Gray, Jeffrey

Chemical And Biomolecular Engineering

Maryland Hall 208
(410) 516-5313

Jump to:


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 […]

Read More

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 […]

Read More


  • Ph.D. 2000, UNIV TEXAS AUSTIN*
  • Bachelor of Science in Engineering 1994, Univ of Michigan Ann Arbor*
  • 2015 - Present:  Faculty Mentor, Martin Ulmschneider (Materials Science)
  • 2015 - Present:  Director, NSF Research Experience for Undergraduates (REU) Program for the Rosetta Commons
  • 2014 - Present:  Faculty Mentor, Margaret Johnson (Biophysics)
  • 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:  Advisor, AIChE
  • 2006 - 2006:  Society for Biological Engineering, Society for Biological Engineering
  • 2006 - 2006:  Academic Advisor, ChemBE
  • 2006 - 2006:  Academic Advisor, ChemBE
  • 2006 - 2006:  Co-leader, Computational Biophysics Journal Club
  • 2005 - 2005:  Co-Chair, Rosetta
  • 2005 - Present:  Joint, SOM Oncology Center
  • 2005 - 2005:  Director, Ingenuity Project
  • 2004 - 2004:  Co-Chair, Rosetta
  • 2004 - 2004:  Project Manager, Rosetta Biomolecular Modeling Suite C++ Conversion and Modernization Project
  • 2003 - 2003:  Mentor, Baltimore Polytechnic Institute
  • 2003 - 2004:  Editorial Manager, Proteins
  • 2002 - 2006:  Academic Advisor, Unspecified
  • 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:  AIMBE College of Fellows
  • 2016:  Himmelblau Award for Innovations in Computer-Based Chemical Engineering Education
  • 2015:  Centennial Lecturer
  • 2015:  Plenary Lecturer
  • 2011:  F. Stuart Hodgson Faculty Scholar
  • 2011:  Fisher Award for Undergraduate Research in Cancer - M.-Y. Lee (*student advised by Jeff Gray)
  • 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:  NIH Ruth L. Kirschstein Graduate Fellowship - M. Berrondo - 2007-2011 (*Student advised by Jeff Gray)
  • 2007:  Provost's Undergraduate Research Award - E. Kim - 2007 (*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)
  • 2006:  JHU Alumni Association Excellence in Teaching Award
  • 2006:  Undergraduate lab members Elizabeth Specht and Sarah Schrier shared an Elenora Streb Muly 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
  • "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
  • "Evolution of CDR H3 Flexibility at an Immunomic Scale", 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
  • "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
  • "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
  • "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
  • "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


