| ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules A Leaver-Fay, M Tyka, SM Lewis, OF Lange, J Thompson, R Jacak, ... Methods in enzymology 487, 545-574, 2011 | 1941 | 2011 |
| Protein–protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations JJ Gray, S Moughon, C Wang, O Schueler-Furman, B Kuhlman, CA Rohl, ... Journal of molecular biology 331 (1), 281-299, 2003 | 1315 | 2003 |
| The Rosetta all-atom energy function for macromolecular modeling and design RF Alford, A Leaver-Fay, JR Jeliazkov, MJ O’Meara, FP DiMaio, H Park, ... Journal of chemical theory and computation 13 (6), 3031-3048, 2017 | 1260 | 2017 |
| The interaction of proteins with solid surfaces JJ Gray Current opinion in structural biology 14 (1), 110-115, 2004 | 1037 | 2004 |
| PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta S Chaudhury, S Lyskov, JJ Gray Bioinformatics 26 (5), 689-691, 2010 | 723 | 2010 |
| The RosettaDock server for local protein–protein docking S Lyskov, JJ Gray Nucleic acids research 36 (suppl_2), W233-W238, 2008 | 640 | 2008 |
| Macromolecular modeling and design in Rosetta: recent methods and frameworks JK Leman, BD Weitzner, SM Lewis, J Adolf-Bryfogle, N Alam, RF Alford, ... Nature methods 17 (7), 665-680, 2020 | 572 | 2020 |
| Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE) S Lyskov, FC Chou, SO Conchuir, BS Der, K Drew, D Kuroda, J Xu, ... PloS one 8 (5), e63906, 2013 | 396 | 2013 |
| A comprehensive, high-resolution map of a gene’s fitness landscape E Firnberg, JW Labonte, JJ Gray, M Ostermeier Molecular biology and evolution 31 (6), 1581-1592, 2014 | 331 | 2014 |
| Benchmarking and analysis of protein docking performance in Rosetta v3. 2 S Chaudhury, M Berrondo, BD Weitzner, P Muthu, H Bergman, JJ Gray PloS one 6 (8), e22477, 2011 | 329 | 2011 |
| Modeling and docking of antibody structures with Rosetta BD Weitzner, JR Jeliazkov, S Lyskov, N Marze, D Kuroda, R Frick, ... Nature protocols 12 (2), 401-416, 2017 | 264 | 2017 |
| High-resolution protein–protein docking JJ Gray Current opinion in structural biology 16 (2), 183-193, 2006 | 260 | 2006 |
| Scientific benchmarks for guiding macromolecular energy function improvement A Leaver-Fay, MJ O'Meara, M Tyka, R Jacak, Y Song, EH Kellogg, ... Methods in enzymology 523, 109-143, 2013 | 244 | 2013 |
| Phosphorylation‐dependent inhibition of mineralization by osteopontin ASARM peptides is regulated by PHEX cleavage WN Addison, DL Masica, JJ Gray, MD McKee Journal of Bone and Mineral Research 25 (4), 695-705, 2010 | 238 | 2010 |
| Toward high‐resolution homology modeling of antibody Fv regions and application to antibody–antigen docking A Sivasubramanian, A Sircar, S Chaudhury, JJ Gray Proteins: Structure, Function, and Bioinformatics 74 (2), 497-514, 2009 | 229 | 2009 |
| Large-scale sequence and structural comparisons of human naive and antigen-experienced antibody repertoires BJ DeKosky, OI Lungu, D Park, EL Johnson, W Charab, C Chrysostomou, ... Proceedings of the National Academy of Sciences 113 (19), E2636-E2645, 2016 | 203 | 2016 |
| RosettaAntibody: antibody variable region homology modeling server A Sircar, ET Kim, JJ Gray Nucleic acids research 37 (suppl_2), W474-W479, 2009 | 198 | 2009 |
