Gray, Jeffrey

Professor
Chemical And Biomolecular Engineering
http://graylab.jhu.edu

Maryland Hall 208
(410) 516-5313
jgray@jhu.edu

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News

ChemBE’s Jeff Gray wins AIChE’s Himmelblau Award

July 13, 2016

Jeffrey Gray, professor in the Department of Chemical and Biomolecular Engineering, has been selected as this year’s recipient of the American Institute for Chemical Engineers’ David Himmelblau Award for Innovations in Computer-Based Chemical Engineering Education. This prestigious award is bestowed annually by AIChE’s Computing & Systems Technology Division to a person or group making new […]

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Student researchers collaborate virtually with help of open-source software

July 29, 2015

A summer research internship for undergraduates is not only helping them learn to build new lifesaving drug molecules and create new biofuels—it’s also testing the concept of a virtual research community. The Johns Hopkins Institute for NanoBioTechnology—with the help of a $200,000, two-year grant from the National Science Foundation—has launched a first-of-its-kind training program in […]

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About

Education
  • Ph.D. 2000, UNIV TEXAS AUSTIN*
Experience
  • 2015 - Present:  Director, NSF Research Experience for Undergraduates (REU) Program for the Rosetta Commons
  • 2013 - 2016:  Co-Chair, Faculty Diversity Subcommittee; Member, Family Support Subcommittee, Diversity Leadership Council
  • 2011 - Present:  Director, ChemBE
  • 2011 - 2012:  Director, ChemBE
  • 2009 - 2012:  Senior Editor, ChemBE Bond Department Alumni Newsletter
  • 2007 - 2007:  Co-Chair, International Conference on Biomolecular Engineering
  • 2006 - 2006:  Co-leader, Computational Biophysics Journal Club
  • 2006 - 2006:  Society for Biological Engineering, Society for Biological Engineering
  • 2005 - 2005:  Director, Ingenuity Project
  • 2005 - 2005:  Co-Chair, Rosetta
  • 2005 - Present:  Joint, SOM Oncology Center
  • 2004 - 2004:  Project Manager, Rosetta Biomolecular Modeling Suite C++ Conversion and Modernization Project
  • 2004 - 2004:  Co-Chair, Rosetta
  • 2003 - 2004:  Editorial Manager, Proteins
Awards
  • 2017:  JHU Provost Discovery Award
  • 2017:  JHU STAR Award - P. Stanley (*A student advised by J. Gray)
  • 2017:  NIH Ruth L. Kirschstein Graduate Fellowship - J. Jeliazko (*Student advised by Jeff Gray)
  • 2016:  Himmelblau Award for Innovations in Computer-Based Chemical Engineering Education
  • 2016:  AIMBE College of Fellows
  • 2015:  Plenary Lecturer
  • 2015:  Centennial Lecturer
  • 2011:  Fisher Award for Undergraduate Research in Cancer - M.-Y. Lee (*student advised by Jeff Gray)
  • 2011:  F. Stuart Hodgson Faculty Scholar
  • 2010:  Provost's Undergraduate Research Award - M.-Y. Lee (*Student Advised by Jeff Gray)
  • 2010:  NSF Graduate Research Fellowship Honorable Mention - S. Schrier (Attending MIT; *Undergraduate advised by J. Gray)
  • 2010:  NSF Graduate Research Fellowship - R. Harrison (To attend Oxford; *Undergraduate advised by J. Gray)
  • 2009:  NSF CAREER Award
  • 2008:  JHU Center for Educational Resources Technology Fellowship - J.D. Bagert & Julian Rosenberg - 2008 (*Student Advised by Jeff Gray)
  • 2007:  Genentech Second Place Poster Award - 1st International Conference on Biomolecular Engineering - D. Masica - 2007 (*Student advised by Jeff Gray)
  • 2007:  Provost's Undergraduate Research Award - E. Kim - 2007 (*Student Advised by Jeff Gray)
  • 2007:  NIH Ruth L. Kirschstein Graduate Fellowship - M. Berrondo - 2007-2011 (*Student advised by Jeff Gray)
  • 2006:  Undergraduate lab members Elizabeth Specht and Sarah Schrier shared an Elenora Streb Muly Award
  • 2006:  JHU Alumni Association Excellence in Teaching Award
  • 2005:  Intel Science Talent Search Finalist awarded to lab member Ryan Harrison (12th grade student)
  • 2005:  Beckman Foundation Young Investigator Award
  • 2003:  Nominee (disqualified due to young age) for JHU Whiting School teaching award
  • 2002:  International Society for Computational Biology travel fellowship
  • 2002:  NIH K01 Mentored Quantitative Research Fellowship in Genomics
  • 2000:  University of Texas Outstanding Doctoral Dissertation - Honorable Mention
Presentations
  • "Predicting and engineering protein complex structures, from antibodies to glycoproteins,”", Chemical Engineering Department Seminar.  Boulder Colorado, United States of America (the).  September 1, 2018
  • "Repertoire Analysis of Antibody CDR-H3 Loops Suggests Affinity Maturation Does Not Typically Result in Rigidification", 14th Annual PEGS: The Protein Engineering Summit.  Boston Maryland, United States of America (the).  April 30, 2018