Journal Articles
  • Roy Burman SS, Yovanno RA, Gray JJ (2019).  Flexible Backbone Assembly and Refinement of Symmetrical Homomeric Complexes.  Structure.  27(6).  1041-1051.e8.
  • Santiago-Frangos A, Fröhlich KS, Jeliazkov JR, Malecka EM, Marino G, Gray JJ, Luisi BF, Woodson SA, Hardwick SW (2019).  Caulobacter crescentus Hfq structure reveals a conserved mechanism of RNA annealing regulation.  Proceedings of the National Academy of Sciences of the United States of America.  166(22).  10978-10987.
  • Høydahl LS, Richter L, Frick R, Snir O, Gunnarsen KS, Landsverk OJB, Iversen R, Jeliazkov JR, Gray JJ, Bergseng E, Foss S, Qiao SW, Lundin KEA, Jahnsen J, Jahnsen FL, Sandlie I, Sollid LM, Løset GÅ (2019).  Plasma Cells Are the Most Abundant Gluten Peptide MHC-expressing Cells in Inflamed Intestinal Tissues From Patients With Celiac Disease.  Gastroenterology.  156(5).  1428-1439.e10.
  • Spear ED, Alford RF, Babatz TD, Wood KM, Mossberg OW, Odinammadu K, Shilagardi K, Gray JJ, Michaelis S (2019).  A humanized yeast system to analyze cleavage of prelamin A by ZMPSTE24.  Methods.  157.  47-55.
  • Long X, Jeliazkov JR, Gray JJ (2019).  Non-H3 CDR template selection in antibody modeling through machine learning.  PeerJ.  2019(1).
  • 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 CM, Dinkova-Kostova AT, Hancock WW, Gray JJ, Bradner JE, Valente S, Mai A, Anders NM, Rudek MA, Hu Y, Ryu B, Schwabe JWR, Mattevi A, Alani RM, Cole PA (2018).  Targeting the CoREST complex with dual histone deacetylase and demethylase inhibitors.  Nature Communications.  9(1).
  • Chien YC, Mansouri A, Jiang W, Khan SR, Gray JJ, McKee MD (2018).  Modulation of calcium oxalate dihydrate growth by phosphorylated osteopontin peptides.  Journal of Structural Biology.  204(2).  131-144.
  • Marze NA, Roy Burman SS, Sheffler W, Gray JJ (2018).  Efficient flexible backbone protein-protein docking for challenging targets.  Bioinformatics.  34(20).  3461-3469.
  • Jiang W, Pacella MS, Vali H, Gray JJ, McKee MD (2018).  Chiral switching in biomineral suprastructures induced by homochiral l-amino acid.  Science Advances.  4(8).
  • Lubin JH, Pacella MS, Gray JJ (2018).  A Parametric Rosetta Energy Function Analysis with LK Peptides on SAM Surfaces.  Langmuir.  34(18).  5279-5289.
  • 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).
  • Pacella MS, Gray JJ (2018).  A Benchmarking Study of Peptide-Biomineral Interactions.  Crystal Growth and Design.  18(2).  607-616.
  • 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).  57-74.
  • 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).  259-268.
  • Kilambi KP, Gray JJ (2017).  Structure-based cross-docking analysis of antibody-antigen interactions.  Scientific Reports.  7(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).
  • Santiago-Frangos A, Jeliazkov JR, Gray JJ, Woodson SA (2017).  Acidic C-terminal domains autoregulate the RNA chaperone Hfq.  eLife.  6.
  • 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.  18(13).  1204-1215.
  • 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, Kuhlman B, Kortemme T, Gray JJ (2017).  The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design.  Journal of Chemical Theory and Computation.  13(6).  3031-3048.
  • 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).  479-486.
  • 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).  276-287.
  • 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).  401-416.
  • Leman JK, Mueller BK, Gray JJ (2017).  Expanding the toolkit for membrane protein modeling in Rosetta.  Bioinformatics.  33(5).  754-756.
  • 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).  505-515.
  • 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).  22924-22935.
  • Kuroda D, Gray JJ (2016).  Pushing the Backbone in Protein-Protein Docking.  Structure.  24(10).  1821-1829.
  • Marze NA, Lyskov S, Gray JJ (2016).  Improved prediction of antibody VL-VH orientation.  Protein Engineering, Design and Selection.  29(10).  409-418.
  • 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).  2451-2456.
  • 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).  E2636-E2645.
  • 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, Lee GR, Seok C, Qin S, Zhou HX, Ritchie DW, Maigret B, Devignes MD, Ghoorah A, Torchala M, Chaleil RAG, Bates PA, Ben-Zeev E, Eisenstein M, Negi SS, Weng Z, Vreven T, Pierce BG, Borrman TM, Yu J, Ochsenbein F, Guerois R, Vangone A, Rodrigues JPGLM, Van Zundert G, Nellen M, Xue L, Karaca E, Melquiond ASJ, Visscher K, Kastritis PL, Bonvin AMJJ, Xu X, Qiu L, Yan C, Li J, Ma Z, Cheng J, Zou X, Shen Y, Peterson LX, Kim HR, Roy A, Han X, Esquivel-Rodriguez J, Kihara D, Yu X, Bruce NJ, Fuller JC, Wade RC, Anishchenko I, Kundrotas PJ, Vakser IA, Imai K, Yamada K, Oda T, Nakamura T, Tomii K, Pallara C, Romero-Durana M, Jiménez-García B, Moal IH, Férnandez-Recio J, Joung JY, Kim JY, Joo K, Lee J, Kozakov D, Vajda S, Mottarella S, Hall DR, Beglov D, Mamonov A, Xia B, Bohnuud T, Del Carpio CA, Ich...Oliva R (2016).  Prediction of homoprotein and heteroprotein complexes by protein docking and template-based modeling: A CASP-CAPRI experiment.  Proteins: Structure, Function and Bioinformatics.  84.  323-348.