| Targeting the CoREST complex with dual histone deacetylase and demethylase inhibitors JH Kalin, M Wu, AV Gomez, Y Song, J Das, D Hayward, N Adejola, M Wu, ... Nature communications 9 (1), 53, 2018 | 196 | 2018 |
| Conformer selection and induced fit in flexible backbone protein–protein docking using computational and NMR ensembles S Chaudhury, JJ Gray Journal of molecular biology 381 (4), 1068-1087, 2008 | 195 | 2008 |
| Deep learning in protein structural modeling and design W Gao, SP Mahajan, J Sulam, JJ Gray Patterns 1 (9), 2020 | 185 | 2020 |
| An integrated framework advancing membrane protein modeling and design RF Alford, J Koehler Leman, BD Weitzner, AM Duran, DC Tilley, A Elazar, ... PLoS computational biology 11 (9), e1004398, 2015 | 169 | 2015 |
| Prediction of homoprotein and heteroprotein complexes by protein docking and template‐based modeling: a CASP‐CAPRI experiment MF Lensink, S Velankar, A Kryshtafovych, SY Huang, ... Proteins: Structure, Function, and Bioinformatics 84, 323-348, 2016 | 166 | 2016 |
| SnugDock: paratope structural optimization during antibody-antigen docking compensates for errors in antibody homology models A Sircar, JJ Gray PloS computational biology 6 (1), e1000644, 2010 | 165 | 2010 |
| Structure-based design of supercharged, highly thermoresistant antibodies AE Miklos, C Kluwe, BS Der, S Pai, A Sircar, RA Hughes, M Berrondo, ... Chemistry & biology 19 (4), 449-455, 2012 | 159 | 2012 |
| Chiral acidic amino acids induce chiral hierarchical structure in calcium carbonate W Jiang, MS Pacella, D Athanasiadou, V Nelea, H Vali, RM Hazen, ... Nature communications 8 (1), 15066, 2017 | 158 | 2017 |
| Community-wide assessment of protein-interface modeling suggests improvements to design methodology SJ Fleishman, TA Whitehead, EM Strauch, JE Corn, S Qin, HX Zhou, ... Journal of molecular biology 414 (2), 289-302, 2011 | 157 | 2011 |
| Structure prediction of protein− solid surface interactions reveals a molecular recognition motif of statherin for hydroxyapatite K Makrodimitris, DL Masica, ET Kim, JJ Gray Journal of the American Chemical Society 129 (44), 13713-13722, 2007 | 153 | 2007 |
| Antibody structure prediction using interpretable deep learning JA Ruffolo, J Sulam, JJ Gray Patterns 3 (2), 2022 | 142 | 2022 |
| Functional loss of semaphorin 3C and/or semaphorin 3D and their epistatic interaction with ret are critical to Hirschsprung disease liability Q Jiang, S Arnold, T Heanue, KP Kilambi, B Doan, A Kapoor, AY Ling, ... The American Journal of Human Genetics 96 (4), 581-596, 2015 | 138 | 2015 |
| Efficient flexible backbone protein–protein docking for challenging targets NA Marze, SS Roy Burman, W Sheffler, JJ Gray Bioinformatics 34 (20), 3461-3469, 2018 | 134 | 2018 |
| Protein–protein docking predictions for the CAPRI experiment JJ Gray, SE Moughon, T Kortemme, O Schueler‐Furman, KMS Misura, ... Proteins: Structure, Function, and Bioinformatics 52 (1), 118-122, 2003 | 133 | 2003 |
| Enzyme replacement therapy prevents dental defects in a model of hypophosphatasia MD McKee, Y Nakano, DL Masica, JJ Gray, I Lemire, R Heft, MP Whyte, ... Journal of dental research 90 (4), 470-476, 2011 | 130 | 2011 |
| Local motions in a benchmark of allosteric proteins MD Daily, JJ Gray Proteins: Structure, function, and bioinformatics 67 (2), 385-399, 2007 | 130 | 2007 |
