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Collaborators
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Key Collaborators and Strategic Alliances
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Steve Almo, Ph.D.
Center for Eukaryotic Structural Biology
Albert Einstein College of Medicine
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Alan Rick Horwitz, Ph.D.
Cell Migration Consortium
University of Virginia School of Medicine
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Roger Kornberg, Ph.D.
Hight Throughput X-ray Analysis of High-Value Targets
Stanford University
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Peter Kuhn, Ph.D.
Functional and Structural Proteomics of SARS
CoV-Related Proteins
The Scripps Research Institute
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James Paulson, Ph.D.
Consortium for Functional Glycomics
The Scripps Research Institute
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Jane and David Richardson
Structure Validation
Duke University Medical Center
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Jeffrey W. Smith, Ph.D.
Center on Proteolytic Pathways
The Burnham Institute
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Susan S. Taylor, Ph.D.
Protein Kinase Resource/Kinase NET
University of California, San Diego (UCSD)
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Richard J. Ulevitch, Ph.D.
Innate Immunity-Inflammation-Sepsis
The Scripps Research Institute
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Virgil L. Woods, Jr.
Deuterium-exchange Mass Spectrometry (DXMS)
University of California, San Diego (UCSD)
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Todd O. Yeates
Computation genomics, non-homology modeling
University of California, Los Angeles (UCLA)
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Other Collaborators
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Paul Adams, Ph.D. and
Sung-Hou Kim, Ph.D.
Berkeley Structural Genomics Center
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Marshall Bern
Palo Alto Research Center (PARC)
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Richard Bruce
Palo Alto Research Center (PARC)
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Tommy Bui
RoboDesign International, Inc.
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Henri Casanova, Ph.D.
University of California, San Diego (UCSD)
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Charles DeLisi, Ph.D.
Boston University
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Tony Fountain
University of California, San Diego (UCSD)
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Jean-Claude Latombe, Ph.D.
Stanford University School of Engineering
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Irimpan I. Mathews, Ph.D.
Stanford Synchrotron Radiation Lightsource (SSRL)
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Ross Overbeek
Fellowship for Interpretation of Genomes (FIG)
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Philip M. Papadopoulos, Ph.D.
San Diego Supercomputer Center
University of California, San Diego (UCSD)
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Anastassis Perrakis
The Netherlands of Cancer Institute
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Ronald D. Ruth
Lyncean Technolgies, Inc.
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Peter Schultz
The Scripps Research Institute (TSRI)
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S. Michael Soltis
Stanford Synchrotron Radiation Lightsource (SSRL)
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Affiliated Partnerships
A number of technology developments have now been implemented in JCSG and have resulted in an extensive network of
funded programs/centers that are leveraged for production.
We have listed these for further exploration.
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Next Generation Crystallization/Imaging Production System (IAVI/TSRI/JCSG-1/RoboDesign)-
A strategic partnership has been formed to keep the crystallization robotic system state-of-the-art.
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Viral Proteome Structural Genomics- http://sars.scripps.edu
The center for Functional and Structural Proteomics of SARS-CoV related proteins was established as a JCSG affiliated center in 2003
in response to the initial SARS outbreak. Its goal is to establish the comprehensive molecular characterization and catloging of all SARS
discovery and comprehensive proteome analysis for the functional mapping of the SARS-CoV proteome and will determine the fuction/biological
role of the SARS-CoV and related proteins. Several approaches are being used to understand the function of each protein and its interactions
including the characterization of the life cycle and host response; the identification and charaterization of protein-protein interactions,
and the identification and characterization of ligands using enthalpy arrays.
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Membrane Protein Production Technologies-
http://jcimpt.scripps.edu
The NIH-funded JCIMPT develops and disseminates methods and technologies for structure-grade production of membrane proteins. JCIMPT is
focusing on integral membrane proteins expressed in cell-free, baculovirus and mammalian cell systems.
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Computational development of a workflow engine for structure refinement and validation and a pending proposal for
computational mapping of crystallization space and identification of crystallization hits, lead by Marshall Bern from Scripps-PARC.
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Development of the enthalpy arrays for thermodynamic characterization of protein interactions; funded by Scripps PARC
and pending proposal as a bioengineering research partnership, headed by Richar Bruce from Scripps-PARC.
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Consortium for Functional Glycomics-
http://web.mit.edu/glycomics/consortium
The Consortium for Functional Glycomics (CFG) is a large research inititiative funded by NIGMS to
understand the rold of carbohydrate-protein interactions at the cell surface in cell-cell communication.
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Cell Migration Consortium- http://www.cellmigration.org/
The molecular complexity and dynamic nature of the supramolecular complexes involved in cell migration have hindered structural studies aimed
at revealing the underlying mechanisms of assembly and breakdown. The structural core, lead by Dr. Robert Liddington focuses on supramolecular
structures of complexes of proteins in cell-cell signaling and cell mobility.
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Alliance for Cell Signaling (AfCS)-
http://www.afcs.org/
The AFCS-Nature Singaline Gateway is a comprehensive and up-to-the minute resource for anyone
interested in signal transduction. This Gateway represents a unique collaboration between
academia and scientific publishing and is designed to facilitate navigation of the complex world
of research into cellular signaling. Information and data presented here are freely available
to all.