  • "Predicting and engineering protein complex structures, from antibodies to glycoproteins,”", Chemical Engineering Department Seminar.  Tempe Arizona, United States of America (the).  April 16, 2018
  • "Predicting and engineering protein complex structures, from antibodies to glycoproteins", Chemical Engineering Department Seminar.  Worcester Massachusetts, United States of America (the).  April 11, 2018
  • "Computational Design of High-Resolution Protein Crystals", Biophysical Society Annual Meeting.  San Francisco California, United States of America (the).  February 21, 2018
  • "Fast Implicit Potentials for Accurate Prediction and Design of Membrane Protein Structures", Biophysical Society Annual Meeting.  San Francisco California, United States of America (the).  February 19, 2018
  • "Efficient Flexible-Backbone Docking of Challenging Protein Complexes", Biophysical Society Annual Meeting.  San Francisco California, United States of America (the).  February 19, 2018
  • "Evolution of CDR H3 Flexibility at an Immunomic Scale", Biophysical Society Annual Meeting.  San Francisco California, United States of America (the).  February 19, 2018
  • "Flexible-Backbone Protein Docking Using Motif Scoring and Large Conformational Ensembles", AlChE Annual Meeting.  Minneapolis Minnesota, United States of America (the).  November 1, 2017
  • "Predicting and Engineering Protein Complex Structures, from Antibodies to Glycoproteins", AlChE Annual Meeting.  Minneapolis Minnesota, United States of America (the).  November 1, 2017
  • "Computation of Amino Acid-Mineral Surface Thermodynamics and Interaction Modes via Importance Sampling", AIChE Annual Meeting.  Minneapolis Minnesota, United States of America (the).  November 1, 2017
  • "Efficient flexible-backbone protein docking using motif scoring of large conformational ensembles", RosettaCon XV.  Leavenworth Washington, United States of America (the).  August 9, 2017
  • "What’s in Pandora’s box? A guide to the Rosetta energy function", RosettaCon XV.  Leavenworth Washington, United States of America (the).  August 8, 2017
  • "RosettaCarbohydrate: A Framework for Residue-Centric Modeling and Design of Saccharide and Glycoconjugate Structures", Carbohydrates Gordon Research Conference.  West Dover Vermont, United States of America (the).  June 26, 2017
  • "Biomolecular Structure Prediction, Docking and Design", University of New Hampshire Annual Symposium in Bioengineering.  Durham New Hampshire, United States of America (the).  May 10, 2017
  • "Modeling and Docking Antibody Structures with Rosetta", PEGS: Protein Engineering Summit.  Boston Massachusetts, United States of America (the).  May 3, 2017
  • "A Deep Dive into the Rosetta Energy Function for Biological Macromolecules", Biophysical Society Annual Meeting.  New Orleans Louisiana, United States of America (the).  February 13, 2017
  • "Pushing the Backbone in Protein-Protein Docking", "Chalk it up to Biophysics" Seminar Series.  Baltimore.  December 14, 2016
  • "Structural Modeling of Glycoproteins and Protein-Sugar Complexes".  Gaithersburg, MD.  June 20, 2016
  • "Accurate global docking in RosettaDock is masked by difficult multi-domain targets in CAPRI rounds 31-35Accurate global docking in RosettaDock is masked by difficult multi-domain targets in CAPRI rounds 31-35", 6th CAPRI Evaluation Meeting.  Tel Aviv, Israel.  April 17, 2016
  • "Computational Protein Engineering of Crystal Growth, Membrane Proteins, and Glycoproteins".  Newark, DE.  March 23, 2016
  • "Toward the Rational Design of Antibodies with Improved Therapeutic Potential", Society for Glycobiology Annual Meeting.  San Francisco.  December 1, 2015
  • "Proteins Dancing the Texas Two-Step", Centennial Lecture Series.  Austin, TX.  December 1, 2015
  • "RosettaCarbohydrates: Expanding the computational tools available to glycoscientists", Society for Glycobiology Annual Meeting.  San Francisco.  December 1, 2015
  • "Toward Structure Prediction and Design of Protein Glycosylations", AIChE Annual Meeting.  Salt Lake City.  November 1, 2015
  • "Modeling chiral recognition between amino acids and vaterite surfaces", AIChE Annual Meeting.  Salt Lake City.  November 1, 2015
  • "How Proteins Dance with their Partners", Inaugural Professorial Lecture.  Baltimore, MD.  September 1, 2015
  • "RosettaCarbohydrates: Expanding the Computational Tools Available to Glycoscientists", RosettaCon XIII.  Leavenworth, WA.  August 1, 2015
  • "The origin of CDR H3 structural diversity", RosettaCon XIII.  Leavenworth, WA.  August 1, 2015
