Jeffrey J. Gray, Ph.D. - Publications

Affiliations: 
2002- Chemical & Biomolecular Engineering Johns Hopkins University, Baltimore, MD 
Area:
Protein docking, structure prediction and design, macromolecular assemblies
Website:
http://graylab.jhu.edu

80 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2015 Cocoros NM, Kleinman K, Priebe GP, Gray JE, Logan LK, Larsen G, Sammons J, Toltzis P, Miroshnik I, Horan K, Burton M, Sims S, Harper M, Coffin S, Sandora TJ, et al. Ventilator-Associated Events in Neonates and Children-A New Paradigm. Critical Care Medicine. PMID 26524075 DOI: 10.1097/CCM.0000000000001372  1
2015 Pierre B, Labonte JW, Xiong T, Aoraha E, Williams A, Shah V, Chau E, Helal KY, Gray JJ, Kim JR. Molecular Determinants for Protein Stabilization by Insertional Fusion to a Thermophilic Host Protein. Chembiochem : a European Journal of Chemical Biology. PMID 26391210 DOI: 10.1002/cbic.201500310  1
2015 Alford RF, Koehler Leman J, Weitzner BD, Duran AM, Tilley DC, Elazar A, Gray JJ. An Integrated Framework Advancing Membrane Protein Modeling and Design. Plos Computational Biology. 11: e1004398. PMID 26325167 DOI: 10.1371/journal.pcbi.1004398  1
2015 Jiang Q, Arnold S, Heanue T, Kilambi KP, Doan B, Kapoor A, Ling AY, Sosa MX, Guy M, Jiang Q, Burzynski G, West K, Bessling S, Griseri P, Amiel J, ... ... Gray JJ, et al. Functional loss of semaphorin 3C and/or semaphorin 3D and their epistatic interaction with ret are critical to Hirschsprung disease liability. American Journal of Human Genetics. 96: 581-96. PMID 25839327 DOI: 10.1016/j.ajhg.2015.02.014  1
2015 Weitzner BD, Dunbrack RL, Gray JJ. The origin of CDR H3 structural diversity. Structure (London, England : 1993). 23: 302-11. PMID 25579815 DOI: 10.1016/j.str.2014.11.010  1
2015 Koehler Leman J, Ulmschneider MB, Gray JJ. Computational modeling of membrane proteins. Proteins. 83: 1-24. PMID 25355688 DOI: 10.1002/prot.24703  1
2015 Matlahov I, Iline-Vul T, Abayev M, Lee EMY, Nadav-Tsubery M, Keinan-Adamsky K, Gray JJ, Goobes G. Interfacial Mineral-Peptide Properties of a Mineral Binding Peptide from Osteonectin and Bone-like Apatite Chemistry of Materials. 27: 5562-5569. DOI: 10.1021/acs.chemmater.5b01696  1
2014 Kilambi KP, Reddy K, Gray JJ. Protein-protein docking with dynamic residue protonation states. Plos Computational Biology. 10: e1004018. PMID 25501663 DOI: 10.1371/journal.pcbi.1004018  1
2014 Firnberg E, Labonte JW, Gray JJ, Ostermeier M. A comprehensive, high-resolution map of a gene's fitness landscape. Molecular Biology and Evolution. 31: 1581-92. PMID 24567513 DOI: 10.1093/molbev/msu081  1
2014 Weitzner BD, Kuroda D, Marze N, Xu J, Gray JJ. Blind prediction performance of RosettaAntibody 3.0: grafting, relaxation, kinematic loop modeling, and full CDR optimization. Proteins. 82: 1611-23. PMID 24519881 DOI: 10.1002/prot.24534  1
2014 Lensink MF, Moal IH, Bates PA, Kastritis PL, Melquiond AS, Karaca E, Schmitz C, van Dijk M, Bonvin AM, Eisenstein M, Jiménez-García B, Grosdidier S, Solernou A, Pérez-Cano L, Pallara C, ... ... Gray JJ, et al. Blind prediction of interfacial water positions in CAPRI. Proteins. 82: 620-32. PMID 24155158 DOI: 10.1002/prot.24439  1
