Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies von Ruffolo, Jeffrey A., Chu, Lee-Shin, Mahajan, Sai Pooja, Gray, Jeffrey J.

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Implicit model to capture electrostatic features of membrane environment von Samanta, Rituparna, Gray, Jeffrey J

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Pushing the Backbone in Protein-Protein Docking von Kuroda, Daisuke, Gray, Jeffrey J.

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Advances to tackle backbone flexibility in protein docking von Harmalkar, Ameya, Gray, Jeffrey J

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Antibody structure prediction using interpretable deep learning von Ruffolo, Jeffrey A., Sulam, Jeremias, Gray, Jeffrey J.

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Benchmarking and analysis of protein docking performance in Rosetta v3.2 von Chaudhury, Sidhartha, Berrondo, Monica, Weitzner, Brian D, Muthu, Pravin, Bergman, Hannah, Gray, Jeffrey J

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PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta von Chaudhury, Sidhartha, Lyskov, Sergey, Gray, Jeffrey J.

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Simultaneous prediction of antibody backbone and side-chain conformations with deep learning von Akpinaroglu, Deniz, Ruffolo, Jeffrey A, Mahajan, Sai Pooja, Gray, Jeffrey J

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Shape complementarity and hydrogen bond preferences in protein-protein interfaces: implications for antibody modeling and protein-protein docking von Kuroda, Daisuke, Gray, Jeffrey J

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SnugDock: paratope structural optimization during antibody-antigen docking compensates for errors in antibody homology models von Sircar, Aroop, Gray, Jeffrey J

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A comprehensive, high-resolution map of a gene's fitness landscape von Firnberg, Elad, Labonte, Jason W, Gray, Jeffrey J, Ostermeier, Marc

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Geometric potentials from deep learning improve prediction of CDR H3 loop structures von Ruffolo, Jeffrey A, Guerra, Carlos, Mahajan, Sai Pooja, Sulam, Jeremias, Gray, Jeffrey J

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Chiral acidic amino acids induce chiral hierarchical structure in calcium carbonate von Jiang, Wenge, Pacella, Michael S., Athanasiadou, Dimitra, Nelea, Valentin, Vali, Hojatollah, Hazen, Robert M., Gray, Jeffrey J., McKee, Marc D.

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Efficient flexible backbone protein–protein docking for challenging targets von Marze, Nicholas A, Roy Burman, Shourya S, Sheffler, William, Gray, Jeffrey J

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Serverification of molecular modeling applications: the Rosetta Online Server that Includes Everyone (ROSIE) von Lyskov, Sergey, Chou, Fang-Chieh, Conchúir, Shane Ó, Der, Bryan S, Drew, Kevin, Kuroda, Daisuke, Xu, Jianqing, Weitzner, Brian D, Renfrew, P Douglas, Sripakdeevong, Parin, Borgo, Benjamin, Havranek, James J, Kuhlman, Brian, Kortemme, Tanja, Bonneau, Richard, Gray, Jeffrey J, Das, Rhiju

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The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design von Alford, Rebecca F, Leaver-Fay, Andrew, Jeliazkov, Jeliazko R, O’Meara, Matthew J, DiMaio, Frank P, Park, Hahnbeom, Shapovalov, Maxim V, Renfrew, P. Douglas, Mulligan, Vikram K, Kappel, Kalli, Labonte, Jason W, Pacella, Michael S, Bonneau, Richard, Bradley, Philip, Dunbrack, Roland L, Das, Rhiju, Baker, David, Kuhlman, Brian, Kortemme, Tanja, Gray, Jeffrey J

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Robustification of RosettaAntibody and Rosetta SnugDock von Jeliazkov, Jeliazko R, Frick, Rahel, Zhou, Jing, Gray, Jeffrey J

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Deep Learning in Protein Structural Modeling and Design von Gao, Wenhao, Mahajan, Sai Pooja, Sulam, Jeremias, Gray, Jeffrey J.

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RosettaDock server for local protein-protein docking von Lyskov, Sergey, Gray, Jeffrey J

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Rapid Calculation of Protein pKa Values Using Rosetta von Kilambi, Krishna Praneeth, Gray, Jeffrey J.

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