  • "Toward structure prediction and design of protein glycosylations", Biochemical and Molecular Engineering XIX.  Puerto Vallarta, Mexico.  July 1, 2015
  • "Teaching Biomolecular Structure Prediction and Design with PyRosetta", Biochemical and Molecular Engineering XIX.  Puerto Vallarta, Mexico.  July 1, 2015
  • "Design and Structure Prediction of Proteins that Control Biomineralization", "From Biomineralization to Materials Science” Seminar Series.  Dresden, Germany.  June 1, 2015
  • "Producing physically realistic structural models with RosettaAntibody", Americas Antibody Congress.  San Diego.  May 1, 2015
  • "Rosetta-MPDock: A novel computational tool for protein-protein docking within the membrane bilayer", Biophysical Society Annual Meeting.  Baltimore, MD.  February 1, 2015
  • "The origin of CDR H3 structural diversity", Biophysical Society Annual Meeting.  Baltimore, MD.  February 1, 2015
  • "Docking and design of oligosaccharides, glycoproteins, and glycolipids: Expanding the computational tools available to glycoscientists", Joint Meeting of the Society for Glycobiology and the Japanese Society of Carbohydrate Research.  Honolulu.  November 19, 2014
  • "Computational Molecular Biophysics: Design Your Future", Grace Hopper Celebration of Women in Computing.  Pheonix, AZ.  October 8, 2014
  • "Computational Design of Peptides to Control Calcite Growth", Gordon Research Conference on Biomineralization.  New London, NH.  August 20, 2014
  • "Diversity Efforts within the Rosetta Commons", Rosetta Conference.  Leavenworth, WA.  August 1, 2014
  • "Computational design of peptides to control calcite growth", Gordon Research Conference on Biomineralization.  New London, NH.  August 1, 2014
  • "Chiral acidic amino acids induce biomineral chirality: Effects of L- and D- Asp and Glu on calcium carbonate (vaterite) growth", Gordon Research Conference on Biomineralization.  New London, NH.  August 1, 2014
  • "Experimental characterization of peptides to control calcite growth", Gordon Research Conference on Biomineralization.  New London, NH.  August 1, 2014
  • "Applying Rosetta to Antibody Loop Modeling and Docking", Protein Engineering Summit (PEGS).  Boston, MA.  May 6, 2014

Publications

Journal Articles
  • Kalin JH, Wu M, Gomez AV, Song Y, Das J, Hayward D, Adejola N, Wu M, Panova I, Chung HJ, Kim E, Roberts HJ, Roberts JM, Prusevich P, Jeliazkov JR, Roy Burman SS, Fairall L, Milano C, Eroglu A, Proby C... (2018).  Targeting the CoREST complex with dual histone deacetylase and demethylase inhibitors.  Nature Communications.  9(1).
  • Lubin JH, Pacella MS, Gray JJ (2018).  A Parametric Rosetta Energy Function Analysis with LK Peptides on SAM Surfaces.  Langmuir.  34(18).
  • Athanasiadou D, Jiang W, Goldbaum D, Saleem A, Basu K, Pacella MS, Böhm CF, Chromik RR, Hincke MT, Rodríguez-Navarro AB, Vali H, Wolf SE, Gray JJ, Bui KH, McKee MD (2018).  Nanostructure, osteopontin, and mechanical properties of calcitic avian eggshell.  Science Advances.  4(3).
  • Jeliazkov JR, Sljoka A, Kuroda D, Tsuchimura N, Katoh N, Tsumoto K, Gray JJ (2018).  Repertoire analysis of antibody CDR-H3 loops suggests affinity maturation does not typically result in rigidification.  Frontiers in Immunology.  9(MAR).
  • Koehler Leman J, D'Avino AR, Bhatnagar Y, Gray JJ (2018).  Comparison of NMR and crystal structures of membrane proteins and computational refinement to improve model quality.  Proteins: Structure, Function and Bioinformatics.  86(1).
  • Moretti R, Lyskov S, Das R, Meiler J, Gray JJ (2018).  Web-accessible molecular modeling with Rosetta: The Rosetta Online Server that Includes Everyone (ROSIE).  Protein Science.  27(1).
  • Alford RF, Leaver-Fay A, Gonzales L, Dolan EL, Gray JJ (2017).  A cyber-linked undergraduate research experience in computational biomolecular structure prediction and design.  PLoS computational biology.  13(12).
  • Kilambi KP, Gray JJ (2017).  Structure-based cross-docking analysis of antibody-antigen interactions.  Scientific Reports.  7(1).
  • Santiago-Frangos A, Jeliazkov JR, Gray JJ, Woodson SA (2017).  Acidic C-terminal domains autoregulate the RNA chaperone Hfq.  eLife.  6.
  • Alford RF, Leaver-Fay A, Jeliazkov JR, O'Meara MJ, DiMaio FP, Park H, Shapovalov MV, Renfrew PD, Mulligan VK, Kappel K, Labonte JW, Pacella MS, Bonneau R, Bradley P, Dunbrack RL, Das R, Baker D, Kuhlm... (2017).  The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design.  Journal of Chemical Theory and Computation.  13(6).
  • Jiang W, Pacella MS, Athanasiadou D, Nelea V, Vali H, Hazen RM, Gray JJ, McKee MD (2017).  Chiral acidic amino acids induce chiral hierarchical structure in calcium carbonate.  Nature Communications.  8.
