Fast detection of common geometric substructure in proteins
RECOMB '99 Proceedings of the third annual international conference on Computational molecular biology
Protein Architecture: A Practical Approach
Protein Architecture: A Practical Approach
A dimensionality reduction approach to modeling protein flexibility
Proceedings of the sixth annual international conference on Computational biology
Geometric suffix tree: a new index structure for protein 3-d structures
CPM'06 Proceedings of the 17th Annual conference on Combinatorial Pattern Matching
Fast Hinge Detection Algorithms for Flexible Protein Structures
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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Protein conformational changes play a critical role in biological functions such as ligand-protein and protein-protein interactions. Due to the noise in structural data, determining salient conformational changes reliably and efficiently is a challenging problem. This paper presents an efficient algorithm for analyzing protein conformational changes, using noisy data. It applies a statistical flexibility test to all contiguous fragments of a protein and combines the information from these tests to compute a consensus flexibility measure for each residue of the protein. We tested the algorithm, using data from the Protein Data Bank and the Macromolecular Movements Database. The results show that our algorithm can reliably detect different types of salient conformational changes, including well-known examples such as hinge and shear, as well as the flap motion of HIV-1 protease. The software implementing our algorithm is available at http://motion.comp.nus.edu.sg/projects/ proflexana/proflexana.html.