Document Type
Conference Proceeding
Publication Date
12-15-2017
Publication Title
Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
Abstract
Pebble game rigidity analysis is a combinatorial method, implemented in our free web server KinariWeb, for extracting protein rigidity and flexibility information without performing costly molecular dynamics simulations. Due to the idiosynchrasies of the data in the Protein Data Bank (PDB), Kinari succeeds only on a fraction of the available files. Motivated by large scale applications, aiming at processing almost all the PDB files, we have recently developed a faster and more robust version, the phased pebble game algorithm. It is specifically designed to take advantage of the sequential structure of biopolymers. However, the structural data available in the Protein Data Bank for proteins solved with X-ray crystallography is very rarely complete: Missing residues induce gaps in the atom sequence, leading to incomplete rigidity analysis results. In this paper, we describe the pre-processing component of the new version Kinari-2, which fixes such gaps for the purpose of producing a valid input for the phased pebble game algorithm described in [19].
Keywords
curation, dilution, flexibility, gaps, PDB file, protein rigidity, rigid clusters, sequence, simulated unfolding
Volume
2017-January
First Page
577
Last Page
580
DOI
10.1109/BIBM.2017.8217714
Recommended Citation
Metlicka, Magdalena; Bygi, Mojtaba Nouri; and Streinu, Ileana, "Repairing Gaps in Kinari-2 for Large Scale Protein and Flexibility Analysis Applications" (2017). Computer Science: Faculty Publications, Smith College, Northampton, MA.
https://scholarworks.smith.edu/csc_facpubs/315
Comments
Peer reviewed accepted manuscript.