GapRepairer: a server to model a structural gap and validate it using topological analysis | Zendy

Aleksandra I. Jarmolinska | Zendy; Michał Kadlof | Zendy; Paweł Dąbrowski-Tumański | Zendy; Joanna I. Sułkowska | Zendy

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GapRepairer: a server to model a structural gap and validate it using topological analysis

Author(s) -

Aleksandra I. Jarmolinska,

Michał Kadlof,

Paweł Dąbrowski-Tumański,

Joanna I. Sułkowska

Publication year - 2018

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/bty334

Subject(s) - modeller , topology (electrical circuits) , computer science , template , computational topology , homology (biology) , theoretical computer science , homology modeling , mathematics , biology , programming language , biochemistry , combinatorics , scalar field , gene , mathematical physics , enzyme

Over 25% of protein structures possess unresolved fragments. On the other hand, approximately 6% of protein chains have non-trivial topology (and form knots, slipknots, lassos and links). As the topology is fundamental for the proper function of proteins, modeling of topologically correct structures is decisive in various fields, including biophysics, biotechnology and molecular biology. However, none of the currently existing tools take into account the topology of the model and those which could be modified to include topology, demand experience in bioinformatics, protein topology and knot theory.

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