Developing algorithms for predicting protein-protein interactions of homology modeled proteins.

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Description

The goal of this project was to examine the protein-protein docking problem, especially as it relates to homology-based structures, identify the key bottlenecks in current software tools, and evaluate and prototype new algorithms that may be developed to improve these bottlenecks. This report describes the current challenges in the protein-protein docking problem: correctly predicting the binding site for the protein-protein interaction and correctly placing the sidechains. Two different and complementary approaches are taken that can help with the protein-protein docking problem. The first approach is to predict interaction sites prior to docking, and uses bioinformatics studies of protein-protein interactions to ... continued below

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37 p.

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Martin, Shawn Bryan; Sale, Kenneth L.; Faulon, Jean-Loup Michel & Roe, Diana C. January 1, 2006.

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Description

The goal of this project was to examine the protein-protein docking problem, especially as it relates to homology-based structures, identify the key bottlenecks in current software tools, and evaluate and prototype new algorithms that may be developed to improve these bottlenecks. This report describes the current challenges in the protein-protein docking problem: correctly predicting the binding site for the protein-protein interaction and correctly placing the sidechains. Two different and complementary approaches are taken that can help with the protein-protein docking problem. The first approach is to predict interaction sites prior to docking, and uses bioinformatics studies of protein-protein interactions to predict theses interaction site. The second approach is to improve validation of predicted complexes after docking, and uses an improved scoring function for evaluating proposed docked poses, incorporating a solvation term. This scoring function demonstrates significant improvement over current state-of-the art functions. Initial studies on both these approaches are promising, and argue for full development of these algorithms.

Physical Description

37 p.

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  • Report No.: SAND2005-7984
  • Grant Number: AC04-94AL85000
  • DOI: 10.2172/883467 | External Link
  • Office of Scientific & Technical Information Report Number: 883467
  • Archival Resource Key: ark:/67531/metadc892709

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Office of Scientific & Technical Information Technical Reports

Reports, articles and other documents harvested from the Office of Scientific and Technical Information.

Office of Scientific and Technical Information (OSTI) is the Department of Energy (DOE) office that collects, preserves, and disseminates DOE-sponsored research and development (R&D) results that are the outcomes of R&D projects or other funded activities at DOE labs and facilities nationwide and grantees at universities and other institutions.

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Creation Date

  • January 1, 2006

Added to The UNT Digital Library

  • Sept. 23, 2016, 2:42 p.m.

Description Last Updated

  • Nov. 23, 2016, 3:22 p.m.

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Martin, Shawn Bryan; Sale, Kenneth L.; Faulon, Jean-Loup Michel & Roe, Diana C. Developing algorithms for predicting protein-protein interactions of homology modeled proteins., report, January 1, 2006; United States. (digital.library.unt.edu/ark:/67531/metadc892709/: accessed October 16, 2017), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.