| Allosteric communication occurs via networks of tertiary and quaternary motions in proteins MD Daily, JJ Gray PLoS computational biology 5 (2), e1000293, 2009 | 127 | 2009 |
| Computational modeling of membrane proteins J Koehler Leman, MB Ulmschneider, JJ Gray Proteins: Structure, Function, and Bioinformatics 83 (1), 1-24, 2015 | 119 | 2015 |
| Community‐wide evaluation of methods for predicting the effect of mutations on protein–protein interactions R Moretti, SJ Fleishman, R Agius, M Torchala, PA Bates, PL Kastritis, ... Proteins: Structure, Function, and Bioinformatics 81 (11), 1980-1987, 2013 | 112 | 2013 |
| Contact rearrangements form coupled networks from local motions in allosteric proteins MD Daily, TJ Upadhyaya, JJ Gray Proteins: Structure, Function, and Bioinformatics 71 (1), 455-466, 2008 | 111 | 2008 |
| Nanostructure, osteopontin, and mechanical properties of calcitic avian eggshell D Athanasiadou, W Jiang, D Goldbaum, A Saleem, K Basu, MS Pacella, ... Science advances 4 (3), eaar3219, 2018 | 107 | 2018 |
| Blind prediction performance of RosettaAntibody 3.0: grafting, relaxation, kinematic loop modeling, and full CDR optimization BD Weitzner, D Kuroda, N Marze, J Xu, JJ Gray Proteins: Structure, Function, and Bioinformatics 82 (8), 1611-1623, 2014 | 104 | 2014 |
| The origin of CDR H3 structural diversity BD Weitzner, RL Dunbrack, JJ Gray Structure 23 (2), 302-311, 2015 | 102 | 2015 |
| Analysis and modeling of the variable region of camelid single-domain antibodies A Sircar, KA Sanni, J Shi, JJ Gray The Journal of Immunology 186 (11), 6357-6367, 2011 | 99 | 2011 |
| Alternative computational protocols for supercharging protein surfaces for reversible unfolding and retention of stability BS Der, C Kluwe, AE Miklos, R Jacak, S Lyskov, JJ Gray, G Georgiou, ... PloS one 8 (5), e64363, 2013 | 94 | 2013 |
| Modulation of calcium oxalate dihydrate growth by selective crystal-face binding of phosphorylated osteopontin and polyaspartate peptide showing occlusion by sectoral … YC Chien, DL Masica, JJ Gray, S Nguyen, H Vali, MD McKee Journal of Biological Chemistry 284 (35), 23491-23501, 2009 | 91 | 2009 |
| Solid-state NMR studies of biomineralization peptides and proteins A Roehrich, J Ash, A Zane, DL Masica, JJ Gray, G Goobes, G Drobny Proteins at Interfaces III State of the Art, 77-96, 2012 | 84 | 2012 |
| Prediction of protein assemblies, the next frontier: The CASP14‐CAPRI experiment MF Lensink, G Brysbaert, T Mauri, N Nadzirin, S Velankar, RAG Chaleil, ... Proteins: Structure, Function, and Bioinformatics 89 (12), 1800-1823, 2021 | 81 | 2021 |
| Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies JA Ruffolo, JJ Gray Biophysical Journal 121 (3), 155a-156a, 2022 | 80 | 2022 |
| Real-time PyMOL visualization for Rosetta and PyRosetta EH Baugh, S Lyskov, BD Weitzner, JJ Gray PloS one 6 (8), e21931, 2011 | 80 | 2011 |
| Structural model of the mAb 806-EGFR complex using computational docking followed by computational and experimental mutagenesis A Sivasubramanian, G Chao, HM Pressler, KD Wittrup, JJ Gray Structure 14 (3), 401-414, 2006 | 80 | 2006 |
| Shape complementarity and hydrogen bond preferences in protein–protein interfaces: implications for antibody modeling and protein–protein docking D Kuroda, JJ Gray Bioinformatics 32 (16), 2451-2456, 2016 | 79 | 2016 |