  • Marze NA, Jeliazkov JR, Roy Burman SS, Boyken SE, DiMaio F, Gray JJ (2017).  Modeling oblong proteins and water-mediated interfaces with RosettaDock in CAPRI rounds 28–35.  Proteins: Structure, Function and Bioinformatics.  85(3).
  • Labonte JW, Adolf-Bryfogle J, Schief WR, Gray JJ (2017).  Residue-centric modeling and design of saccharide and glycoconjugate structures.  Journal of Computational Chemistry.  38(5).
  • Newman HA, Meluh PB, Lu J, Vidal J, Carson C, Lagesse E, Gray JJ, Boeke JD, Matunis MJ (2017).  A high throughput mutagenic analysis of yeast sumo structure and function.  PLoS Genetics.  13(2).
  • Weitzner BD, Jeliazkov JR, Lyskov S, Marze N, Kuroda D, Frick R, Adolf-Bryfogle J, Biswas N, Dunbrack RL, Gray JJ (2017).  Modeling and docking of antibody structures with Rosetta.  Nature Protocols.  12(2).
  • Pacella MS, Gray JJ (2017).  A Benchmark Study of Peptide-Biomineral Interactions.  Crystal Growth and Design.  (2).
  • Mathew MP, Tan E, Labonte JW, Shah S, Saeui CT, Liu L, Bhattacharya R, Bovonratwet P, Gray JJ, Yarema KJ (2017).  Glycoengineering of Esterase Activity through Metabolic Flux-Based Modulation of Sialic Acid.  ChemBioChem.
  • Weitzner BD, Gray JJ (2017).  Accurate structure prediction of CDR H3 loops enabled by a novel structure-based C-terminal constraint.  Journal of Immunology.  198(1).
  • Leman JK, Mueller BK, Gray JJ (2017).  Expanding the toolkit for membrane protein modeling in Rosetta.  Bioinformatics.  33(5).
  • Mathew MP, Tan E, Labonte JW, Shah S, Saeui CT, Liu L, Bhattacharya R, Bovonratwet P, Gray JJ, Yarema KJ (2017).  Glycoengineering of Esterase Activity through Metabolic Flux-Based Modulation of Sialic Acid.  ChemBioChem.  (13).
  • Koehler Leman J, Mueller BK, Gray J (2016).  Expanding the toolkit for membrane protein modeling in Rosetta..  Bioinformatics (Oxford, England).
  • Piepenbrink KH, Lillehoj E, Harding CM, Labonte JW, Zuo X, Rapp CA, Munson RS, Goldblum SE, Feldman MF, Gray JJ, Sundberg EJ (2016).  Structural diversity in the type IV Pili of multidrug-resistant acinetobacter.  Journal of Biological Chemistry.  291(44).
  • Piepenbrink KH, Lillehoj E, Harding CM, Labonte J, Zuo X, Rapp CA, Munson, Jr RS, Goldblum SE, Feldman M, Gray J, Sundberg EJ (2016).  Structural Diversity in the Type IV Pili of Multidrug-resistant Acinetobacter..  The Journal of biological chemistry.  291(44).  22924-22935.
  • Kuroda D, Gray J (2016).  Pushing the Backbone in Protein-Protein Docking..  Structure (London, England : 1993).  24(10).  1821-1829.
  • Kuroda D, Gray JJ (2016).  Pushing the Backbone in Protein-Protein Docking.  Structure.  24(10).
  • Marze NA, Lyskov S, Gray JJ (2016).  Improved prediction of antibody VL-VH orientation.  Protein Engineering, Design and Selection.  29(10).
  • Marze NA, Lyskov S, Gray J (2016).  Improved prediction of antibody VL-VH orientation..  Protein engineering, design & selection : PEDS.  29(10).  409-18.
  • Lensink MF, Velankar S, Kryshtafovych A, Huang S, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie Lee G, Seok C, Qin S, Zhou HX, Ritchie DW, Maigret B, D... (2016).  Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment..  Proteins.  84 Suppl 1.  323-48.
  • Kuroda D, Gray JJ (2016).  Shape complementarity and hydrogen bond preferences in protein-protein interfaces: Implications for antibody modeling and protein-protein docking.  Bioinformatics.  32(16).
  • Kuroda D, Gray J (2016).  Shape complementarity and hydrogen bond preferences in protein-protein interfaces: implications for antibody modeling and protein-protein docking..  Bioinformatics (Oxford, England).  32(16).  2451-6.
  • DeKosky BJ, Lungu OI, Park D, Johnson EL, Charab W, Chrysostomou C, Kuroda D, Ellington AD, Ippolito GC, Gray JJ, Georgiou G (2016).  Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires.  Proceedings of the National Academy of Sciences of the United States of America.  113(19).
  • DeKosky BJ, Lungu OI, Park D, Johnson EL, Charab W, Chrysostomou C, Kuroda D, Ellington AD, Ippolito GC, Gray J, Georgiou G (2016).  Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires..  Proceedings of the National Academy of Sciences of the United States of America.  113(19).  E2636-45.
