Jeffrey J. Gray's research group at the Johns Hopkins University studies the computational structural prediction and design of glycans, membrane proteins, antibodies, and various complexes. The GrayLab is a member of the RosettaCommons, responsible for creating PyRosetta and co-developing the Rosetta biomolecular modeling suite.
http://graylab.jhu.edu/
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GrayLab at Johns Hopkins University | graylab.jhu.edu Reviews
https://graylab.jhu.edu
Jeffrey J. Gray's research group at the Johns Hopkins University studies the computational structural prediction and design of glycans, membrane proteins, antibodies, and various complexes. The GrayLab is a member of the RosettaCommons, responsible for creating PyRosetta and co-developing the Rosetta biomolecular modeling suite.
ROSIE: The Rosetta Online Server that Includes Everyone
Welcome to ROSIE Rosetta Online Server that Includes Everyone. See more info at our About. Get Started with ROSIE. Server related documentation and info. This is a list of forums for Rosetta users to discuss problems with running Rosetta and is monitored by Rosetta developers. Latest Rosetta User Guide. Rosetta Protocols opened for academic users:. Rosetta Protocols under beta testing (for developers only):. ROSIE is web front-end for Rosetta software suite. Developed by Sergey Lyskov, GrayLab at JHU.
ROSIE: The Rosetta Online Server that Includes Everyone
Welcome to ROSIE Rosetta Online Server that Includes Everyone. See more info at our About. Get Started with ROSIE. Server related documentation and info. This is a list of forums for Rosetta users to discuss problems with running Rosetta and is monitored by Rosetta developers. Latest Rosetta User Guide. Rosetta Protocols opened for academic users:. Rosetta Protocols under beta testing (for developers only):. ROSIE is web front-end for Rosetta software suite. Developed by Sergey Lyskov, GrayLab at JHU.
ROSIE: The Rosetta Online Server that Includes Everyone
Welcome to ROSIE Rosetta Online Server that Includes Everyone. See more info at our About. Get Started with ROSIE. Server related documentation and info. This is a list of forums for Rosetta users to discuss problems with running Rosetta and is monitored by Rosetta developers. Latest Rosetta User Guide. Rosetta Protocols opened for academic users:. Rosetta Protocols under beta testing (for developers only):. ROSIE is web front-end for Rosetta software suite. Developed by Sergey Lyskov, GrayLab at JHU.
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:...
ROSIE: The Rosetta Online Server that Includes Everyone
Welcome to ROSIE Rosetta Online Server that Includes Everyone. See more info at our About. Get Started with ROSIE. Server related documentation and info. This is a list of forums for Rosetta users to discuss problems with running Rosetta and is monitored by Rosetta developers. Latest Rosetta User Guide. Rosetta Protocols opened for academic users:. Rosetta Protocols under beta testing (for developers only):. ROSIE is web front-end for Rosetta software suite. Developed by Sergey Lyskov, GrayLab at JHU.
graylab.jhu.edu
Positions Available in Gray Lab
http://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...
Courses Taught By Prof. Jeffrey J. Gray
http://graylab.jhu.edu/courses.html
Welcome to the Gray Lab. Courses taught by Prof. Gray. ChemBE 101: Chemical and Biomolecular Engineering in Today's World. ChemBE 202: Introduction to Chemical and Biological Process Analysis. Fall 2011, Fall 2012, Spring 2014, Spring 2015, Fall 2015]. Lectures from this course are on YouTube:. ChemBE 409: Modeling, Dynamics and Control of Chemical and Biological Processes. Spring 2003, Fall 2003-2010]. ChemBE 406/606: Molecular Simulations and Multiscale Modeling, taught with German Drazer.
Lab Members in Gray Lab
http://graylab.jhu.edu/members.html
Welcome to the Gray Lab. Jeffrey J. Gray, Ph.D. Email: jgray at jhu dot edu. Jason W. Labonte, Ph.D. PhD, Chemistry, Johns Hopkins University. BS, Biochemistry, Grove City College. Julia Koehler Leman, Ph.D. PhD, Chemical and Physical Biology, Vanderbilt University. MS, Physics, Leipzig, Germany. Email: julia.koehler[at]jhu.edu. Brian Weitzner, Ph.D. 2015. PhD, Chemical and Biomolecular Engineering, Johns Hopkins University. BS, Chemical Engineering, Cornell. Email: brian.weitzner at jhu dot edu. BS, Bio...
Docking Decoys
http://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...
Rosetta Docking Software
http://graylab.jhu.edu/docking/rosetta
Welcome to the Gray Lab. RosettaDock predicts the structure of a protein-protein complex from the individual structures of the monomer components. RosettaDock is distributed as part of the Rosetta Protein Structure Prediction and Design Suite. Rosetta is available from the RosettaCommons. Chaudhury, S. and Gray, J. J. Conformer selection and induced fit in flexible backbone protein-protein docking using computational and NMR ensembles, J. Mol. Biol. 4), 1068-1087 (2008). Online. Updated 8/13/2008 graylab...
