(Taken from the Application): The Albert Einstein College of Medicine, the Department of Biology at Brookhaven National Laboratory, Mount Sinai School of Medicine, the Rockefeller University, and the Weill Medical College of Cornell University have formed the New York Structural Genomics Research Consortium (NYSGRC) for high-throughput, structural and functional studies of proteins. The research program takes the form of a Pilot Study focused on establishing a fully-integrated, high-throughput system for protein family classification and target selection, target protein expression, purification, biophysical characterization and crystallization, target protein structure determination by X-ray crystallography, and analyses and dissemination of the results. The long-term goal of the NYSGRC is to create an efficient, cost-effective Structural Genomics Center that will contribute substantially to the task of determining the 10,000 plus three-dimensional protein structures envisaged by the National Institute of General Medical Sciences Protein Structure Initiative.
The specific aims of the NYSGRC application are:
Aim 1. Identify target protein sequences for structural genomics.
Aim 2. Develop high-throughput E. coli expression of soluble target proteins.
Aim 3. Develop high-throughput production of target proteins.
Aim 4. Develop high-throughput biophysical characterization of target proteins.
Aim 5. Develop high-throughput crystallization of target proteins.
Aim 6. Develop efficient experimental strategies for MAD crystallography.
Aim 7. Develop high-throughput synchrotron data collection with target protein crystals.
Aim 8. Develop and use an Internet-based computational pipeline for protein crystallography.
Aim 9. Develop high-throughput molecular replacement tools for crystallography.
Aim 1 0 Develop high-throughput comparative modeling for structural genomics.
Aim 1 1. Develop efficient annotation and dissemination of protein structures and models.
Aim 1 2. Develop an Internet-based """"""""web-book"""""""" for use by the NYSGRC.
| Webb, Benjamin; Sali, Andrej (2016) Comparative Protein Structure Modeling Using MODELLER. Curr Protoc Bioinformatics 54:5.6.1-5.6.37 |
| Webb, Benjamin; Sali, Andrej (2014) Comparative Protein Structure Modeling Using MODELLER. Curr Protoc Bioinformatics 47:5.6.1-32 |
| Madhusudhan, M S; Webb, Benjamin M; Marti-Renom, Marc A et al. (2009) Alignment of multiple protein structures based on sequence and structure features. Protein Eng Des Sel 22:569-74 |
| Melo, Francisco; Sali, Andrej (2007) Fold assessment for comparative protein structure modeling. Protein Sci 16:2412-26 |
| Velge, P; Herler, M; Johansson, J et al. (2007) A naturally occurring mutation K220T in the pleiotropic activator PrfA of Listeria monocytogenes results in a loss of virulence due to decreasing DNA-binding affinity. Microbiology 153:995-1005 |
| Marti-Renom, Marc A; Pieper, Ursula; Madhusudhan, M S et al. (2007) DBAli tools: mining the protein structure space. Nucleic Acids Res 35:W393-7 |
| Soranzo, Nicole; Kelly, Libusha; Martinian, Lillian et al. (2007) Lack of support for a role for RLIP76 (RALBP1) in response to treatment or predisposition to epilepsy. Epilepsia 48:674-83 |
| Agarwal, Rakhi; Burley, Stephen K; Swaminathan, Subramanyam (2007) Structural analysis of a ternary complex of allantoate amidohydrolase from Escherichia coli reveals its mechanics. J Mol Biol 368:450-63 |
| Feyfant, Eric; Sali, Andrej; Fiser, Andras (2007) Modeling mutations in protein structures. Protein Sci 16:2030-41 |
| Eswar, Narayanan; Webb, Ben; Marti-Renom, Marc A et al. (2007) Comparative protein structure modeling using MODELLER. Curr Protoc Protein Sci Chapter 2:Unit 2.9 |
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