2014 Xu J, Tack D, Hughes RA, Ellington AD, Gray JJ. Structure-based non-canonical amino acid design to covalently crosslink an antibody-antigen complex. Journal of Structural Biology. 185: 215-22. PMID 23680795 DOI: 10.1016/j.jsb.2013.05.003  1
2014 Chaikind B, Kilambi KP, Gray JJ, Ostermeier M. Correction: Targeted dna methylation using an artificially bisected m.hhai fused to zinc fingers (PLoS ONE) Plos One. 9. DOI: 10.1371/annotation/b1f48851-2dd7-438f-938e-6bac0b4d8c94  1
2013 Pacella MS, Koo da CE, Thottungal RA, Gray JJ. Using the RosettaSurface algorithm to predict protein structure at mineral surfaces. Methods in Enzymology. 532: 343-66. PMID 24188775 DOI: 10.1016/B978-0-12-416617-2.00016-3  1
2013 Kilambi KP, Pacella MS, Xu J, Labonte JW, Porter JR, Muthu P, Drew K, Kuroda D, Schueler-Furman O, Bonneau R, Gray JJ. Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20-27. Proteins. 81: 2201-9. PMID 24123494 DOI: 10.1002/prot.24425  1
2013 Drew K, Renfrew PD, Craven TW, Butterfoss GL, Chou FC, Lyskov S, Bullock BN, Watkins A, Labonte JW, Pacella M, Kilambi KP, Leaver-Fay A, Kuhlman B, Gray JJ, Bradley P, et al. Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design. Plos One. 8: e67051. PMID 23869206 DOI: 10.1371/journal.pone.0067051  1
2013 Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JP, Trellet M, Bonvin AM, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, ... ... Gray JJ, et al. Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions. Proteins. 81: 1980-7. PMID 23843247 DOI: 10.1002/prot.24356  1
2013 Der BS, Kluwe C, Miklos AE, Jacak R, Lyskov S, Gray JJ, Georgiou G, Ellington AD, Kuhlman B. Alternative computational protocols for supercharging protein surfaces for reversible unfolding and retention of stability. Plos One. 8: e64363. PMID 23741319 DOI: 10.1371/journal.pone.0064363  1
2013 Lyskov S, Chou FC, Conchúir SÓ, Der BS, Drew K, Kuroda D, Xu J, Weitzner BD, Renfrew PD, Sripakdeevong P, Borgo B, Havranek JJ, Kuhlman B, Kortemme T, Bonneau R, ... Gray JJ, et al. Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE). Plos One. 8: e63906. PMID 23717507 DOI: 10.1371/journal.pone.0063906  1
2013 Tarasevich BJ, Perez-Salas U, Masica DL, Philo J, Kienzle P, Krueger S, Majkrzak CF, Gray JL, Shaw WJ. Neutron reflectometry studies of the adsorbed structure of the amelogenin, LRAP. The Journal of Physical Chemistry. B. 117: 3098-109. PMID 23477285 DOI: 10.1021/jp311936j  1
2013 Leaver-Fay A, O'Meara MJ, Tyka M, Jacak R, Song Y, Kellogg EH, Thompson J, Davis IW, Pache RA, Lyskov S, Gray JJ, Kortemme T, Richardson JS, Havranek JJ, Snoeyink J, et al. Scientific benchmarks for guiding macromolecular energy function improvement. Methods in Enzymology. 523: 109-43. PMID 23422428 DOI: 10.1016/B978-0-12-394292-0.00006-0  1
2012 Chaikind B, Kilambi KP, Gray JJ, Ostermeier M. Targeted DNA Methylation Using an Artificially Bisected M.HhaI Fused to Zinc Fingers Plos One. 7. PMID 22984575 DOI: 10.1371/journal.pone.0044852  1
2012 Kilambi KP, Gray JJ. Rapid calculation of protein pKa values using rosetta Biophysical Journal. 103: 587-595. PMID 22947875 DOI: 10.1016/j.bpj.2012.06.044  1
