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    2017
  1. Alford RF, Leaver-Fay A, Jeliazkov JR, O'Meara MJ, DiMaio FD, Park H, Shapovalov MV, Renfrew PD, Mulligan VK, Kappel K, Labonte JW, Pacella MS, Bonneau R, Bradley P, Dunbrack RL, Das R, Baker D, Kuhlman B, Kortemme T & Gray JJ "The Rosetta all-atom energy function for macromolecular modeling and design," J. Chem. Theor. Comput. (Web) (2017) Online
  2. Jiang W, Pacella MS, Athansiadou D, Nelea V, Vali H, Hazen RM, Gray JJ, & McKee MD "Chiral acidic amino acids induce chiral hierarchical structure in calcium carbonate," Nature Communications 8 (2017)
  3. Labonte JW, Adolf-Bryfogle J, Schief WR, & Gray JJ "Residue-Centric Modeling and Design of Saccharide and Glycoconjugate Structures," J. Comput. Chem. 38(5) (2017) Online
  4. Weitzner BD, Jeliazkov JR, Lyskov S, Marze N, Kuroda D, Frick R, Adolf-Bryfogle A, Biswas N & Gray JJ "Modeling and docking antibody structures with Rosetta," Nature Protocols 12(2) (2017) Online
  5. 2016
  6. Marze, N. A. & Gray, J. J. "Improved Prediction of Antibody VL-VH Orientation," Protein Eng. Des. Sel. 29(10) (2016) Online
  7. Koehler Leman J., Muller K. & Gray J.J. "Expanding the toolkit for membrane protein modeling in Rosetta," Bioinformatics In Press (2016) Online
  8. Weitzner BD & Gray JJ "Accurate structure prediction of CDR H3 loops enabled by a novel structure-based C-terminal constraint," J. Immunol In Press (2016) Online
  9. Piepenbrik KH, Lillehoj E, Harding CM, Labonte JW, Zuo X, Rapp CA, Munson RS, Goldblum SE, Feldman MF, Gray JJ & Sundberg EJ "Structural diversity in the type IV pili of multidrug-resistant Acinetobacter," J. Biol. Chem. 291 (2016) Online
  10. Marze NA, Jeliazkov JR, Roy Burman SS, Boyken SE & Gray JJ "Modeling oblong proteins and water-mediated interfaces with RosettaDock in CAPRI rounds 28-35," Proteins Early View (2016) Online
  11. Kuroda, D & Gray, J.J. "Pushing the Backbone in Protein-Protein Docking," Structure 24(10) (2016) Online
  12. 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 84(51) (2016)
  13. Kuroda, D. & Gray, J. J. "Shape complementarity of hydrogen bond preferences in protein-protein interfaces: Implications for antibody modeling and protein-protein docking," Bioinformatics 32(16) (2016) Online
  14. 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. USA 113(19) (2016) Online (*these authors contriubted equally to this work)
  15. 2015
  16. 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) (2015) Online
  17. 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) (2015) Online
  18. 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) (2015) Online
  19. Functional Loss of Semaphorin 3C and/or Semaphorin 3D and Their Epistatic Interaction with Ret Are Critical to Hirschsprung Disease LiabilityJiang, 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) (2015) Online
  20. Weitzner, B. D., Dunbrack, R. & J. J. Gray. "The origin of CDR H3 structural diversity," Structure 23(2) (2015) Online
  21. J. Koehler Leman, M. B. Ulmschneider & J. J. Gray. "Computational Modeling of Membrane Proteins," Proteins 83(1) (2015) Online
  22. 2014
  23. Kilambi, K. P., Reddy, K. & J. J. Gray. "Protein-protein docking with dynamic residue protonation states," PLoS Computational Biology 10(12) (2014) Online
  24. 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) (2014) Online (*these authors contriubted equally to this work)
  25. A Comprehensive, High-Resolution Map of a Gene's Fitness LandscapeFirnberg, 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) (2014) Online
  26. 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) (2014) Online
  27. 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) (2014) Online
  28. 2013
  29. 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) (2013) Online
  30. 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 (2013) Online
  31. 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) (2013) Online
  32. 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) (2013) Online
  33. 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) (2013) Online
  34. 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) (2013) Online (*these authors contriubted equally to this work; ;co-corresponding authors)
  35. 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 (2013) Online
  36. 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) (2013) Online
  37. 2012
  38. 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) (2012) Online
  39. K. P. Kilambi and J. J. Gray "Rapid Calculation of Protein pKa Values using Rosetta," Biophys. J. 103(3) (2012) Online
  40. 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) (2012) Online
  41. 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) (2012) Online
  42. 2011
  43. 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) (2011) Online
  44. 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) (2011) Online
  45. Benchmarking and analysis of protein docking performance in RosettaDock 3.2S. 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) (2011) Online
  46. E. Baugh, S. Lyskov, B. D. Weitzner, & J. J. Gray "Real-time PyMOL visualization for Rosetta and PyRosetta," PLoS One 6(8) (2011) Online
  47. M. Berrondo & J. J. Gray "Computed structures of point deletion mutants and their enzymatic activities," Proteins 79(10) (2011) Online (Featured Cover Art)
  48. 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) (2011) Online (co-corresponding authors)