  • Lensink MF, Velankar S, Kryshtafovych A, Huang SY, Schneidman-Duhovny D, Sali A, Segura J, Fernandez-Fuentes N, Viswanath S, Elber R, Grudinin S, Popov P, Neveu E, Lee H, Baek M, Park S, Heo L, Rie Le... (2016).  Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.  Proteins: Structure, Function and Bioinformatics.
  • Pierre B, Labonte J, Xiong T, Aoraha E, Williams A, Shah V, Chau E, Helal KY, Gray J, Kim J (2015).  Molecular Determinants for Protein Stabilization by Insertional Fusion to a Thermophilic Host Protein..  Chembiochem : a European journal of chemical biology.  16(16).  2392-402.
  • Pierre B, Labonte JW, Xiong T, Aoraha E, Williams A, Shah V, Chau E, Helal KY, Gray JJ, Kim JR (2015).  Molecular Determinants for Protein Stabilization by Insertional Fusion to a Thermophilic Host Protein.  ChemBioChem.  16(16).
  • Alford RF, Koehler Leman J, Weitzner BD, Duran AM, Tilley DC, Elazar A, Gray J (2015).  An Integrated Framework Advancing Membrane Protein Modeling and Design..  PLoS computational biology.  11(9).  e1004398.
  • Matlahov I, Iline-Vul T, Abayev M, Lee EMY, Nadav-Tsubery M, Keinan-Adamsky K, Gray JJ, Goobes G (2015).  Interfacial Mineral-Peptide Properties of a Mineral Binding Peptide from Osteonectin and Bone-like Apatite.  Chemistry of Materials.  27(16).
  • 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, Fernandez RM, Verheij JB, Hofstra RM, Borrego S, Lyonnet S, Ceccherini I, Gray J, Pachnis V, McCallion AS,... (2015).  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(4).  581-96.
  • Weitzner BD, Dunbrack, Jr RL, Gray J (2015).  The origin of CDR H3 structural diversity..  Structure (London, England : 1993).  23(2).  302-11.
  • Weitzner BD, Dunbrack RL, Gray JJ (2015).  The origin of CDR H3 structural diversity.  Structure.  23(2).
  • Weitzner BD, Dunbrack RL, Gray J (2015).  The Origin of CDR H3 Structural Diversity.  Structure.
  • Koehler Leman J, Ulmschneider MB, Gray JJ (2015).  Computational modeling of membrane proteins.  Proteins: Structure, Function and Bioinformatics.  83(1).
  • Labonte J, Gray J (2015).  Docking and Design of Oligosaccharides, Glycoproteins, and Glycolipids.  Biophysical Journal.  108(2).  470a.
  • 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, Fernandez RM, Verheij JBGM, Hofstra RMW, Borrego S, Ly... (2015).  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(4).
  • Alford RF, Koehler Leman J, Weitzner BD, Duran AM, Tilley DC, Elazar A, Gray JJ (2015).  An Integrated Framework Advancing Membrane Protein Modeling and Design.  PLoS Computational Biology.  11(9).
  • Leman JK, Alford RF, Gray J (2015).  Rosetta-MPDock: A Novel Computational Tool for Protein-Protein Docking within the Membrane Bilayer.  Biophysical Journal.  108(2).  250a.
  • Koehler Leman J, Ulmschneider M, Gray J (2015).  Computational modeling of membrane proteins..  Proteins.  83(1).  1-24.
  • Roy Burman SS, Pacella MS, De Yoreo JJ, Gray J (2015).  Characterization of Peptides Designed to Control Crystal Nucleation and Growth.  Biophysical Journal.  108(2).  633a.
  • Matlahov I, Iline-Vul T, Abayev M, Lee EM, Nadav-Tsubery M, Keinan-Adamsky K, Gray J, Goobes G (2015).  Interfacial Mineral-Peptide Properties of a Mineral Binding Peptide from Osteonectin and Bone-like Apatite.  Chemistry of Materials.  27(16).  5562-5569.
  • Leman JK, Ulmschneider M, Gray J (2015).  Computational modeling of membrane proteins.  Proteins-Structure Function and Bioinformatics.  83(1).  1-24.
  • Firnberg E, Labonte J, Gray J, Ostermeier M (2014).  A comprehensive, high-resolution map of a gene's fitness landscape..  Molecular Biology and Evolution.  31(6).  1581-92.
  • Xu J, Tack D, Hughes RA, Ellington AD, Gray JJ (2014).  Structure-based non-canonical amino acid design to covalently crosslink an antibody-antigen complex.  Journal of Structural Biology.  185(2).
  • Weitzner BD, Kuroda D, Marze N, Xu J, Gray J (2014).  Blind prediction performance of RosettaAntibody 3.0: grafting, relaxation, kinematic loop modeling, and full CDR optimization.  Proteins: Structure, Function, and Bioinformatics.  82(8).  1611-1623.
  • Kilambi KP, Reddy K, Gray JJ (2014).  Protein-Protein Docking with Dynamic Residue Protonation States.  PLoS Computational Biology.  10(12).
  • Xu J, Tack D, Hughes RA, Ellington AD, Gray J (2014).  Structure-based non-canonical amino acid design to covalently crosslink an antibody-antigen complex.  Journal of structural biology.  185(2).  215-222.
