Genus for biomolecules

Paweł Rubach; Sebastian Zajac; Borys Jastrzebski; Joanna I Sulkowska; Piotr Sułkowski

doi:10.1093/nar/gkz845

Genus for biomolecules

Nucleic Acids Res. 2020 Jan 8;48(D1):D1129-D1135. doi: 10.1093/nar/gkz845.

Authors

Paweł Rubach^{1

2}, Sebastian Zajac², Borys Jastrzebski¹, Joanna I Sulkowska^{1

3}, Piotr Sułkowski^{4

5}

Affiliations

¹ Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland.
² Warsaw School of Economics, Al. Niepodległości 162, 02-554 Warsaw, Poland.
³ Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
⁴ Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland.
⁵ Walter Burke Institute for Theoretical Physics, California Institute of Technology, Pasadena, CA 91125, USA.

Abstract

The 'Genus for biomolecules' database (http://genus.fuw.edu.pl) collects information about topological structure and complexity of proteins and RNA chains, which is captured by the genus of a given chain and its subchains. For each biomolecule, this information is shown in the form of a genus trace plot, as well as a genus matrix diagram. We assemble such information for all and RNA structures deposited in the Protein Data Bank (PDB). This database presents also various statistics and extensive information about the biological function of the analyzed biomolecules. The database is regularly self-updating, once new structures are deposited in the PDB. Moreover, users can analyze their own structures.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Computational Biology / methods*
Databases, Genetic*
Models, Molecular
Proteins* / chemistry
Proteins* / genetics
RNA* / chemistry
RNA* / genetics
Software
Structure-Activity Relationship
User-Computer Interface
Web Browser

Substances

Proteins
RNA