2012 Ye Y, Stahley MR, Xu J, Friedman JI, Sun Y, McKnight JN, Gray JJ, Bowman GD, Stivers JT. Enzymatic excision of uracil residues in nucleosomes depends on the local DNA structure and dynamics. Biochemistry. 51: 6028-38. PMID 22784353 DOI: 10.1021/bi3006412  1
2012 Miklos AE, Kluwe C, Der BS, Pai S, Sircar A, Hughes RA, Berrondo M, Xu J, Codrea V, Buckley PE, Calm AM, Welsh HS, Warner CR, Zacharko MA, Carney JP, ... Gray JJ, et al. Structure-based design of supercharged, highly thermoresistant antibodies. Chemistry & Biology. 19: 449-55. PMID 22520751 DOI: 10.1016/j.chembiol.2012.01.018  1
2012 Roehrich A, Ash J, Zane A, Masica DL, Gray JJ, Goobes G, Drobny G. Solid-state NMR studies of biomineralization peptides and proteins Acs Symposium Series. 1120: 77-96. DOI: 10.1021/bk-2012-1120.ch004  1
2011 Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M, Terashi G, Moal IH, Li X, Bates PA, Zacharias M, Park H, ... ... Gray JJ, et al. Community-wide assessment of protein-interface modeling suggests improvements to design methodology. Journal of Molecular Biology. 414: 289-302. PMID 22001016 DOI: 10.1016/j.jmb.2011.09.031  1
2011 Berrondo M, Gray JJ. Computed structures of point deletion mutants and their enzymatic activities Proteins: Structure, Function and Bioinformatics. 79: 2844-2860. PMID 21905110 DOI: 10.1002/prot.23109  1
2011 Baugh EH, Lyskov S, Weitzner BD, Gray JJ. Real-time PyMOL visualization for Rosetta and PyRosetta Plos One. 6. PMID 21857909 DOI: 10.1371/journal.pone.0021931  1
2011 Masica DL, Gray JJ, Shaw WJ. Partial high-resolution structure of phosphorylated and non-phosphorylated leucine-rich amelogenin protein adsorbed to hydroxyapatite. The Journal of Physical Chemistry. C, Nanomaterials and Interfaces. 115: 13775-13785. PMID 21845207 DOI: 10.1021/jp202965h  1
2011 Chaudhury S, Berrondo M, Weitzner BD, Muthu P, Bergman H, Gray JJ. Benchmarking and analysis of protein docking performance in Rosetta v3.2. Plos One. 6: e22477. PMID 21829626 DOI: 10.1371/journal.pone.0022477  1
2011 Schrier SB, Sayeg MK, Gray JJ. Prediction of calcite morphology from computational and experimental studies of mutations of a de Novo-designed peptide Langmuir. 27: 11520-11527. PMID 21797243 DOI: 10.1021/la201904k  1
2011 Sircar A, Sanni KA, Shi J, Gray JJ. Analysis and modeling of the variable region of camelid single-domain antibodies Journal of Immunology. 186: 6357-6367. PMID 21525384 DOI: 10.4049/jimmunol.1100116  1
2011 McKee MD, Nakano Y, Masica DL, Gray JJ, Lemire I, Heft R, Whyte MP, Crine P, Millán JL. Enzyme replacement therapy prevents dental defects in a model of hypophosphatasia Journal of Dental Research. 90: 470-476. PMID 21212313 DOI: 10.1177/0022034510393517  1
2011 Leaver-Fay A, Tyka M, Lewis SM, Lange OF, Thompson J, Jacak R, Kaufman K, Renfrew PD, Smith CA, Sheffler W, Davis IW, Cooper S, Treuille A, Mandell DJ, Richter F, ... ... Gray JJ, et al. ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods in Enzymology. 487: 545-74. PMID 21187238 DOI: 10.1016/B978-0-12-381270-4.00019-6  1
2011 Bocik WE, Sircar A, Gray JJ, Tolman JR. Mechanism of polyubiquitin chain recognition by the human ubiquitin conjugating enzyme Ube2g2. The Journal of Biological Chemistry. 286: 3981-91. PMID 21098018 DOI: 10.1074/jbc.M110.189050  1
