Protein structure alignment using elastic shape analysis
Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology
Graph Comparison by Log-Odds Score Matrices with Application to Protein Topology Analysis
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Touring Protein Space with Matt
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Touring protein space with matt
ISBRA'10 Proceedings of the 6th international conference on Bioinformatics Research and Applications
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Motivation: Throughout evolution, homologous proteins have common regions that stay semi-rigid relative to each other and other parts that vary in a more noticeable way. In order to compare the increasing number of structures in the PDB, flexible geometrical alignments are needed, that are reliable and easy to use. Results: We present a protein structure alignment method whose main feature is the ability to consider different rigid transformations at different sites, allowing for deformations beyond a global rigid transformation. The performance of the method is comparable with that of the best ones from 10 aligners tested, regarding both the quality of the alignments with respect to hand curated ones, and the classification ability. An analysis of some structure pairs from the literature that need to be matched in a flexible fashion are shown. The use of a series of local transformations can be exported to other classifiers, and a future golden protein similarity measure could benefit from it. Availability: A public server for the program is available at http://dmi.uib.es/ProtDeform/. Contact: jairo@uib.es Supplementary information: All data used, results and examples are available at http://dmi.uib.es/people/jairo/bio/ProtDeform.Supplementary data are available at Bioinformatics online.