JCSG Acknowledgements

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JCSG Acknowledgements

JCSG Acknowledgements

Supporting Institution

Collaborators

Affiliated Partnerships

Tools

Supporting Institutions

The JCSG is a multi-institutional consortium with major activities at The Scripps Research Institute (TSRI) [Administrative Core and Crystallomics Core], the Genomics Institute of the Novartis Research Foundation (GNF) [Crystallomics Core], the University of California, San Diego (UCSD) [Bioinformatics Core], the Burnham Institute [Bioinformatics Core] and the Stanford Synchrotron Radiation Laboratory (SSRL) at Stanford University [Structure Determination Core].

	The Scripps Research Institute (TSRI) Richard A. Lerner, President	http://www.scripps.edu
	Genomics Institute of the Novartis Foundation (GNF) Peter Schultz, Director	http://web.gnf.org/index.shtml
	University of California, San Diego (UCSD) Richard Attiyeh, Vice Chancellor for Research	http://www.ucsd.edu
	The Burnham Institute John C. Reed, President & CEO	http://www.burnham-inst.org/
	Stanford Synchrotron Radiation Laboratory (SSRL) Keith O. Hodgson, Director	http://www-ssrl.slac.stanford.edu/welcome.html

Collaborators

Key Collaborators and Strategic Alliances

	Steve Almo, Ph.D. Center for Eukaryotic Structural Biology Albert Einstein College of Medicine		Alan Rick Horwitz, Ph.D. Cell Migration Consortium University of Virginia School of Medicine
	Roger Kornberg, Ph.D. Hight Throughput X-ray Analysis of High-Value Targets Stanford University		Peter Kuhn, Ph.D. Functional and Structural Proteomics of SARS CoV-Related Proteins The Scripps Research Institute
	James Paulson, Ph.D. Consortium for Functional Glycomics The Scripps Research Institute		Jane and David Richardson Structure Validation Duke University Medical Center
	Jeffrey W. Smith, Ph.D. Center on Proteolytic Pathways The Burnham Institute		Susan S. Taylor, Ph.D. Protein Kinase Resource/Kinase NET University of California, San Diego (UCSD)
	Richard J. Ulevitch, Ph.D. Innate Immunity-Inflammation-Sepsis The Scripps Research Institute		Virgil L. Woods, Jr. Deuterium-exchange Mass Spectrometry (DXMS) University of California, San Diego (UCSD)
	Todd O. Yeates Computation genomics, non-homology modeling University of California, Los Angeles (UCLA)

Other Collaborators

	Paul Adams, Ph.D. and Sung-Hou Kim, Ph.D. Berkeley Structural Genomics Center		Marshall Bern Palo Alto Research Center (PARC)
	Richard Bruce Palo Alto Research Center (PARC)		Tommy Bui RoboDesign International, Inc.
	Henri Casanova, Ph.D. University of California, San Diego (UCSD)		Charles DeLisi, Ph.D. Boston University
	Tony Fountain University of California, San Diego (UCSD)		Jean-Claude Latombe, Ph.D. Stanford University School of Engineering
	Irimpan I. Mathews, Ph.D. Stanford Synchrotron Radiation Laboratory (SSRL)		Ross Overbeek Fellowship for Interpretation of Genomes (FIG)
	Philip M. Papadopoulos, Ph.D. San Diego Supercomputer Center University of California, San Diego (UCSD)		Anastassis Perrakis The Netherlands of Cancer Institute
	Ronald D. Ruth Lyncean Technolgies, Inc.		Peter Schultz The Scripps Research Institute (TSRI)
	S. Michael Soltis Stanford Synchrotron Radiation Laboratory (SSRL)

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.

	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.
	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.
	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.
	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.
	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.
	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.
	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.
	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.
	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.
	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.
	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.
	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.

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.

	CD-HI Dr. Adam Godzik's Laboratory, The Burnham Institute Tool for clustering large protein databases at high sequence identity threshold (>70%).
	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]
	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.]
	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]
	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]
	NNPredict University of California, San Francisco Tool that predicts the secondary structure type for each residue in an amino acid sequence.
	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�nchez, F. Melo and A. Sali (2000) Annu. Rev. Biophys. Biomol. Struct. 29, 291-325]
	PROSITE Swiss Institute of Bioinformatics Database of protein families and domains from The ExPASy (Expert Protein Analysis System) proteomics server.
	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]
	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]
	Prove SCMBB - Service de Conformation des Macromol�cules Biologiques et de Bioinformatique Universit� 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];
	ERRAT UCLA-DOE Institute for Genomics and Proteomics Tool for structure validation. [C. Colovos and T.O. Yeates (1993) Protein Sci 2:1511-9]
	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]
	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]
	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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