2010 Masica DL, Ash JT, Ndao M, Drobny GP, Gray JJ. Toward a structure determination method for biomineral-associated protein using combined solid- state NMR and computational structure prediction. Structure (London, England : 1993). 18: 1678-87. PMID 21134646 DOI: 10.1016/j.str.2010.09.013  1
2010 Keshet B, Gray JJ, Good TA. Structurally distinct toxicity inhibitors bind at common loci on β-amyloid fibril. Protein Science : a Publication of the Protein Society. 19: 2291-304. PMID 20882638 DOI: 10.1002/pro.509  1
2010 Masica DL, Schrier SB, Specht EA, Gray JJ. De novo design of peptide-calcite biomineralization systems Journal of the American Chemical Society. 132: 12252-12262. PMID 20712308 DOI: 10.1021/ja1001086  1
2010 Sircar A, Chaudhury S, Kilambi KP, Berrondo M, Gray JJ. A generalized approach to sampling backbone conformations with RosettaDock for CAPRI rounds 13-19 Proteins: Structure, Function and Bioinformatics. 78: 3115-3123. PMID 20535822 DOI: 10.1002/prot.22765  1
2010 Berrondo M, Gray JJ, Schleif R. Computational Predictions of the Mutant Behavior of AraC Journal of Molecular Biology. 398: 462-470. PMID 20338183 DOI: 10.1016/j.jmb.2010.03.021  1
2010 Sircar A, Gray JJ. SnugDock: Paratope structural optimization during antibody-antigen docking compensates for errors in antibody homology models Plos Computational Biology. 6. PMID 20098500 DOI: 10.1371/journal.pcbi.1000644  1
2010 Chaudhury S, Lyskov S, Gray JJ. PyRosetta: A script-based interface for implementing molecular modeling algorithms using Rosetta Bioinformatics. 26: 689-691. PMID 20061306 DOI: 10.1093/bioinformatics/btq007  1
2010 Addison WN, Masica DL, Gray JJ, McKee MD. Phosphorylation-dependent inhibition of mineralization by osteopontin ASARM peptides is regulated by PHEX cleavage Journal of Bone and Mineral Research. 25: 695-705. PMID 19775205 DOI: 10.1359/jbmr.090832  1
2009 Chaudhury S, Gray JJ. Identification of Structural Mechanisms of HIV-1 Protease Specificity Using Computational Peptide Docking: Implications for Drug Resistance Structure. 17: 1636-1648. PMID 20004167 DOI: 10.1016/j.str.2009.10.008  1
2009 Chien YC, Masica DL, Gray JJ, Nguyen S, Vali H, McKee MD. Modulation of calcium oxalate dihydrate growth by selective crystal-face binding of phosphorylated osteopontin and polyaspartate peptide showing occlusion by sectoral (compositional) zoning Journal of Biological Chemistry. 284: 23491-23501. PMID 19581305 DOI: 10.1074/jbc.M109.021899  1
2009 Sircar A, Kim ET, Gray JJ. RosettaAntibody: Antibody variable region homology modeling server Nucleic Acids Research. 37: W474-W479. PMID 19458157 DOI: 10.1093/nar/gkp387  1
2009 Masica DL, Gray JJ. Solution- and adsorbed-state structural ensembles predicted for the statherin-hydroxyapatite system Biophysical Journal. 96: 3082-3091. PMID 19383454 DOI: 10.1016/j.bpj.2009.01.033  1
2009 Daily MD, Gray JJ. Allosteric communication occurs via networks of tertiary and quaternary motions in proteins Plos Computational Biology. 5. PMID 19229311 DOI: 10.1371/journal.pcbi.1000293  1