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The Protein Kinase Resource (PKR) -
http://pkr.sdsc.edu/html/index.shtml
The Protein Kinase Resource (PKR) aims to become a web accessible compendium of information
on the protein kinase family of enzymes. This resource will include tools for structural and
computational analyses as well as links to related information maintained by others. The PKR is
a collaborative project of protein kinase researchers and computational biologists working to
create a datase integrating molecular and cellular information.
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Center on Proteolytic Pathways-
http://www.ncrrprog/roadmap/ntcnpdirectory.asp
CPP is a National Resource for the study of proteases, their inhibitors, their products, and upstream and downstream regulatory pathways.
The strategic goal of the CPP is to develop the Protease Pathway Interrogation Platform (PPIP) technology. A key and unique feature of this
technology platform is its focus on measuring activity, as opposed to just expression levels or presence of a given protein, in a cell.
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Systems Approach to Innate Immunity-Inflammaton-
http://www.septicshock.org/
This multi-institution consortium focuses on understanding and modeling of the human cell response to sepsis. Innate immunity protects the body
from infection by a very broad range of microbes, the vast microbial flora that normally inhabit the surfaces of human skin and mucosae. Innate
immunity is regulated by serveral groups of proteins, containing specific domains - many of them with unknown structure. Most proteins innate
immunity form large paralogous families, where subtle functional difference are caused by relatively small sequence differences, often enhanced
by disease-causing mutations. These proteins are very challenging and often have folds which are recalcitrant ot strucutre study.
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Scripps PARC Institute for Advance Biomedical Sciences
http://www.scrippsparc.org
The Scripps-PARC Institute for Advanced Biomedical Sciences is a partnership between the Palo
Alto Research Center (PARC) and The Scripps Research Institute (TSRI). The Institute's purpose
is to invent and deliver novel instrumentation and information systems to accelerate understanding
and discovery in the life sciences.
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Tools
We are grateful to the many scientists who have contributed to our effort by creating tools that they are willing to share with
our center and/or with the entire community. In particular, we wish to express our thanks to Adam Godzik's research group at the
Burnham Institute, who have shared freely the tools they have created for their research purposes.
We list these tools with links to their home pages for further exploration.
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CD-HI
Dr. Adam Godzik's Laboratory, The Burnham Institute
Tool for clustering large protein databases at high sequence identity threshold (>70%).
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Fold Family Assignment Tool (FFAS)
Dr. Adam Godzik's Laboratory, The Burnham Institute
Tool for identifying folds whose structure can be predicted with high confidence.
[L. Rychlewski, L. Jaroszewski, W. Li, A. Godzik (2000), Protein Science 9, 232-241]
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PSQS
Dr. Adam Godzik's Laboratory, The Burnham Institute
Tool for checking Proteins Model Quality.
[L. Jaroszewski L., K. Pawlowski and A. Godzik (1998) J.Mol.Model. 4, 294-309.]
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PFA-HMM
Washington University in St. Louis
Tool for Hidden Markov Models for detecting protein sequence homology
[A. Bateman, E. Birney, R. Durbin, S. R. Eddy, K. L. Howe and E. L. L. Sonnhammer (2000) Nucl. Acids Res. 28:263-266]
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TMHMM
Center for Biological Sequence Analysis (CBS), Technical University of Denmark DTU
Tool for transmembrane region prediction
[A. Krogh, B. Larsson, G. von Heijne and E. L. L. Sonnhammer (2001) J. Mol. Biol. 305:567-580]
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NNPredict
University of California, San Francisco
Tool that predicts the secondary structure type for each residue in an amino acid sequence.
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Modeller
Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and California Institute for
Quantitative Biomedical Research, Univ. of Calif., San Francisco
Tool for creating 3D models based on sequence alignments.
[M. A. Marti-Renom, A. Stuart, A. Fiser, R. S\341nchez, F. Melo and A. Sali (2000) Annu. Rev. Biophys. Biomol. Struct. 29, 291-325]
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PROSITE
Swiss Institute of Bioinformatics
Database of protein families and domains from The ExPASy (Expert Protein Analysis System) proteomics server.
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PROCHECK
European Bioinformatics Institute
Tool for evaluation of model geometry.
[R. A. Laskowski, V. MacArthur, D. S. Moss and J. M. Thornton (1993) J. Appl. Cryst. 26: 283-291]
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SFCHECK
Tool for evaluating the quality of macromolecular structure-factor data and their agreement
with atomic model.
[A. A. Vaguine, J. Richelle and S. J. Wodak (1999) Acta Cryst. D55, 191-205]
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Prove
SCMBB - Service de Conformation des Macromol\351cules Biologiques et de Bioinformatique
Universit\351 Libre de Bruxelles
Tool for evaluating model quality based in molecular volume.
[J. Pontius, J. Richelle, and S. J. Wodak (1996) J. Mol. Biol. 264: 121-136];
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ERRAT
UCLA-DOE Institute for Genomics and Proteomics
Tool for structure validation.
[C. Colovos and T.O. Yeates (1993) Protein Sci 2:1511-9]
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WASP
Washington University School of Medicine
Tool for screening solvent for ions that are called as water molecules.
[M. Nayal and E. Di Cera (1996) JMB 256, 228-234]
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DDQ
The Lerner Institute
Tool for evaluation of model quality by solvent density.
[F. van den Akker and W. Hol (1999) Acta Cryst. D55, 206-218]
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What Check
Tool for Errors in protein structures.
[R. W. W. Hooft, G. Vriend, C. Sander and E. E. Abola (1996) Nature 381, 272-272]
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