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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
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128 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, 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
2020 Ruffolo JA, Guerra C, Mahajan SP, Sulam J, Gray JJ. Geometric potentials from deep learning improve prediction of CDR H3 loop structures. Bioinformatics (Oxford, England). 36: i268-i275. PMID 32657412 DOI: 10.1093/Bioinformatics/Btaa457  0.342
2020 Alford RF, Smolin N, Young HS, Gray JJ, Robia SL. Protein docking and steered molecular dynamics suggest alternative phospholamban-binding sites on the SERCA calcium transporter. The Journal of Biological Chemistry. PMID 32554805 DOI: 10.1074/Jbc.Ra120.012948  0.311
2020 Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, ... ... Gray JJ, et al. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature Methods. PMID 32483333 DOI: 10.1038/S41592-020-0848-2  0.748
2020 Koehler Leman J, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, ... ... Gray JJ, et al. Better together: Elements of successful scientific software development in a distributed collaborative community. Plos Computational Biology. 16: e1007507. PMID 32365137 DOI: 10.1371/Journal.Pcbi.1007507  0.77
2020 Lee J, Der BS, Karamitros CS, Li W, Marshall NM, Lungu OI, Miklos AE, Xu J, Kang TH, Lee CH, Tan B, Hughes RA, Jung ST, Ippolito GC, Gray JJ, et al. Computer-based Engineering of Thermostabilized Antibody Fragments. Aiche Journal. American Institute of Chemical Engineers. 66. PMID 32336757 DOI: 10.1002/Aic.16864  0.57
2020 Alford RF, Fleming PJ, Fleming KG, Gray JJ. Protein Structure Prediction and Design in a Biologically Realistic Implicit Membrane. Biophysical Journal. PMID 32224301 DOI: 10.1016/J.Bpj.2020.03.006  0.366
2020 Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, ... ... Gray JJ, et al. Members of the RosettaCommons Consortium. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S009  0.737
2020 Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, ... ... Gray JJ, et al. Details of Remaining Collective Challenges. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S008  0.751
2020 Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, ... ... Gray JJ, et al. Commercial spin-off companies from the Rosetta community. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S007  0.74
2020 Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, ... ... Gray JJ, et al. Values Statement: Equality and Inclusion in the RosettaCommons. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S005  0.729
2020 Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, ... ... Gray JJ, et al. Descriptions of the Rosetta board positions. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S004  0.737
2020 Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, ... ... Gray JJ, et al. Typical development workflow in the Rosetta community. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S003  0.755
2020 Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, ... ... Gray JJ, et al. Specific tests for Rosetta running on our automated testing framework. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S002  0.743
2020 Leman JK, Weitzner BD, Renfrew PD, Lewis SM, Moretti R, Watkins AM, Mulligan VK, Lyskov S, Adolf-Bryfogle J, Labonte JW, Krys J, Bystroff C, Schief W, Gront D, Schueler-Furman O, ... ... Gray JJ, et al. Growth in Rosetta PIs and conference attendees. Plos Computational Biology. DOI: 10.1371/Journal.Pcbi.1007507.S001  0.732
2019 Roy Burman SS, Nance ML, Jeliazkov JR, Labonte JW, Lubin JH, Biswas N, Gray JJ. Novel sampling strategies and a coarse-grained score function for docking homomers, flexible heteromers, and oligosaccharides using Rosetta in CAPRI Rounds 37-45. Proteins. PMID 31742764 DOI: 10.1002/Prot.25855  0.734
