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PvSOAR: detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins.

ABSTRACT: Detecting similar protein surfaces provides an important route for discovering unrecognized or novel functional relationship between proteins. The web server pvSOAR (pocket and void Surfaces Of Amino acid Residues) provides an online resource to identify similar protein surface regions. pvSOAR can take a structure either uploaded by a user or obtained from the Protein Data Bank, and identifies similar surface patterns based on geometrically defined pockets and voids. It provides several search modes to compare protein surfaces by similarity in local sequence, local shape and local orientation. Statistically significant search results are reported for visualization and interactive exploration. pvSOAR can be used to predict biological functions of proteins with known three-dimensional structures but unknown biological roles. It can also be used to study functional relationship between proteins and for exploration of the evolutionary origins of structural elements important for protein function. We present an example using pvSOAR to explore the biological roles of a protein whose structure was solved by the structural genomics project. The pvSOAR web server is available at http://pvsoar.bioengr.uic.edu/.

SUBMITTER: Binkowski TA

PROVIDER: S-EPMC441528 | biostudies-literature | 2004 Jul

REPOSITORIES: biostudies-literature

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pvSOAR: detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins.

Binkowski T Andrew TA Freeman Patrick P Liang Jie J

Nucleic acids research 20040701 Web Server issue

Detecting similar protein surfaces provides an important route for discovering unrecognized or novel functional relationship between proteins. The web server pvSOAR (pocket and void Surfaces Of Amino acid Residues) provides an online resource to identify similar protein surface regions. pvSOAR can take a structure either uploaded by a user or obtained from the Protein Data Bank, and identifies similar surface patterns based on geometrically defined pockets and voids. It provides several search m ...[more]

PMID: 15215448

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Project description:BACKGROUND:Understanding the genetic structure of natural populations provides insight into the demographic and adaptive processes that have affected those populations. Such information, particularly when integrated with geospatial data, can have translational applications for a variety of fields, including public health. Estimated effective migration surfaces (EEMS) is an approach that allows visualization of the spatial patterns in genomic data to understand population structure and migration. In this study, we developed a workflow to optimize the resolution of spatial grids used to generate EEMS migration maps and applied this optimized workflow to estimate migration of Plasmodium falciparum in Cambodia and bordering regions of Thailand and Vietnam. METHODS:The optimal density of EEMS grids was determined based on a new workflow created using density clustering to define genomic clusters and the spatial distance between genomic clusters. Topological skeletons were used to capture the spatial distribution for each genomic cluster and to determine the EEMS grid density; i.e., both genomic and spatial clustering were used to guide the optimization of EEMS grids. Model accuracy for migration estimates using the optimized workflow was tested and compared to grid resolutions selected without the optimized workflow. As a test case, the optimized workflow was applied to genomic data generated from P. falciparum sampled in Cambodia and bordering regions, and migration maps were compared to estimates of malaria endemicity, as well as geographic properties of the study area, as a means of validating observed migration patterns. RESULTS:Optimized grids displayed both high model accuracy and reduced computing time compared to grid densities selected in an unguided manner. In addition, EEMS migration maps generated for P. falciparum using the optimized grid corresponded to estimates of malaria endemicity and geographic properties of the study region that might be expected to impact malaria parasite migration, supporting the validity of the observed migration patterns. CONCLUSIONS:Optimized grids reduce spatial uncertainty in the EEMS contours that can result from user-defined parameters, such as the resolution of the spatial grid used in the model. This workflow will be useful to a broad range of EEMS users as it can be applied to analyses involving other organisms of interest and geographic areas.

Dataset Information

PvSOAR: detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins.

Publications

pvSOAR: detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins.

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