  • 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).  2392-2402.
  • 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).  5562-5569.
  • Weitzner BD, Dunbrack RL, Gray JJ (2015).  The origin of CDR H3 structural diversity.  Structure.  23(2).  302-311.
  • 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).
  • 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, Lyonnet S, Ceccherini I, Gray JJ, Pachnis V, McCallion AS, Chakravarti A (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).  581-596.
  • Koehler Leman J, Ulmschneider MB, Gray JJ (2015).  Computational modeling of membrane proteins.  Proteins: Structure, Function and Bioinformatics.  83(1).  1-24.
  • 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).  215-222.
  • 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).  1611-1623.
  • Kilambi KP, Reddy K, Gray JJ (2014).  Protein-Protein Docking with Dynamic Residue Protonation States.  PLoS Computational Biology.  10(12).
  • 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-Recio J, Xu J, Muthu P, Praneeth Kilambi K, Gray JJ, Grudinin S, Derevyanko G, Mitchell JC, Wieting J, Kanamori E, Tsuchiya Y, Murakami Y, Sarmiento J, Standley DM, Shirota M, Kinoshita K, Nakamura H, Chavent M, Ritchie DW, Park H, Ko J, Lee H, Seok C, Shen Y, Kozakov D, Vajda S, Kundrotas PJ, Vakser IA, Pierce BG, Hwang H, Vreven T, Weng Z, Buch I, Farkash E, Wolfson HJ, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Wojdyla JA, Kleanthous C, Wodak SJ (2014).  Blind prediction of interfacial water positions in CAPRI.  Proteins: Structure, Function and Bioinformatics.  82(4).  620-632.
  • 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).  1581-1592.
  • 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).  2201-2209.
  • 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, Jimenez B, Fernandez-Recio J, Flores S, Pacella M, Praneeth Kilambi K, Gray JJ, Popov P, Grudinin S, Esquivel-Rodríguez J, Kihara D, Zhao N, Korkin D, Zhu X, Demerdash ONA, Mitchell JC, Kanamori E, Tsuchiya Y, Nakamura H, Lee H, Park H, Seok C, Sarmiento J, Liang S, Teraguchi S, Standley DM, Shimoyama H, Terashi G, Takeda-Shitaka M, Iwadate M, Umeyama H, Beglov D, Hall DR, Kozakov D, Vajda S, Pierce BG, Hwang H, Vreven T, Weng Z, Huang Y, Li H, Yang X, Ji X, Liu S, Xiao Y, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Velankar S, Janin J, Wodak SJ, Baker D (2013).  Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions.  Proteins: Structure, Function and Bioinformatics.  81(11).  1980-1987.
  • 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, Bonneau 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).  3098-3109.
  • 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.  77-96.
  • 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).  587-595.
  • 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).  6028-6038.
  • 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).  449-455.
  • 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 T, Bernauer J, Poupon A, Azé J, Soner S, Ovali SK, Ozbek P, Tal NB, Haliloglu T, Hwang H, Vreven T, Pierce BG, Weng Z, Pérez-Cano L, Pons C, Fernández-Recio J, Jiang F, Yang F, Gong X, Cao L, Xu X, Liu B, Wang P, Li C, Wang C, Robert CH, Guharoy M, Liu S, Huang Y, Li L, Guo D, Chen Y, Xiao Y, London N, Itzhaki Z, Schueler-Furman O, Inbar Y, Potapov V, Cohen M, Schreiber G, Tsuchiya Y, Kanamori E, Standley DM, Nakamura H, Kinoshita K, Driggers CM, Hall RG, Morgan JL, Hsu VL, Zhan J, Yang Y, Zhou Y, Kastritis PL, Bonvin AMJJ, Zhang W, Camacho CJ, Kilambi KP, Sircar A, Gray JJ, Ohue M, Uchikoga N, Matsuzaki Y, Ishida T, Akiyama Y, Khashan R, Bush S, Fouches D, Tropsha A, Esquivel-Rodríguez J, Kihara D, Stranges PB, Jacak R, Kuhlman B, Huang SY, Zou X, Wodak SJ, Janin J, Baker D (2011).  Community-wide assessment of protein-interface modeling suggests improvements to design methodology.  Journal of Molecular Biology.  414(2).  289-302.
  • Berrondo M, Gray JJ (2011).  Computed structures of point deletion mutants and their enzymatic activities.  Proteins: Structure, Function and Bioinformatics.  79(10).  2844-2860.
  • 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).  11520-11527.
  • 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).  13775-13785.
  • 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).  6357-6367.
  • 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).  470-476.