  49. Analysis and Modeling of the Variable Region of Camelid Single Domain AntibodiesA. 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) (2011) Online | Supplementary Material
  50. 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) (2011) Online (Featured Cover Art)
  51. 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 (2011) Online
  52. Mechanism of polyubiquitin chain recognition by the human ubiquitin conjugating enzyme Ube2g2W. 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) (2011) Online (co-corresponding authors)
  53. 2010
  54. 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) (2010) Online
  55. B. Keshet, J. J. Gray & T. A. Good "Structurally distinct toxicity inhibitors bind at common loci on beta-amyloid fibril," Prot. Sci. 19(12) (2010) Online
  56. 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) (2010) Online
  57. 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) (2010) Online
  58. M. Berrondo, J. J. Gray & R. Schleif "Computational predictions of the mutant behavior of AraC," J. Mol. Biol. 398(3) (2010) Online
  59. PyRosetta: a script-based interface for implementing molecular modeling algorithms using RosettaS. Chaudhury, S. Lyskov & J. J. Gray "PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta," Bioinformatics 26(5) (2010) Online
  60. 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) (2010) Online
  61. 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) (2010) Online
  62. 2009
  63. 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) (2009) Online
  64. 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 (2009) Online
  65. A. Sircar,* E. Kim* & J. J. Gray "RosettaAntibody: Antibody Variable Region Homology Modeling Server," Nucleic Acids Research 37(Web Server Issue) (2009) Online (*these authors contriubted equally to this work)
  66. D. L. Masica & J. J. Gray "Solution- and adsorbed-state structural ensembles predicted for the statherin-hydroxyapatite system," Biophys. J. 96(8) (2009) Online
  67. M.D. Daily & J. J. Gray "Allosteric communication occurs via networks of tertiary and quaternary motions in proteins," PLoS Comput. Biol. 5(2) (2009) Online
  68. Toward high-resolution homology modeling of antibody Fv regions and application to antibody-antigen docking 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) (2009) Online (*these authors contriubted equally to this work)
  69. 2008
  70. 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) (2008) Online
  71. S. Lyskov & J. J. Gray "The RosettaDock server for local protein-protein docking," Nucleic Acids Research 36(Web Server Issue) (2008) Online
  72. 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) (2008) Online
  73. Structure prediction of domain insertion proteins from structures of the individual domainsM. Berrondo, M. Ostermeier & J. J. Gray "Structure prediction of domain insertion proteins from structures of the individual domains," Structure 16(4) (2008) Online
  74. M.D. Daily, T.J. Upadhyaya & J. J. Gray "Contact rearrangements form coupled networks from local motions in allosteric proteins," Proteins 71(1) (2008) Online | Supplementary Material
  75. Modeling the structure of mAb 14B7 bound to the anthrax protective antigenA. Sivasubramanian, J. A. Maynard, & J. J. Gray "Modeling the structure of mAb 14B7 bound to the anthrax protective antigen," Proteins 70(1) (2008) Online
  76. 2007
  77. 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) (2007) Online
  78. 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) (2007) Online (*these authors contriubted equally to this work)
  79. 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) (2007) Online
  80. M. D. Daily & J. J. Gray "Local motions in a benchmark of allosteric proteins," Proteins 67(2) (2007) Online | Supplementary Material
  81. 2006
  82. Gray, J.J. "Biomolecular Modeling in a Process Dynamics and Control Course," Chemical Engineering Education 40(4) (2006) Online
  83. High-resolution protein-protein dockingGray, J.J. "High-resolution protein-protein docking," Curr. Op. Struct. Biol. 16(2) (2006) Online
  84. 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) (2006) Online
  85. 2005
  86. 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) (2005) Online
  87. 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) (2005) Online
  88. 2004
  89. Gray, J.J. "The Interaction of Proteins with Solid Surfaces," Curr. Op. Struct. Biol. 14(1) (2004) Online
  90. 2003
  91. 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) (2003) Online
  92. 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) (2003) Online
  93. 2001
  94. 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) (2001) Online
  95. Adsorption of colloidal particles by Brownian dynamics simulation: kinetics and surface structuresGray, J.J., R.T. Bonnecaze "Adsorption of colloidal particles by Brownian dynamics simulation: kinetics and surface structures," J. Chem. Phys. 114(3) (2001) Online
  96. Gray, J.J., R. T. Bonnecaze "Adsorption of charge-bidisperse mixtures of colloidal particles," Langmuir 17(25) (2001) Online
  97. 2000 & Older
  98. 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) (2000) Online
  99. Origin of anomalous multibody interactionsGray, J.J., B. Chiang, R.T. Bonnecaze "Origin of anomalous multibody interactions," Nature 402 (1999) Online (brief communication)
  100. Gray, J.J., R.T. Bonnecaze "Rheology and dynamics of sheared arrays of colloidal particles," J. Rheology 42(5) (1998) Online
  101. Lee, G.M., J.J. Gray, and B.O. Palsson "Effect of trisodium citrate treatment on hybridoma cell viability," Biotechnology Techniques 5(4) (1991)