  • Firnberg E, Labonte JW, Gray JJ, Ostermeier M (2014).  A comprehensive, high-resolution map of a Gene's fitness landscape.  Molecular Biology and Evolution.  31(6).
  • Lensink MF, Moal IH, Bates PA, Kastritis PL, Melquiond ASJ, Karaca E, Schmitz C, van Dijk M, Bonvin AMJJ, Eisenstein M, Jiménez-García B, Grosdidier S, Solernou A, Pérez-Cano L, Pallara C, Fernández-R... (2014).  Blind prediction of interfacial water positions in CAPRI.  Proteins: Structure, Function and Bioinformatics.  82(4).
  • Weitzner BD, Kuroda D, Marze N, Xu J, Gray JJ (2014).  Blind prediction performance of RosettaAntibody 3.0: Grafting, relaxation, kinematic loop modeling, and full CDR optimization.  Proteins: Structure, Function and Bioinformatics.  82(8).
  • Kilambi KP, Reddy K, Gray J (2014).  Protein-Protein Docking with Dynamic Residue Protonation States.  PLoS computational biology.  10(12).  e1004018.
  • Kilambi KP, Pacella MS, Xu J, Labonte JW, Porter JR, Muthu P, Drew K, Kuroda D, Schueler-Furman O, Bonneau R, Gray JJ (2013).  Extending RosettaDock with water, sugar, and pH for prediction of complex structures and affinities for CAPRI rounds 20-27.  Proteins: Structure, Function and Bioinformatics.  81(12).
  • Pacella MS, Koo DCE, Thottungal RA, Gray JJ (2013).  Using the Rosetta surface algorithm to predict protein structure at mineral surfaces.  Methods in Enzymology.  532.
  • Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JPGLM, Trellet M, Bonvin AMJJ, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, Perez-Cano L, Pallara C, J... (2013).  Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions.  Proteins: Structure, Function and Bioinformatics.  81(11).
  • 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, Kirshenbaum K, Arora PS, Das R, ... (2013).  Adding Diverse Noncanonical Backbones to Rosetta: Enabling Peptidomimetic Design.  PLoS ONE.  8(7).
  • Der BS, Kluwe C, Miklos AE, Jacak R, Lyskov S, Gray JJ, Georgiou G, Ellington AD, Kuhlman B (2013).  Alternative Computational Protocols for Supercharging Protein Surfaces for Reversible Unfolding and Retention of Stability.  PLoS ONE.  8(5).
  • Lyskov S, Chou FC, Conchúir SO, 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, Das R (2013).  Serverification of Molecular Modeling Applications: The Rosetta Online Server That Includes Everyone (ROSIE).  PLoS ONE.  8(5).
  • Tarasevich BJ, Perez-Salas U, Masica DL, Philo J, Kienzle P, Krueger S, Majkrzak CF, Gray JL, Shaw WJ (2013).  Neutron reflectometry studies of the adsorbed structure of the amelogenin, LRAP.  Journal of Physical Chemistry B.  117(11).
  • 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, Baker D, Kuhlman B (2013).  Scientific benchmarks for guiding macromolecular energy function improvement.  Methods in Enzymology.  523.
  • Roehrich A, Ash J, Zane A, Masica DL, Gray JJ, Goobes G, Drobny G (2012).  Solid-state NMR studies of biomineralization peptides and proteins.  ACS Symposium Series.  1120.
  • Chaikind B, Kilambi KP, Gray JJ, Ostermeier M (2012).  Targeted DNA Methylation Using an Artificially Bisected M.HhaI Fused to Zinc Fingers.  PLoS ONE.  7(9).
  • Kilambi KP, Gray JJ (2012).  Rapid calculation of protein pKa values using rosetta.  Biophysical Journal.  103(3).
  • Ye Y, Stahley MR, Xu J, Friedman JI, Sun Y, McKnight JN, Gray JJ, Bowman GD, Stivers JT (2012).  Enzymatic excision of uracil residues in nucleosomes depends on the local DNA structure and dynamics.  Biochemistry.  51(30).
  • 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, Georgiou G, Kuhlman B, Ellington AD (2012).  Structure-based design of supercharged, highly thermoresistant antibodies.  Chemistry and Biology.  19(4).
  • Chaikind B, Kilambi KP, Gray J, Ostermeier M (2012).  Targeted DNA methylation using an artificially bisected M.HhaI fused to zinc fingers.  PLoS One.  7(9).  e44852.
  • Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ONA, Takeda-Shitaka M, Terashi G, Moal IH, Li X, Bates PA, Zacharias M, Park H, Ko JS, Lee H, Seok C, Bourquard ... (2011).  Community-wide assessment of protein-interface modeling suggests improvements to design methodology.  Journal of Molecular Biology.  414(2).
  • Berrondo M, Gray JJ (2011).  Computed structures of point deletion mutants and their enzymatic activities.  Proteins: Structure, Function and Bioinformatics.  79(10).
  • Schrier SB, Sayeg MK, Gray JJ (2011).  Prediction of calcite morphology from computational and experimental studies of mutations of a de Novo-designed peptide.  Langmuir.  27(18).