2009 Sivasubramanian A, Sircar A, Chaudhury S, Gray JJ. Toward high-resolution homology modeling of antibody F v regions and application to antibody-antigen docking Proteins: Structure, Function and Bioinformatics. 74: 497-514. PMID 19062174 DOI: 10.1002/prot.22309  1
2008 Chaudhury S, Gray JJ. Conformer Selection and Induced Fit in Flexible Backbone Protein-Protein Docking Using Computational and NMR Ensembles Journal of Molecular Biology. 381: 1068-1087. PMID 18640688 DOI: 10.1016/j.jmb.2008.05.042  1
2008 Lyskov S, Gray JJ. The RosettaDock server for local protein-protein docking Nucleic Acids Research. 36: W233-238. PMID 18442991 DOI: 10.1093/nar/gkn216  1
2008 Berrondo M, Ostermeier M, Gray JJ. Structure Prediction of Domain Insertion Proteins from Structures of Individual Domains Structure. 16: 513-527. PMID 18400174 DOI: 10.1016/j.str.2008.01.012  1
2008 Pickin KA, Chaudhury S, Dancy BCR, Gray JJ, Cole PA. Analysis of protein kinase autophosphorylation using expressed protein ligation and computational modeling Journal of the American Chemical Society. 130: 5667-5669. PMID 18396877 DOI: 10.1021/ja711244h  1
2008 Daily MD, Upadhyaya TJ, Gray JJ. Contact rearrangements form coupled networks from local motions in allosteric proteins Proteins: Structure, Function and Genetics. 71: 455-466. PMID 17957766 DOI: 10.1002/prot.21800  1
2008 Sivasubramanian A, Maynard JA, Gray JJ. Modeling the structure of mAb 14B7 bound to the anthrax protective antigen. Proteins. 70: 218-30. PMID 17671962 DOI: 10.1002/prot.21595  1
2008 Masica D, Gray JJ. High-resolution adsorbed and solution-state ensembles of a naturally evolved biomineralization protein: Blind and nmr-guided predictions Aiche Annual Meeting, Conference Proceedings 1
2008 Berrondo M, Gray J. Computational predictions of the enzymatic activity of single deletion mutants Aiche Annual Meeting, Conference Proceedings 1
2008 Sivasubramanian A, Sircar A, Chaudhury S, Gray JJ. High-resolution homology modeling of antibody fv regions and application to antibody-antigen docking Aiche Annual Meeting, Conference Proceedings 1
2007 Makrodimitris K, Masica DL, Kim ET, Gray JJ. Structure prediction of protein-solid surface interactions reveals a molecular recognition motif of statherin for hydroxyapatite Journal of the American Chemical Society. 129: 13713-13722. PMID 17929924 DOI: 10.1021/ja074602v  1
2007 Chaudhury S, Sircar A, Sivasubramanian A, Berrondo M, Gray JJ. Incorporating biochemical information and backbone flexibility in RosettaDock for CAPRI rounds 6-12 Proteins: Structure, Function and Genetics. 69: 793-800. PMID 17894347 DOI: 10.1002/prot.21731  1
2007 Meitzler JL, Gray JJ, Hendrickson TL. Truncation of the caspase-related subunit (Gpi8p) of Saccharomyces cerevisiae GPI transamidase: Dimerization revealed Archives of Biochemistry and Biophysics. 462: 83-93. PMID 17475206 DOI: 10.1016/j.abb.2007.03.035  1
2007 Daily MD, Gray JJ. Local motions in a benchmark of allosteric proteins Proteins: Structure, Function and Genetics. 67: 385-399. PMID 17295319 DOI: 10.1002/prot.21300  1
2006 Gray JJ. High-resolution protein-protein docking Current Opinion in Structural Biology. 16: 183-193. PMID 16546374 DOI: 10.1016/j.sbi.2006.03.003  1
