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OBSTRUCT: a program to obtain largest cliques from a protein sequence set according to structural resolution and
J Heringa1, H Sommerfeldt, D Higgins
1European Molecular Biology Laboratory, Heidelberg, Germany.
Computer Applications in the Biosciences : CABIOS
|December 1, 1992
Summary
A new program, OBSTRUCT, identifies the largest protein sequence subsets meeting user-defined criteria from crystallographically determined structures. It allows adjustable sequence similarity and structural resolution, optionally including NMR data for comprehensive analysis.
Area of Science:
- Structural Biology
- Bioinformatics
- Computational Biology
Background:
- Protein tertiary structures are crucial for function.
- Analyzing large datasets of protein structures presents computational challenges.
- Identifying subsets of proteins with specific structural and sequence properties is essential for various biological studies.
Purpose of the Study:
- To develop a computational tool for selecting optimal subsets of protein sequences based on structural and sequence constraints.
- To provide researchers with a flexible program for data mining in structural biology databases.
Main Methods:
- Development of the OBSTRUCT program.
- Implementation of user-defined constraints for sequence similarity and structural resolution.
- Optional integration of Nuclear Magnetic Resonance (NMR) data for three-dimensional folds.
Main Results:
- OBSTRUCT successfully identifies the largest possible subsets of protein sequences meeting specified criteria.
- The program offers adjustable parameters for sequence similarity and structural resolution.
- Inclusion of NMR-derived structures enhances the comprehensiveness of the analyzed datasets.
Conclusions:
- OBSTRUCT is an effective tool for subset selection in protein structural biology.
- The program facilitates efficient analysis of large protein structure datasets.
- OBSTRUCT aids researchers in exploring structure-function relationships by enabling targeted data retrieval.