2019 Jeliazkov JR, Robinson AC, García-Moreno E B, Berger JM, Gray JJ. Toward the computational design of protein crystals with improved resolution. Acta Crystallographica. Section D, Structural Biology. 75: 1015-1027. PMID 31692475 DOI: 10.1107/S2059798319013226  0.327
2019 Roy Burman SS, Yovanno RA, Gray JJ. Flexible Backbone Assembly and Refinement of Symmetrical Homomeric Complexes. Structure (London, England : 1993). PMID 31006588 DOI: 10.1016/J.Str.2019.03.014  0.35
2019 Long X, Jeliazkov JR, Gray JJ. Non-H3 CDR template selection in antibody modeling through machine learning. Peerj. 7: e6179. PMID 30648015 DOI: 10.7717/Peerj.6179  0.315
2019 Santiago-Frangos A, Fröhlich KS, Jeliazkov JR, Małecka EM, Marino G, Gray JJ, Luisi BF, Woodson SA, Hardwick SW. 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. 116: 10978-10987. DOI: 10.2210/Pdb6Gwk/Pdb  0.311
2019 Srinivasan Y, Pooja Mahajan S, Labonte J, DeLisa MP, Gray JJ. Structure-Based Prediction of Polypeptide Substrate Specificities of Glycosyltransferases Biophysical Journal. 116: 68a. DOI: 10.1016/J.Bpj.2018.11.410  0.708
2019 Alford RF, Fleming P, Fleming KG, Gray JJ. A Thermodynamically-Rigorous, Biologically-Driven Energy Function for Membrane Protein Modeling and Design Biophysical Journal. 116: 58a. DOI: 10.1016/J.Bpj.2018.11.358  0.316
2018 Marze NA, Roy Burman SS, Sheffler W, Gray JJ. Efficient Flexible Backbone Protein-Protein Docking for Challenging Targets. Bioinformatics (Oxford, England). PMID 29718115 DOI: 10.1093/Bioinformatics/Bty355  0.708
2018 Lubin JH, Pacella MS, Gray JJ. A Parametric Rosetta Energy Function Analysis with LK Peptides on SAM Surfaces. Langmuir : the Acs Journal of Surfaces and Colloids. PMID 29630384 DOI: 10.1021/Acs.Langmuir.8B00212  0.359
2018 Jeliazkov JR, Sljoka A, Kuroda D, Tsuchimura N, Katoh N, Tsumoto K, Gray JJ. Repertoire Analysis of Antibody CDR-H3 Loops Suggests Affinity Maturation Does Not Typically Result in Rigidification. Frontiers in Immunology. 9: 413. PMID 29545810 DOI: 10.3389/Fimmu.2018.00413  0.575
2018 Pacella MS, Gray JJ. A Benchmarking Study of Peptide–Biomineral Interactions Crystal Growth & Design. 18: 607-616. DOI: 10.1021/Acs.Cgd.7B00109  0.317
2018 Alford RF, Fleming P, Fleming KG, Gray JJ. Fast Implicit Potentials for Accurate Prediction and Design of Membrane Protein Structures Biophysical Journal. 114: 345a. DOI: 10.1016/J.Bpj.2017.11.1923  0.337
2018 Roy Burman SS, Marze NA, Sheffler W, Gray JJ. Efficient Flexible-Backbone Docking of Challenging Protein Complexes Biophysical Journal. 114: 344a. DOI: 10.1016/J.Bpj.2017.11.1919  0.695
2018 Jeliazkov JR, Slojka A, Kuroda D, Tsutchimura N, Tsumoto K, Katoh N, Gray JJ. Evolution of CDR H3 Flexibility at an Immunomic Scale Biophysical Journal. 114. DOI: 10.1016/J.Bpj.2017.11.1060  0.512
2017 Alford RF, Leaver-Fay A, Gonzales L, Dolan EL, Gray JJ. A cyber-linked undergraduate research experience in computational biomolecular structure prediction and design. Plos Computational Biology. 13: e1005837. PMID 29216185 DOI: 10.1371/Journal.Pcbi.1005837  0.683
2017 Koehler Leman J, D'Avino AR, Bhatnagar Y, Gray JJ. Comparison of NMR and crystal structures of membrane proteins and computational refinement to improve model quality. Proteins. PMID 29044728 DOI: 10.1002/Prot.25402  0.3
2017 Moretti R, Lyskov S, Das R, Meiler J, Gray JJ. Web-accessible molecular modeling with Rosetta: The Rosetta Online Server That Includes Everyone (ROSIE). Protein Science : a Publication of the Protein Society. PMID 28960691 DOI: 10.1002/Pro.3313  0.641
2017 Kilambi KP, Gray JJ. Structure-based cross-docking analysis of antibody-antigen interactions. Scientific Reports. 7: 8145. PMID 28811664 DOI: 10.1038/S41598-017-08414-Y  0.783
2017 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, ... ... Gray JJ, et al. The Rosetta all-atom energy function for macromolecular modeling and design. Journal of Chemical Theory and Computation. PMID 28430426 DOI: 10.1021/Acs.Jctc.7B00125  0.788
