A geometric invariant-based framework for the analysis of protein conformational space

Motivation: Characterization of the restricted nature of the protein local conformational space has remained a challenge, thereby necessitating a computationally expensive conformational search in protein modeling. Moreover, owing to the lack of unilateral structural descriptors, conventional data m...

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Bibliographic Details
Published in:Bioinformatics 2005-09, Vol.21 (18), p.3622-3628
Main Authors: Tendulkar, Ashish V., Sohoni, Milind A., Ogunnaike, Babatunde, Wangikar, Pramod P.
Format: Article
Language:English
Subjects:
Algorithms
Biological and medical sciences
Cluster Analysis
Computational Biology - methods
Computer Simulation
Fundamental and applied biological sciences. Psychology
General aspects
Internet
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Models, Theoretical
Molecular Conformation
Peptides - chemistry
Principal Component Analysis
Probability
Protein Conformation
Sequence Alignment
Sequence Analysis, Protein
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Summary:Motivation: Characterization of the restricted nature of the protein local conformational space has remained a challenge, thereby necessitating a computationally expensive conformational search in protein modeling. Moreover, owing to the lack of unilateral structural descriptors, conventional data mining techniques, such as clustering and classification, have not been applied in protein structure analysis. Results: We first map the local conformations in a fixed dimensional space by using a carefully selected suite of geometric invariants (GIs) and then reduce the number of dimensions via principal component analysis (PCA). Distribution of the conformations in the space spanned by the first four PCs is visualized as a set of conditional bivariate probability distribution plots, where the peaks correspond to the preferred conformations. The locations of the different canonical structures in the PC-space have been interpreted in the context of the weights of the GIs to the first four PCs. Clustering of the available conformations reveals that the number of preferred local conformations is several orders of magnitude smaller than that suggested previously. Contact: pramodw@iitb.ac.in Supplementary information: www.it.iitb.ac.in/~ashish/bioinfo2005/
ISSN:1367-4803
1460-2059
1367-4811
DOI:10.1093/bioinformatics/bti621