Genus for biomolecules.

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

doi:10.1093/nar/gkz845

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.

Highlights

Biomolecules are often characterized by their primary, secondary, or tertiary structures, which describe the sequence of their fundamental constituents, and their configuration in physical space
The database ‘Genus for biomolecules’ that we present in this work assembles information about another important topological property, which is encoded in the genus of a given biomolecular chain or its various subchains
The Genus database collects information about the genus characteristics of biomolecular chains deposited in the Protein Data Bank (PDB) [7]

Summary

Introduction

Biomolecules are often characterized by their primary, secondary, or tertiary structures, which describe the sequence of their fundamental constituents (such as nucleotides or amino acids), and their configuration in physical space. Each backbone represents one biomolecular chain (so for a single biomolecule it is sufficient to consider one backbone, b = 1), and each chord represents one bond (a base pair for RNA, or a contact for proteins).

Results

Conclusion