2017 Mathew M, Tan E, Labonte JW, Shah S, Saeui CT, Liu L, Bhattacharya R, Bovonratwet P, Gray JJ, Yarema K. GLYCOENGINEERING OF ESTERASE ACTIVITY THROUGH METABOLIC FLUX-BASED MODULATION OF SIALIC ACID. Chembiochem : a European Journal of Chemical Biology. PMID 28218815 DOI: 10.1002/Cbic.201600698  0.677
2017 Newman HA, Meluh PB, Lu J, Vidal J, Carson C, Lagesse E, Gray JJ, Boeke JD, Matunis MJ. A high throughput mutagenic analysis of yeast sumo structure and function. Plos Genetics. 13: e1006612. PMID 28166236 DOI: 10.1371/Journal.Pgen.1006612  0.337
2017 Weitzner BD, Jeliazkov JR, Lyskov S, Marze N, Kuroda D, Frick R, Adolf-Bryfogle J, Biswas N, Dunbrack RL, Gray JJ. Modeling and docking of antibody structures with Rosetta. Nature Protocols. 12: 401-416. PMID 28125104 DOI: 10.1038/Nprot.2016.180  0.793
2017 Alford RF, Leaver-Fay A, Jeliazkov JR, Pacella MS, Kuhlman B, Kortemme T, Gray JJ. A Deep-Dive into the Rosetta Energy Function for Biological Macromolecules Biophysical Journal. 112: 194a. DOI: 10.1016/J.Bpj.2016.11.1078  0.785
2016 Koehler Leman J, Mueller BK, Gray JJ. Expanding the toolkit for membrane protein modeling in Rosetta. Bioinformatics (Oxford, England). PMID 28011777 DOI: 10.1093/Bioinformatics/Btw716  0.333
2016 Labonte JW, Adolf-Bryfogle J, Schief WR, Gray JJ. Residue-centric modeling and design of saccharide and glycoconjugate structures. Journal of Computational Chemistry. PMID 27900782 DOI: 10.1002/Jcc.24679  0.747
2016 Weitzner BD, Gray JJ. Accurate Structure Prediction of CDR H3 Loops Enabled by a Novel Structure-Based C-Terminal Constraint. Journal of Immunology (Baltimore, Md. : 1950). PMID 27872211 DOI: 10.4049/Jimmunol.1601137  0.768
2016 Marze NA, Jeliazkov JR, Roy Burman SS, Boyken SE, DiMaio F, Gray JJ. Modeling oblong proteins and water-mediated interfaces with RosettaDock in CAPRI rounds 28-35. Proteins. PMID 27667482 DOI: 10.1002/Prot.25168  0.37
2016 Piepenbrink KJ, Lillehoj EP, Harding CM, Labonte JW, Zuo X, Rapp CA, Munson RS, Goldblum SE, Feldman MF, Gray JJ, Sundberg EJ. Structural diversity in the type IV pili of multidrug-resistant Acinetobacter. The Journal of Biological Chemistry. PMID 27634041 DOI: 10.1074/Jbc.M116.751099  0.684
2016 Kuroda D, Gray JJ. Pushing the Backbone in Protein-Protein Docking. Structure (London, England : 1993). PMID 27568930 DOI: 10.1016/J.Str.2016.06.025  0.603
2016 Marze NA, Lyskov S, Gray JJ. Improved prediction of antibody VL-VH orientation. Protein Engineering, Design & Selection : Peds. PMID 27276984 DOI: 10.1093/Protein/Gzw013  0.371
2016 Kuroda D, Gray JJ. Shape complementarity and hydrogen bond preferences in protein-protein interfaces: Implications for antibody modeling and protein-protein docking. Bioinformatics (Oxford, England). PMID 27153634 DOI: 10.1093/Bioinformatics/Btw197  0.585
2016 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, ... ... Gray JJ, et al. Prediction of homo- and hetero-protein complexes by protein docking and template-based modeling: a CASP-CAPRI experiment. Proteins. PMID 27122118 DOI: 10.1002/Prot.25007  0.628
2016 DeKosky BJ, Lungu OI, Park D, Johnson EL, Charab W, Chrysostomou C, Kuroda D, Ellington AD, Ippolito GC, Gray JJ, Georgiou G. 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. PMID 27114511 DOI: 10.1073/Pnas.1525510113  0.557
2016 Firnberg E, Labonte JW, Gray JJ, Ostermeier M. A Comprehensive, High-Resolution Map of a Gene's Fitness Landscape. Molecular Biology and Evolution. PMID 26912810 DOI: 10.1093/Molbev/Msw021  0.742
2015 Khachatryan V, Sirunyan AM, Tumasyan A, Adam W, Bergauer T, Dragicevic M, Erö J, Friedl M, Frühwirth R, Ghete VM, Hartl C, Hörmann N, Hrubec J, Jeitler M, Kiesenhofer W, ... Gray J, et al. Measurements of the [Formula: see text][Formula: see text] production cross sections in the [Formula: see text] channel in proton-proton collisions at [Formula: see text] and [Formula: see text] and combined constraints on triple gauge couplings. The European Physical Journal. C, Particles and Fields. 75: 511. PMID 26549982 DOI: 10.1140/Epjc/S10052-015-3706-0  0.381
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  0.7
