Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017
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 .
curation, dilution, flexibility, gaps, PDB file, protein rigidity, rigid clusters, sequence, simulated unfolding
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.