeling in a Process Dyanmics and Control Course," Chemical Engineering Education 40(4), 297-306 (Fall 2006). PDF
  62. Gray, J.J., "High-resolution protein-protein docking," Curr. Op. Struct. Biol. 16(2), 183-193 (2006). Online

  63. 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

  64. 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

  65. 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

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

  67. 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

  68. 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

  69. 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

  70. 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

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

  72. 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

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

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

  75. 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).

  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
  6. Computational Prediction of Protein-Protein Interactions, Dr. Krishna Praneeth Kilambi, 2015
  7. Next-Generation Antibody Modeling, Dr. Brian Weitzner, 2015

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