  • Baugh EH, Lyskov S, Weitzner BD, Gray JJ (2011).  Real-time PyMOL visualization for Rosetta and PyRosetta.  PLoS ONE.  6(8).
  • Chaudhury S, Berrondo M, Weitzner BD, Muthu P, Bergman H, Gray JJ (2011).  Benchmarking and analysis of protein docking performance in Rosetta v3.2.  PLoS ONE.  6(8).
  • Masica DL, Gray JJ, Shaw WJ (2011).  Partial High-resolution structure of phosphorylated and non-phosphorylated leucine-rich amelogenin protein adsorbed to hydroxyapatite.  Journal of Physical Chemistry C.  115(28).
  • Sircar A, Sanni KA, Shi J, Gray JJ (2011).  Analysis and modeling of the variable region of camelid single-domain antibodies.  Journal of Immunology.  186(11).
  • McKee MD, Nakano Y, Masica DL, Gray JJ, Lemire I, Heft R, Whyte MP, Crine P, Millán JL (2011).  Enzyme replacement therapy prevents dental defects in a model of hypophosphatasia.  Journal of Dental Research.  90(4).
  • Bocik WE, Sircar A, Gray JJ, Tolman JR (2011).  Mechanism of polyubiquitin chain recognition by the human ubiquitin conjugating enzyme Ube2g2.  Journal of Biological Chemistry.  286(5).
  • 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, Ban YEA, Fleishman SJ, Corn JE, Kim D... (2011).  Rosetta3: An object-oriented software suite for the simulation and design of macromolecules.  Methods in Enzymology.  487(C).
  • Masica DL, Ash JT, Ndao M, Drobny GP, Gray JJ (2010).  Toward a structure determination method for biomineral-associated protein using combined solid- State NMR and computational structure prediction.  Structure.  18(12).
  • Keshet B, Gray JJ, Good TA (2010).  Structurally distinct toxicity inhibitors bind at common loci on β-amyloid fibril.  Protein Science.  19(12).
  • Sircar A, Chaudhury S, Kilambi KP, Berrondo M, Gray JJ (2010).  A generalized approach to sampling backbone conformations with RosettaDock for CAPRI rounds 13-19.  Proteins: Structure, Function and Bioinformatics.  78(15).
  • Masica DL, Schrier SB, Specht EA, Gray JJ (2010).  De novo design of peptide-calcite biomineralization systems.  Journal of the American Chemical Society.  132(35).
  • Berrondo M, Gray JJ, Schleif R (2010).  Computational Predictions of the Mutant Behavior of AraC.  Journal of Molecular Biology.  398(3).
  • Addison WN, Masica DL, Gray JJ, McKee MD (2010).  Phosphorylation-dependent inhibition of mineralization by osteopontin ASARM peptides is regulated by PHEX cleavage.  Journal of Bone and Mineral Research.  25(4).
  • Sircar A, Gray JJ (2010).  SnugDock: Paratope structural optimization during antibody-antigen docking compensates for errors in antibody homology models.  PLoS Computational Biology.  6(1).
  • Chaudhury S, Gray JJ (2009).  Identification of Structural Mechanisms of HIV-1 Protease Specificity Using Computational Peptide Docking: Implications for Drug Resistance.  Structure.  17(12).
  • Chien YC, Masica DL, Gray JJ, Nguyen S, Vali H, McKee MD (2009).  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(35).
  • Masica DL, Gray JJ (2009).  Solution- and adsorbed-state structural ensembles predicted for the statherin-hydroxyapatite system.  Biophysical Journal.  96(8).
  • Sircar A, Kim ET, Gray JJ (2009).  RosettaAntibody: Antibody variable region homology modeling server.  Nucleic Acids Research.  37(SUPPL. 2).
  • Sivasubramanian A, Sircar A, Chaudhury S, Gray JJ (2009).  Toward high-resolution homology modeling of antibody F v regions and application to antibody-antigen docking.  Proteins: Structure, Function and Bioinformatics.  74(2).
  • Daily MD, Gray JJ (2009).  Allosteric communication occurs via networks of tertiary and quaternary motions in proteins.  PLoS Computational Biology.  5(2).
  • Sivasubramanian A, Sircar A, Chaudhury S, Gray JJ (2008).  High-resolution homology modeling of antibody fv regions and application to antibody-antigen docking.  AIChE Annual Meeting, Conference Proceedings.
  • Masica D, Gray JJ (2008).  High-resolution adsorbed and solution-state ensembles of a naturally evolved biomineralization protein: Blind and nmr-guided predictions.  AIChE Annual Meeting, Conference Proceedings.
  • Berrondo M, Gray J (2008).  Computational predictions of the enzymatic activity of single deletion mutants.  AIChE Annual Meeting, Conference Proceedings.
  • Chaudhury S, Gray JJ (2008).  Conformer Selection and Induced Fit in Flexible Backbone Protein-Protein Docking Using Computational and NMR Ensembles.  Journal of Molecular Biology.  381(4).
  • Lyskov S, Gray JJ (2008).  The RosettaDock server for local protein-protein docking..  Nucleic acids research.  36(Web Server issue).
