rosettatests.graylab.jhu.edu rosettatests.graylab.jhu.edu

rosettatests.graylab.jhu.edu

Jeffrey J. Gray Research Group, Johns Hopkins University

Welcome to the Gray Lab. Department of Chemical and Biomolecular Engineering. And Program in Molecular and Computational Biophysics. Baltimore, Maryland 21218. The goal of our research is to create and apply protein structure prediction methods to solve practical problems in self-assembly and function in biomolecular engineering. Package for interactive protein structure prediction and design. The Rosetta Online Server that Includes Everyone (includes RosettaAntibody and RosettaDock servers). Bottom row:...

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Jeffrey J. Gray Research Group, Johns Hopkins University | rosettatests.graylab.jhu.edu Reviews
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Welcome to the Gray Lab. Department of Chemical and Biomolecular Engineering. And Program in Molecular and Computational Biophysics. Baltimore, Maryland 21218. The goal of our research is to create and apply protein structure prediction methods to solve practical problems in self-assembly and function in biomolecular engineering. Package for interactive protein structure prediction and design. The Rosetta Online Server that Includes Everyone (includes RosettaAntibody and RosettaDock servers). Bottom row:...
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Jeffrey J. Gray Research Group, Johns Hopkins University | rosettatests.graylab.jhu.edu Reviews

https://rosettatests.graylab.jhu.edu

Welcome to the Gray Lab. Department of Chemical and Biomolecular Engineering. And Program in Molecular and Computational Biophysics. Baltimore, Maryland 21218. The goal of our research is to create and apply protein structure prediction methods to solve practical problems in self-assembly and function in biomolecular engineering. Package for interactive protein structure prediction and design. The Rosetta Online Server that Includes Everyone (includes RosettaAntibody and RosettaDock servers). Bottom row:...

INTERNAL PAGES

rosettatests.graylab.jhu.edu rosettatests.graylab.jhu.edu
1

Links

http://rosettatests.graylab.jhu.edu/links.html

Welcome to the Gray Lab. Directions to the JHU Homewood Campus. Academic Advising Appointments with Dr. Gray. CAPRI: Critical Assessment of PRediction of Interactions. Department of Chemical and Biomolecular Engineering. Program in Molecular Biophysics. The Protein Data Bank - www.pdb.org. The Sheridan Libraries Selected Science and Engineering Journals. Welch Library Electronic Journals.

2

Selected Publications

http://rosettatests.graylab.jhu.edu/publications.html

Welcome to the Gray Lab. Journal Publications: (Additional listings at Google Scholar. Kuroda, D. and Gray, J. J. "Shape complementarity of hydrogen bond preferences in protein-protein interfaces: Implications for antibody modeling and protein-protein docking," Bioinformatics. 2016) (*These authors contributed equally to this work). 9): e1004398 (2015). Online. 16), 2392-2402 (2015). Online. 16), 5562-5569 (2015). Online. 4), 581-596 (2015). Online. 2), 302-311 (2015). Online. 1), 1-24 (2015). Online.

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Docking Decoys

http://rosettatests.graylab.jhu.edu/docking/decoys

Welcome to the Gray Lab. There are three sets of decoys:. Bound perturbations": from perturbations of the bound complex structure (with native sidechains removed and rebuilt from rotamers). 1000 decoys for each of 54 targets. bound perturb.tgz. Unbound perturbations": from perturbations of the unbound component structures which were superimposed on the bound backbones (again, with sidechains removed and rebuilt). 1000 decoys for each of 54 targets. unbound perturb.tgz. Some oddities (Thanks to Yaoqi Zhou...

4

Facilities in Gray Lab

http://rosettatests.graylab.jhu.edu/facilities.html

Welcome to the Gray Lab. System: Dell PowerEdge High-Performance Computing Cluster. Processors: 8 dual-hex-core nodes, 13 dual-quad-core nodes, and 32 quad-core nodes for a total of 328 CPUs. RAM Memory: 1-2 GB/core. Network: 1 GB Ethernet High Speed Adapter. Capable of producing 10. We host the Rosetta Commons. Cluster, used (1) to test every incremental revision of the Rosetta code and (2) to run free calculations for the academic scientific community through our ROSIE. RAM Memory: 8 GB/node.

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Positions Available in Gray Lab

http://rosettatests.graylab.jhu.edu/positions.html

Welcome to the Gray Lab. We accept applicants throughout the year on the following broad projects:. Docking of Therapeutic Antibodies. To improve the protein-protein docking algorithm RosettaDock especially for application to therapeutic antibodies, one of the fastest-growing class of new drugs. Protein Interactions with Solid Surfaces. To apply email a CV and three references to jgray@jhu.edu. Or related field, or serious experience in computer programming. Applicants should email a resume and a transcr...

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Developer Resources | RosettaCommons

https://www.rosettacommons.org/dev

The hub for Rosetta modeling software. The following links are intended for Rosetta Developers, who have the passwords to these protected areas. If you need the password, please contact your PI. List of current developers. Access to the GitHub respositories and to the Wiki is restricted to developers. The Next Steps for Rosetta and the RosettaCommons (2013 and beyond). Expanding two scripting interfaces for generating custom protocols. Increasing the speed of Rosetta calculations.

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Jeffrey J. Gray Research Group, Johns Hopkins University

Welcome to the Gray Lab. Department of Chemical and Biomolecular Engineering. And Program in Molecular and Computational Biophysics. Baltimore, Maryland 21218. The goal of our research is to create and apply protein structure prediction methods to solve practical problems in self-assembly and function in biomolecular engineering. Package for interactive protein structure prediction and design. The Rosetta Online Server that Includes Everyone (includes RosettaAntibody and RosettaDock servers). Bottom row:...

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