| Structural diversity in the type IV pili of multidrug-resistant Acinetobacter KH Piepenbrink, E Lillehoj, CM Harding, JW Labonte, X Zuo, CA Rapp, ... Journal of Biological Chemistry 291 (44), 22924-22935, 2016 | 78 | 2016 |
| An expanded benchmark for antibody-antigen docking and affinity prediction reveals insights into antibody recognition determinants JD Guest, T Vreven, J Zhou, I Moal, JR Jeliazkov, JJ Gray, Z Weng, ... Structure 29 (6), 606-621. e5, 2021 | 76 | 2021 |
| Plasma cells are the most abundant gluten peptide MHC-expressing cells in inflamed intestinal tissues from patients with celiac disease LS Høydahl, L Richter, R Frick, O Snir, KS Gunnarsen, OJB Landsverk, ... Gastroenterology 156 (5), 1428-1439. e10, 2019 | 73 | 2019 |
| Adding diverse noncanonical backbones to rosetta: enabling peptidomimetic design K Drew, PD Renfrew, TW Craven, GL Butterfoss, FC Chou, S Lyskov, ... PLoS One 8 (7), e67051, 2013 | 73 | 2013 |
| Rapid calculation of protein pKa values using Rosetta KP Kilambi, JJ Gray Biophysical journal 103 (3), 587-595, 2012 | 73 | 2012 |
| CAPRI rounds 3–5 reveal promising successes and future challenges for RosettaDock MD Daily, D Masica, A Sivasubramanian, S Somarouthu, JJ Gray PROTEINS: Structure, Function, and Bioinformatics 60 (2), 181-186, 2005 | 72 | 2005 |
| Deciphering antibody affinity maturation with language models and weakly supervised learning JA Ruffolo, JJ Gray, J Sulam arXiv preprint arXiv:2112.07782, 2021 | 71 | 2021 |
| Solution-and adsorbed-state structural ensembles predicted for the statherin-hydroxyapatite system DL Masica, JJ Gray Biophysical Journal 96 (8), 3082-3091, 2009 | 71 | 2009 |
| Adsorption of colloidal particles by Brownian dynamics simulation: Kinetics and surface structures JJ Gray, RT Bonnecaze The Journal of Chemical Physics 114 (3), 1366-1381, 2001 | 71 | 2001 |
| De Novo Design of Peptide− Calcite Biomineralization Systems DL Masica, SB Schrier, EA Specht, JJ Gray Journal of the American Chemical Society 132 (35), 12252-12262, 2010 | 68 | 2010 |
| Acidic C-terminal domains autoregulate the RNA chaperone Hfq A Santiago-Frangos, JR Jeliazkov, JJ Gray, SA Woodson Elife 6, e27049, 2017 | 64 | 2017 |
| Improved prediction of antibody VL–VH orientation NA Marze, S Lyskov, JJ Gray Protein Engineering, Design and Selection 29 (10), 409-418, 2016 | 63 | 2016 |
| A generalized approach to sampling backbone conformations with RosettaDock for CAPRI rounds 13–19 A Sircar, S Chaudhury, KP Kilambi, M Berrondo, JJ Gray Proteins: Structure, Function, and Bioinformatics 78 (15), 3115-3123, 2010 | 63 | 2010 |
| Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies JA Ruffolo, LS Chu, SP Mahajan, JJ Gray Nature communications 14 (1), 2389, 2023 | 62 | 2023 |
| Generative language modeling for antibody design RW Shuai, JA Ruffolo, JJ Gray BioRxiv, 2021.12. 13.472419, 2021 | 61 | 2021 |
| Blind prediction of interfacial water positions in CAPRI MF Lensink, IH Moal, PA Bates, PL Kastritis, ASJ Melquiond, E Karaca, ... Proteins: Structure, Function, and Bioinformatics 82 (4), 620-632, 2014 | 61 | 2014 |
| Microstructure formation and kinetics in the random sequential adsorption of polydisperse tethered nanoparticles modeled as hard disks JJ Gray, DH Klein, BA Korgel, RT Bonnecaze Langmuir 17 (8), 2317-2328, 2001 | 61 | 2001 |