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What is PyRosetta? - PyRosetta
http://www.pyrosetta.org/home/what-is-pyrosetta
PyRosetta is a Python-based interface to the Rosetta molecular modeling suite. It enables a user to create custom molecular modeling algorithms with Rosetta sampling and scoring functions using Python scripting. PyRosetta is designed to make the sophisticated Rosetta molecular modeling suite accessible to a broader audience of scientists in the life sciences. Users can implement new algorithms or edit existing ones by writing Python scripts using the appropriate Rosetta objects and functions. The use...
PyRosetta
http://www.pyrosetta.org/home
PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling suite. It enables users to design their own custom molecular modeling algorithms using Rosetta sampling methods and energy functions. PyRosetta was created at Johns Hopkins University. By Jeffrey J. Gray, Sergey Lyskov, and the PyRosetta Team. Its development is supported by:. Videos from JHU Computational Protein Structure Prediction and Design graduate course. Posted Apr 1, 2015, 1:48 PM. By Jeffrey J. Gray.
About ROSIE
http://rosie.graylab.jhu.edu/about
Welcome to ROSIE Rosetta Online Server that Includes Everyone. See more info at our About. Get Started with ROSIE. Server related documentation and info. This is a list of forums for Rosetta users to discuss problems with running Rosetta and is monitored by Rosetta developers. Latest Rosetta User Guide. Is a web front-end to the Rosetta 3.x. Is an easy-to-use web interface for selected Rosetta protocols. Framework is developed by Sergey Lyskov at GrayLab at JHU. Average waiting time in queue:.
[ROSIE] Docking Protocol
http://rosie.graylab.jhu.edu/docking2
Welcome to ROSIE Rosetta Online Server that Includes Everyone. Please cite the following article when referring to results from our ROSIE server:. Lyskov S., Gray J.J. "The RosettaDock server for local protein-protein docking" Nucleic Acids Research. 36 (Web Server Issue), W233-W238 (2008). Online. 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. Modeling tools developed by GrayLab.
[ROSIE] FARFAR (RNA De Novo) Protocol
http://rosettaserver.graylab.jhu.edu/rna_denovo
Welcome to ROSIE Rosetta Online Server that Includes Everyone. Rosetta FARFAR (RNA De Novo) Protocol. Please cite the following article when referring to results from our ROSIE server:. Das, R., Karanicolas, J., and Baker, D. (2010), "Atomic accuracy in predicting and designing noncanonical RNA structure". Nature Methods 7:291-294. Link. This is the primary citation for these algorithms]. PLoS One. 2013 May 22;8(5):e63906. doi: 10.1371/journal.pone.0063906. Print 2013. Link. For fragment assembly witout ...
[ROSIE] Ligand Docking Protocol
http://rosettaserver.graylab.jhu.edu/ligand_docking
Welcome to ROSIE Rosetta Online Server that Includes Everyone. Rosetta Ligand Docking Protocol. Submit Ligand Docking task]. Ligand Docking Server Documentation]. Please cite the following article when referring to results from our ROSIE server:. Combs, S. A., Deluca, S. L., DeLuca, S. H., Lemmon, G. H., Nannemann, D. P., Nguyen, E. D., et al. (2013). Small-molecule ligand docking into comparative models with Rosetta. Nature Protocols, 8(7), 1277 1298. doi:10.1038/nprot.2013.074.
[ROSIE] Supercharge Protocol
http://rosettaserver.graylab.jhu.edu/supercharge
Welcome to ROSIE Rosetta Online Server that Includes Everyone. ROSIE is web front-end for Rosetta software suite. Developed by Sergey Lyskov, GrayLab at JHU.
[ROSIE] Sequence Tolerance Protocol
http://rosettaserver.graylab.jhu.edu/sequence_tolerance
Welcome to ROSIE Rosetta Online Server that Includes Everyone. Rosetta Sequence Tolerance Protocol. Submit Sequence Tolerance task]. ROSIE is web front-end for Rosetta software suite. Developed by Sergey Lyskov, GrayLab at JHU.
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Home Page | David Gray Lab
Skip to main content. The development of antibody responses to most antigens and pathogens requires interaction between B and T cells. So helper signals from CD4 (helper) T cells are delivered to B cells, facilitating their differentiation into antibody secreting plasma cells. Although many details remain to be discovered, we know much about the molecular nature of T cell help for B cells (contact signals such as CD40 and soluble cytokines). Our work leads us to a better understanding of the development ...
Gray laboratory
Biological and physical responses to environmental change. Why is a particular species abundant in one area but rare or absent in another? The answer to this fundamental question might seem obvious on the surface, but ecologists have spent decades trying to answer it! Back to the original question: what factors control the distribution and abundance of organisms? Some of the basic questions I hope to answer with my research are:. What role do dispersal and colonization processes play in determining the d...
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The Nathanael Gray Laboratory | Home
Despite the tremendous increase in understanding of basic cancer mechanisms and potential targets there has only been a moderate increase in effective new therapies to treat cancer. The Gray Laboratory seeks to develop first-in-class chemical inhibitors that can be used to pharmacologically validate new potential targets to treat cancer and other diseases. October 29, 2015. We won group costume contest on BCMP retreat party! October 19, 2015. Welcome to Lena Muenzker joining us as visiting student.
GrayLab at Johns Hopkins University
Department of Chemical and Biomolecular Engineering. Program in Molecular and Computational Biophysics. Developed by Kayvon Tabrizi.
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