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  0.768
2015 Khachatryan V, Sirunyan AM, Tumasyan A, Adam W, Bergauer T, Dragicevic M, Erö J, Friedl M, Frühwirth R, Ghete VM, Hartl C, Hörmann N, Hrubec J, Jeitler M, Kiesenhofer W, ... Gray J, et al. Evidence for Collective Multiparticle Correlations in p-Pb Collisions. Physical Review Letters. 115: 012301. PMID 26182092 DOI: 10.1103/Physrevlett.115.012301  0.394
2015 Khachatryan V, Sirunyan AM, Tumasyan A, Adam W, Bergauer T, Dragicevic M, Erö J, Friedl M, Frühwirth R, Ghete VM, Hartl C, Hörmann N, Hrubec J, Jeitler M, Kiesenhofer W, ... Gray J, et al. Search for a standard model Higgs boson produced in association with a top-quark pair and decaying to bottom quarks using a matrix element method. The European Physical Journal. C, Particles and Fields. 75: 251. PMID 26097407 DOI: 10.1140/Epjc/S10052-015-3454-1  0.411
2015 Aad G, Abbott B, Abdallah J, Abdinov O, Aben R, Abolins M, AbouZeid OS, Abramowicz H, Abreu H, Abreu R, Abulaiti Y, Acharya BS, Adamczyk L, Adams DL, Adelman J, ... Gray J, et al. Combined Measurement of the Higgs Boson Mass in pp Collisions at sqrt[s]=7 and 8 TeV with the ATLAS and CMS Experiments. Physical Review Letters. 114: 191803. PMID 26024162 DOI: 10.1103/Physrevlett.114.191803  0.376
2015 Khachatryan V, Sirunyan AM, Tumasyan A, Adam W, Bergauer T, Dragicevic M, Erö J, Friedl M, Frühwirth R, Ghete VM, Hartl C, Hörmann N, Hrubec J, Jeitler M, Kiesenhofer W, ... Gray J, et al. Measurement of J/ψ and ψ(2S) Prompt Double-Differential Cross Sections in pp Collisions at sqrt[s]=7 TeV. Physical Review Letters. 114: 191802. PMID 26024161 DOI: 10.1103/Physrevlett.114.191802  0.376
2015 Khachatryan V, Sirunyan AM, Tumasyan A, Adam W, Bergauer T, Dragicevic M, Erö J, Friedl M, Frühwirth R, Ghete VM, Hartl C, Hörmann N, Hrubec J, Jeitler M, Kiesenhofer W, ... Gray J, et al. Precise determination of the mass of the Higgs boson and tests of compatibility of its couplings with the standard model predictions using proton collisions at 7 and 8[Formula: see text]. The European Physical Journal. C, Particles and Fields. 75: 212. PMID 25999783 DOI: 10.1140/Epjc/S10052-015-3351-7  0.405
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  0.757
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  0.791
2015 Koehler Leman J, Ulmschneider MB, Gray JJ. Computational modeling of membrane proteins. Proteins. 83: 1-24. PMID 25355688 DOI: 10.1002/Prot.24703  0.377
2015 Labonte JW, Gray JJ. Docking and Design of Oligosaccharides, Glycoproteins, and Glycolipids Biophysical Journal. 108: 470a. DOI: 10.1016/J.Bpj.2014.11.2568  0.752
2015 Leman JK, Alford RF, Gray JJ. Rosetta-MPDock: A Novel Computational Tool for Protein-Protein Docking within the Membrane Bilayer Biophysical Journal. 108: 250a. DOI: 10.1016/J.Bpj.2014.11.1382  0.753
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  0.79
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  0.759
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  0.802
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  0.345
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  0.3
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  0.77
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  0.389
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  0.811
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  0.804
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  0.463
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  0.546
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  0.796
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  0.771
2013 Mansouri A, Masica D, Gray J, McKee M. Osteopontin ASARM peptide binding to crystal faces of hydroxyapatite [ndash] computational simulations Bone Abstracts. DOI: 10.1530/Boneabs.1.Pp460  0.652
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  0.772
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  0.786
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  0.787