| Geometric potentials from deep learning improve prediction of CDR H3 loop structures JA Ruffolo, C Guerra, SP Mahajan, J Sulam, JJ Gray Bioinformatics 36 (Supplement_1), i268-i275, 2020 | 60 | 2020 |
| Protein structure prediction and design in a biologically realistic implicit membrane RF Alford, PJ Fleming, KG Fleming, JJ Gray Biophysical journal 118 (8), 2042-2055, 2020 | 57 | 2020 |
| Incorporating biochemical information and backbone flexibility in RosettaDock for CAPRI rounds 6–12 S Chaudhury, A Sircar, A Sivasubramanian, M Berrondo, JJ Gray PROTEINS: Structure, Function, and Bioinformatics 69 (4), 793-800, 2007 | 56 | 2007 |
| Pushing the backbone in protein-protein docking D Kuroda, JJ Gray Structure 24 (10), 1821-1829, 2016 | 53 | 2016 |
| Repertoire analysis of antibody CDR-H3 loops suggests affinity maturation does not typically result in rigidification JR Jeliazkov, A Sljoka, D Kuroda, N Tsuchimura, N Katoh, K Tsumoto, ... Frontiers in immunology 9, 338525, 2018 | 51 | 2018 |
| Partial high-resolution structure of phosphorylated and non-phosphorylated leucine-rich amelogenin protein adsorbed to hydroxyapatite DL Masica, JJ Gray, WJ Shaw The Journal of Physical Chemistry C 115 (28), 13775-13785, 2011 | 51 | 2011 |
| Web‐accessible molecular modeling with Rosetta: the Rosetta online server that includes everyone (ROSIE) R Moretti, S Lyskov, R Das, J Meiler, JJ Gray Protein Science 27 (1), 259-268, 2018 | 50 | 2018 |
| Enzymatic excision of uracil residues in nucleosomes depends on the local DNA structure and dynamics Y Ye, MR Stahley, J Xu, JI Friedman, Y Sun, JN McKnight, JJ Gray, ... Biochemistry 51 (30), 6028-6038, 2012 | 50 | 2012 |
| Toward a structure determination method for biomineral-associated protein using combined solid-state NMR and computational structure prediction DL Masica, JT Ash, M Ndao, GP Drobny, JJ Gray Structure 18 (12), 1678-1687, 2010 | 47 | 2010 |
| Modeling the structure of mAb 14B7 bound to the anthrax protective antigen A Sivasubramanian, JA Maynard, JJ Gray Proteins: Structure, Function, and Bioinformatics 70 (1), 218-230, 2008 | 47 | 2008 |
| Nonequilibrium phase behavior during the random sequential adsorption of tethered hard disks JJ Gray, DH Klein, RT Bonnecaze, BA Korgel Physical Review Letters 85 (21), 4430, 2000 | 47 | 2000 |
| Advances to tackle backbone flexibility in protein docking A Harmalkar, JJ Gray Current opinion in structural biology 67, 178-186, 2021 | 45 | 2021 |
| Chiral switching in biomineral suprastructures induced by homochiral L-amino acid W Jiang, MS Pacella, H Vali, JJ Gray, MD McKee Science advances 4 (8), eaas9819, 2018 | 45 | 2018 |
| Residue‐centric modeling and design of saccharide and glycoconjugate structures JW Labonte, J Adolf‐Bryfogle, WR Schief, JJ Gray Journal of computational chemistry 38 (5), 276-287, 2017 | 45 | 2017 |
| Accurate structure prediction of CDR H3 loops enabled by a novel structure-based C-terminal constraint BD Weitzner, JJ Gray The Journal of Immunology 198 (1), 505-515, 2017 | 45 | 2017 |
| Identification of structural mechanisms of HIV-1 protease specificity using computational peptide docking: implications for drug resistance S Chaudhury, JJ Gray Structure 17 (12), 1636-1648, 2009 | 45 | 2009 |
