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TOPOFIT-DB


NAR Molecular Biology Database Collection entry number 941
Leslin C., Abyzov A. and Ilyin V.
Northeastern University, Biology Department, Theoretical and Molecular Biology Laboratory, Boston, MA 02115, USA

Database Description

Similarity of protein structure has been analyzed using the TOPOFIT method on a large scale and placed into the publicly available TOPOFIT database (TOPOFIT-DB). Using TOPOFIT, structurally related proteins have been found to share a common spatial invariant part, a set of tetrahedrons, mathematically described as a common spatial sub-graph volume of the three-dimensional contact graph derived from Delaunay tessellation. Using the TOPOFIT method, we present TOPOFIT-DB (release 0.9), which currently contains 86,033,950 structural alignments between all proteins in the PDB as of July 2005. Structural neighbors to the query protein structure can be retrieved by PDB code and chain id, or ASTRAL domain codes. All data from a search is presented in row format, similar to other structural databases, pairwise structural alignments can be visualized over the internet with the FRIEND applet, and alignment plots with colored alignments are produced for the user. PDB codes not found in TOPOFIT-DB can be searched for structural neighbors using T-Server, a utility for comparison of a user given PDB code against the entire current PDB release using the TOPOFIT method, all results can seen on the web or optionally emailed. Pairwise comparison between two user give PDB codes, or PDB formatted coordinate files can be done using the T-Pair utility. TOPOFIT’s non-parametric and objective way to separate the common part from the variable part, along with TOPOFIT-DB’s accessibility will provide the scientific community with another resource for protein structure comparison.

References

1. Abyzov,A., Errami,M., Leslin,C.M. and Ilyin,V.A. (2005) Friend, an integrated analytical front-end application for bioinformatics. Bioinformatics. 2005, 18, 3677-3678
2. Ilyin,V.A., Abyzov,A. and Leslin,C.M. (2004) Structural alignment of proteins by a novel TOPOFIT method, as a superimposition of common volumes at a topomax point. Protein Science, 13, 1865-1874

Subcategory: Protein structure

Go to the abstract in the NAR 2007 Database Issue.
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