  • Pickin KA, Chaudhury S, Dancy BCR, Gray JJ, Cole PA (2008).  Analysis of protein kinase autophosphorylation using expressed protein ligation and computational modeling.  Journal of the American Chemical Society.  130(17).
  • Berrondo M, Ostermeier M, Gray JJ (2008).  Structure Prediction of Domain Insertion Proteins from Structures of Individual Domains.  Structure.  16(4).
  • Daily MD, Upadhyaya TJ, Gray JJ (2008).  Contact rearrangements form coupled networks from local motions in allosteric proteins.  Proteins: Structure, Function and Genetics.  71(1).
  • Berrondo M, Ostermeier M, Gray J (2008).  Structure prediction of domain insertion proteins from structures of individual domains.  Structure.  16(4).  513-27.
  • Sivasubramanian A, Maynard JA, Gray JJ (2008).  Modeling the structure of mAb 14B7 bound to the anthrax protective antigen.  Proteins: Structure, Function and Genetics.  70(1).
  • Chaudhury S, Sircar A, Sivasubramanian A, Berrondo M, Gray JJ (2007).  Incorporating biochemical information and backbone flexibility in RosettaDock for CAPRI rounds 6-12.  Proteins: Structure, Function and Genetics.  69(4).
  • Makrodimitris K, Masica DL, Kim ET, Gray JJ (2007).  Structure prediction of protein-solid surface interactions reveals a molecular recognition motif of statherin for hydroxyapatite.  Journal of the American Chemical Society.  129(44).
  • Meitzler JL, Gray JJ, Hendrickson TL (2007).  Truncation of the caspase-related subunit (Gpi8p) of Saccharomyces cerevisiae GPI transamidase: Dimerization revealed.  Archives of Biochemistry and Biophysics.  462(1).
  • Daily MD, Gray JJ (2007).  Local motions in a benchmark of allosteric proteins.  Proteins: Structure, Function and Genetics.  67(2).
  • Gray JJ (2006).  Biomolecular modeling in a process dynamics and control course.  Chemical Engineering Education.  40(4).
  • Gray JJ (2006).  High-resolution protein-protein docking.  Current Opinion in Structural Biology.  16(2).
  • Sivasubramanian A, Chao G, Pressler HM, Wittrup KD, Gray JJ (2006).  Structural model of the mAb 806-EGFR complex using computational docking followed by computational and experimental mutagenesis.  Structure.  14(3).
  • Harrison RM, Gray JJ (2005).  Prediction of pKa shifts in proteins using a discrete rotamer search and the Rosetta energy function.  AIChE Annual Meeting, Conference Proceedings.
  • Sivasubramanian A, Chao G, Wittrup KD, Gray JJ (2005).  Computational prediction of the mab 806-egfr complex structure by combining protein docking with computational and experimental mutagenesis.  AIChE Annual Meeting, Conference Proceedings.
  • Daily MD, Masica D, Sivasubramanian A, Somarouthu S, Gray JJ (2005).  CAPRI rounds 3-5 reveal promising successes and future challenges for RosettaDock.  Proteins: Structure, Function and Genetics.  60(2).
  • Singh P, Mhaka AM, Christensen SB, Gray JJ, Denmeade SR, Isaacs JT (2005).  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(8).
  • Gray JJ (2004).  The interaction of proteins with solid surfaces.  Current Opinion in Structural Biology.  14(1).
  • Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D (2003).  Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations.  Journal of Molecular Biology.  331(1).
  • Gray JJ, Moughon SE, Kortemme T, Schueler-Furman O, Misura K, Morozov AV, Baker D (2003).  Protein-protein docking predictions for the CAPRI experiment.  Proteins: Structure, Function and Genetics.  52(1).
  • Gray JJ, Bonnecaze RT (2001).  Adsorption of charge-bidisperse mixtures of colloidal particles.  Langmuir.  17(25).
  • Gray JJ, Klein DH, Korgel BA, Bonnecaze RT (2001).  Microstructure formation and kinetics in the random sequential adsorption of polydisperse tethered nanoparticles modeled as hard disks.  Langmuir.  17(8).
  • Gray JJ, Bonnecaze RT (2001).  Adsorption of colloidal particles by Brownian dynamics simulation: Kinetics and surface structures.  Journal of Chemical Physics.  114(3).
  • Gray JJ, Klein DH, Bonnecaze RT, Korgel BA (2000).  Nonequilibrium phase behavior during the random sequential adsorption of tethered hard disks.  Physical Review Letters.  85(21).
  • Gray JJ, Chiang B, Bonnecaze RT (1999).  Origin of anomalous multibody interactions.  Nature.  402(6763).
  • Gray JJ, Bonnecaze RT (1998).  Rheology and dynamics of sheared arrays of colloidal particles.  Journal of Rheology.  42(5).
  • Lee GM, Gray JJ, Palsson B (1991).  Effect of trisodium citrate treatment on hybridoma cell viability.  Biotechnology Techniques.  5(4).
  • Gray J, Jiang W, Pacella M, Athanasiadou D, Nelea V, Vali H, Hazen R, McKee M (2017).  Chiral amino acids induce hierarchical structure in calcium carbonate.  Nature Communications.  accepted.
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