The primary goal of this project is to provide the infrastructure for the Critical Assessment of Protein Structure Prediction (CASP) prediction experiments. With the success of the sequencing projects, the structural characterization of the genome-encoded proteins becomes increasingly important. Extensive knowledge of protein structure will significantly aid the investigation of protein function, protein interactions, and biochemical pathways. It will also have a major impact on our understanding of biology and human disease, and eventually on drug design. Experimental determination of structure is inherently time-consuming and costly. Currently there is a two order-of-magnitude gap in numbers between proteins characterized by sequencing and by structure determination efforts. Computational techniques of structure modeling and prediction hold great promise for narrowing this gap. The CASP process was established to answer two main questions: First, what level of prediction quality can be expected of these techniques? And second, which methods offer the most promise for continued development? CASP is a community-wide program, with approximately 200 research groups world-wide submitting over 40,000 predictions in the last round. Our group is the primary infrastructure resource for CASP, and handles processing of predictions, develops and implements evaluation software, performs prediction assessment, develops analysis and display tools, and facilitates access to predictions and their evaluation data. We propose to support the continuing operation of CASP and to expand its infrastructure, including an increased capacity for assessing predictions, further development and refinement of the evaluation software, and improved prediction analysis methods. In addition, we will conduct a series of specialized off-CASP experiments dedicated to overcoming the most significant obstacles to progress in structure prediction. We will also provide the infrastructure for a community-wide program to build useful structural models of biologically important proteins. Finally, we will place special emphasis on interactions with lecturers and researchers throughout academia with the goal of disseminating the experience and the wealth of data gained through CASP.

Agency
National Institute of Health (NIH)
Institute
National Library of Medicine (NLM)
Type
Biotechnology Resource Grants (P41)
Project #
5P41LM007085-12
Application #
8117576
Study Section
Biomedical Library and Informatics Review Committee (BLR)
Program Officer
Ye, Jane
Project Start
2004-08-01
Project End
2012-06-14
Budget Start
2011-06-15
Budget End
2012-06-14
Support Year
12
Fiscal Year
2011
Total Cost
$515,168
Indirect Cost
Name
University of California Davis
Department
Genetics
Type
Schools of Arts and Sciences
DUNS #
047120084
City
Davis
State
CA
Country
United States
Zip Code
95618
Monastyrskyy, Bohdan; Fidelis, Krzysztof; Tramontano, Anna et al. (2011) Evaluation of residue-residue contact predictions in CASP9. Proteins 79 Suppl 10:119-25
Kryshtafovych, Andriy; Fidelis, Krzysztof; Tramontano, Anna (2011) Evaluation of model quality predictions in CASP9. Proteins 79 Suppl 10:91-106
Kryshtafovych, Andriy; Fidelis, Krzysztof; Moult, John (2011) CASP9 results compared to those of previous CASP experiments. Proteins 79 Suppl 10:196-207
Monastyrskyy, Bohdan; Fidelis, Krzysztof; Moult, John et al. (2011) Evaluation of disorder predictions in CASP9. Proteins 79 Suppl 10:107-18
Kryshtafovych, Andriy; Moult, John; Bartual, Sergio G et al. (2011) Target highlights in CASP9: Experimental target structures for the critical assessment of techniques for protein structure prediction. Proteins 79 Suppl 10:6-20
Moult, John; Fidelis, Krzysztof; Kryshtafovych, Andriy et al. (2009) Critical assessment of methods of protein structure prediction - Round VIII. Proteins 77 Suppl 9:1-4
Schwede, Torsten; Sali, Andrej; Honig, Barry et al. (2009) Outcome of a workshop on applications of protein models in biomedical research. Structure 17:151-9
Kryshtafovych, Andriy; Fidelis, Krzysztof (2009) Protein structure prediction and model quality assessment. Drug Discov Today 14:386-93
Hvidsten, Torgeir R; Kryshtafovych, Andriy; Fidelis, Krzysztof (2009) Local descriptors of protein structure: a systematic analysis of the sequence-structure relationship in proteins using short- and long-range interactions. Proteins 75:870-84
Cozzetto, Domenico; Kryshtafovych, Andriy; Fidelis, Krzysztof et al. (2009) Evaluation of template-based models in CASP8 with standard measures. Proteins 77 Suppl 9:18-28

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