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  0.629
2012 Praneeth Kilambi K, Gray JJ. Towards Fast and Accurate Calculation of Protein pKa Values Exploiting Various Degrees of Conformational Flexibility Biophysical Journal. 102: 169a-170a. DOI: 10.1016/J.Bpj.2011.11.921  0.38
2012 Xu J, Miklos AE, Hughes R, Kuhlman B, Georgiou G, Ellington AD, Gray JJ. A Systematic Computational Method to Predict and Enhance Antibody-Antigen Binding in the Absence of Antibody Crystal Structures Biophysical Journal. 102: 621a. DOI: 10.1016/J.Bpj.2011.11.3382  0.602
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  0.798
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  0.794
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  0.758
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  0.684
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  0.789
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  0.344
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  0.775
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  0.646
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  0.761
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  0.777
2011 Kilambi KP, Gray JJ. Incorporating the Effects of pH in Protein-Protein Docking Biophysical Journal. 100: 216a. DOI: 10.1016/J.Bpj.2010.12.1391  0.789
2011 Young M, Lee L, Cao B, Mao C, Gray JJ. Fd Bacteriophage Coat Protein Structure Prediction and Design for the Assembly of Hydroxyapatite Nanorods and Bone Tissue Regeneration Biophysical Journal. 100: 158a. DOI: 10.1016/J.Bpj.2010.12.1077  0.307
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  0.704
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  0.688
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  0.795
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  0.793
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  0.803
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  0.686
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  0.66
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  0.637
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  0.656
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  0.794
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  0.704
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  0.725
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  0.8
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  0.69
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  0.403
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  0.799
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  0.643
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  0.724
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  0.776
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  0.702
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  0.788
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  0.728
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  0.42
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  0.768
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  0.786
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  0.321
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  0.343
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  0.811
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  0.802
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  0.544
2001 Gray JJ, Bonnecaze RT. Adsorption of charge-bidisperse mixtures of colloidal particles Langmuir. 17: 7935-7947. DOI: 10.1021/La0012844  0.537
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  0.551
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  0.533
1999 Gray JJ, Chiang B, Bonnecaze RT. Origin of anomalous multibody interactions Nature. 402: 750. DOI: 10.1038/45445  0.524
1998 Gray JJ, Bonnecaze RT. Rheology and dynamics of sheared arrays of colloidal particles Journal of Rheology. 42: 1121-1151. DOI: 10.1122/1.550923  0.532
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