| Applying linear interaction energy method for rational design of noncompetitive allosteric inhibitors of the sarco-and endoplasmic reticulum calcium-ATPase P Singh, AM Mhaka, SB Christensen, JJ Gray, SR Denmeade, JT Isaacs Journal of medicinal chemistry 48 (8), 3005-3014, 2005 | 43 | 2005 |
| Targeted DNA methylation using an artificially bisected M. HhaI fused to zinc fingers B Chaikind, KP Kilambi, JJ Gray, M Ostermeier Public Library of Science 7 (9), e44852, 2012 | 42 | 2012 |
| Rheology and dynamics of sheared arrays of colloidal particles JJ Gray, RT Bonnecaze Journal of Rheology 42 (5), 1121-1151, 1998 | 42 | 1998 |
| Expanding the toolkit for membrane protein modeling in Rosetta J Koehler Leman, BK Mueller, JJ Gray Bioinformatics 33 (5), 754-756, 2017 | 39 | 2017 |
| Structure-based cross-docking analysis of antibody–antigen interactions KP Kilambi, JJ Gray Scientific reports 7 (1), 8145, 2017 | 37 | 2017 |
| Better together: Elements of successful scientific software development in a distributed collaborative community J Koehler Leman, BD Weitzner, PD Renfrew, SM Lewis, R Moretti, ... PLoS computational biology 16 (5), e1007507, 2020 | 34 | 2020 |
| Neutron Reflectometry Studies of the Adsorbed Structure of the Amelogenin, LRAP WJ Tarasevich, B. J., Perez-Salas, U. Masica, D. L., Philo, J., Kienzle, P ... J. Phys. Chem. B 117 (11), 3098, 2013 | 33 | 2013 |
| Using the RosettaSurface algorithm to predict protein structure at mineral surfaces MS Pacella, RA Thottungal, JJ Gray Methods in enzymology 532, 343-366, 2013 | 31 | 2013 |
| Structurally distinct toxicity inhibitors bind at common loci on β‐amyloid fibril B Keshet, JJ Gray, TA Good Protein science 19 (12), 2291-2304, 2010 | 30 | 2010 |
| Origin of anomalous multibody interactions JJ Gray, B Chiang, RT Bonnecaze Nature 402 (6763), 750-750, 1999 | 28 | 1999 |
| Structure-based non-canonical amino acid design to covalently crosslink an antibody–antigen complex J Xu, D Tack, RA Hughes, AD Ellington, JJ Gray Journal of structural biology 185 (2), 215-222, 2014 | 27 | 2014 |
| Protein-protein docking with dynamic residue protonation states KP Kilambi, K Reddy, JJ Gray PLoS computational biology 10 (12), e1004018, 2014 | 25 | 2014 |
| Structure prediction of domain insertion proteins from structures of individual domains M Berrondo, M Ostermeier, JJ Gray Structure 16 (4), 513-527, 2008 | 25 | 2008 |
| Robustification of rosettaantibody and rosetta snugdock JR Jeliazkov, R Frick, J Zhou, JJ Gray PloS one 16 (3), e0234282, 2021 | 24 | 2021 |
| " Necessary thought": Frank Bidart and the postconfessional J Gray Contemporary Literature 34 (4), 714-739, 1993 | 24 | 1993 |
| A high throughput mutagenic analysis of yeast sumo structure and function HA Newman, PB Meluh, J Lu, J Vidal, C Carson, E Lagesse, JJ Gray, ... PLoS genetics 13 (2), e1006612, 2017 | 23 | 2017 |
| Interfacial mineral–peptide properties of a mineral binding peptide from osteonectin and bone-like apatite I Matlahov, T Iline-Vul, M Abayev, EMY Lee, M Nadav-Tsubery, ... Chemistry of Materials 27 (16), 5562-5569, 2015 | 23 | 2015 |
| Analysis of protein kinase autophosphorylation using expressed protein ligation and computational modeling KA Pickin, S Chaudhury, BCR Dancy, JJ Gray, PA Cole Journal of the American Chemical Society 130 (17), 5667-5669, 2008 | 23 | 2008 |
Brian KuhlmanUniversity of North CarolinaVerified email at email.unc.edu