2006 Sivasubramanian A, Chao G, Pressler HM, Wittrup KD, Gray JJ. Structural model of the mAb 806-EGFR complex using computational docking followed by computational and experimental mutagenesis. Structure (London, England : 1993). 14: 401-14. PMID 16531225 DOI: 10.1016/j.str.2005.11.022  1
2006 Gray JJ. Biomolecular modeling in a process dynamics and control course Chemical Engineering Education. 40: 297-306.  1
2005 Daily MD, Masica D, Sivasubramanian A, Somarouthu S, Gray JJ. CAPRI rounds 3-5 reveal promising successes and future challenges for RosettaDock Proteins: Structure, Function and Genetics. 60: 181-186. PMID 15981262 DOI: 10.1002/prot.20555  1
2005 Singh P, Mhaka AM, Christensen SB, Gray JJ, Denmeade SR, Isaacs JT. Applying linear interaction energy method for rational design of noncompetitive allosteric inhibitors of the sarco- and endoplasmic reticulum calcium-ATPase. Journal of Medicinal Chemistry. 48: 3005-14. PMID 15828839 DOI: 10.1021/jm049319a  1
2005 Harrison RM, Gray JJ. Prediction of pKa shifts in proteins using a discrete rotamer search and the Rosetta energy function Aiche Annual Meeting, Conference Proceedings. 10466.  1
2005 Sivasubramanian A, Chao G, Wittrup KD, Gray JJ. Computational prediction of the mab 806-egfr complex structure by combining protein docking with computational and experimental mutagenesis Aiche Annual Meeting, Conference Proceedings. 8064.  1
2004 Gray JJ. The interaction of proteins with solid surfaces Current Opinion in Structural Biology. 14: 110-115. PMID 15102457 DOI: 10.1016/j.sbi.2003.12.001  1
2003 Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D. Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. Journal of Molecular Biology. 331: 281-99. PMID 12875852 DOI: 10.1016/S0022-2836(03)00670-3  1
2003 Gray JJ, Moughon SE, Kortemme T, Schueler-Furman O, Misura KM, Morozov AV, Baker D. Protein-protein docking predictions for the CAPRI experiment. Proteins. 52: 118-22. PMID 12784377 DOI: 10.1002/prot.10384  1
2001 Gray JJ, Bonnecaze RT. Adsorption of colloidal particles by Brownian dynamics simulation: Kinetics and surface structures Journal of Chemical Physics. 114: 1366-1381. DOI: 10.1063/1.1319317  1
2001 Gray JJ, Bonnecaze RT. Adsorption of charge-bidisperse mixtures of colloidal particles Langmuir. 17: 7935-7947. DOI: 10.1021/la0012844  1
2001 Gray JJ, Klein DH, Korgel BA, Bonnecaze RT. Microstructure formation and kinetics in the random sequential adsorption of polydisperse tethered nanoparticles modeled as hard disks Langmuir. 17: 2317-2328. DOI: 10.1021/la001029j  1
2000 Gray JJ, Klein DH, Bonnecaze RT, Korgel BA. Nonequilibrium phase behavior during the random sequential adsorption of tethered hard disks Physical Review Letters. 85: 4430-4433. DOI: 10.1103/PhysRevLett.85.4430  1
1999 Gray JJ, Chiang B, Bonnecaze RT. Origin of anomalous multibody interactions Nature. 402: 750.  1
1998 Gray JJ, Bonnecaze RT. Rheology and dynamics of sheared arrays of colloidal particles Journal of Rheology. 42: 1121-1151.  1
1991 Lee GM, Gray JJ, Palsson B. Effect of trisodium citrate treatment on hybridoma cell viability Biotechnology Techniques. 5: 295-298. DOI: 10.1007/BF02438666  1
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