  • 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).  3981-3991.
  • 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).  1678-1687.
  • Keshet B, Gray JJ, Good TA (2010).  Structurally distinct toxicity inhibitors bind at common loci on β-amyloid fibril.  Protein Science.  19(12).  2291-2304.
  • 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).  3115-3123.
  • 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).  12252-12262.
  • Berrondo M, Gray JJ, Schleif R (2010).  Computational Predictions of the Mutant Behavior of AraC.  Journal of Molecular Biology.  398(3).  462-470.
  • 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).  695-705.
  • 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).  1636-1648.
  • 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).  23491-23501.
  • Sircar A, Kim ET, Gray JJ (2009).  RosettaAntibody: Antibody variable region homology modeling server.  Nucleic Acids Research.  37(SUPPL. 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 (2009).  Toward high-resolution homology modeling of antibody F v regions and application to antibody-antigen docking.  Proteins: Structure, Function and Bioinformatics.  74(2).  497-514.
  • Masica DL, Gray JJ (2009).  Solution- and adsorbed-state structural ensembles predicted for the statherin-hydroxyapatite system.  Biophysical Journal.  96(8).  3082-3091.
  • Berrondo M, Gray J (2008).  Computational predictions of the enzymatic activity of single deletion mutants.  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.
  • 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.
  • 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).  1068-1087.
  • 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).  5667-5669.
  • Berrondo M, Ostermeier M, Gray JJ (2008).  Structure Prediction of Domain Insertion Proteins from Structures of Individual Domains.  Structure.  16(4).  513-527.
  • 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).  455-466.
  • Lyskov S, Gray JJ (2008).  The RosettaDock server for local protein-protein docking..  Nucleic acids research.  36(Web Server issue).
  • 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).  218-230.
  • 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).  793-800.
  • 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).  13713-13722.
  • 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).  83-93.
  • Daily MD, Gray JJ (2007).  Local motions in a benchmark of allosteric proteins.  Proteins: Structure, Function and Genetics.  67(2).  385-399.
  • Gray JJ (2006).  Biomolecular modeling in a process dynamics and control course.  Chemical Engineering Education.  40(4).  297-306.
  • Gray JJ (2006).  High-resolution protein-protein docking.  Current Opinion in Structural Biology.  16(2).  183-193.
  • 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).  401-414.
  • 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.  8064.
  • 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.  10466.
  • 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).  181-186.
  • 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).  3005-3014.
  • Gray JJ (2004).  The interaction of proteins with solid surfaces.  Current Opinion in Structural Biology.  14(1).  110-115.
  • 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).  281-299.
  • 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).  118-122.
  • Gray JJ, Bonnecaze RT (2001).  Adsorption of charge-bidisperse mixtures of colloidal particles.  Langmuir.  17(25).  7935-7947.
  • 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).  2317-2328.
  • Gray JJ, Bonnecaze RT (2001).  Adsorption of colloidal particles by Brownian dynamics simulation: Kinetics and surface structures.  Journal of Chemical Physics.  114(3).  1366-1381.
  • 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).  4430-4433.
  • Gray JJ, Chiang B, Bonnecaze RT (1999).  Origin of anomalous multibody interactions.  Nature.  402(6763).  750.
  • Gray JJ, Bonnecaze RT (1998).  Rheology and dynamics of sheared arrays of colloidal particles.  Journal of Rheology.  42(5).  1121-1151.
  • Lee GM, Gray JJ, Palsson B (1991).  Effect of trisodium citrate treatment on hybridoma cell viability.  Biotechnology Techniques.  5(4).  295-298.
  • 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.
Book Chapters
  • 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.  343-366.
  • 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.  109-143.
  • 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 DE, Lyskov S, Berrondo M, Mentzer S, Popovic Z, Havranek JJ, Karanicolas J, Das R, Meiler J, Kortemme T, Gray JJ, Kuhlman B, Baker D, Bradley P (2011).  Rosetta3: An object-oriented software suite for the simulation and design of macromolecules.  Methods in Enzymology.  487(C).  545-574.
Back to top