Tunque Cahui, R. R. | Search bioRxiv

bioRxiv2022

CoDNaS-Q: a database of conformational diversity of the native state of proteins with quaternary structure

SummaryA collection of conformers that exist in a dynamical equilibrium defines the native state of a protein. The structural differences between them describe their conformational diversity, a defining characteristic of the protein with an essential role in multiple cellular processes. Since most proteins carry out their functions by assembling into complexes, we have developed CoDNaS-Q, the first online resource to explore conformational diversity in homooligomeric proteins. It features a curated collection of redundant protein structures with known quaternary structure. CoDNaS-Q integrates relevant annotations that allow researchers to identify and explore the extent and possible reasons of conformational diversity in homooligomeric protein complexes. Availability and implementationCoDNaS-Q is freely accessible at http://ufq.unq.edu.ar/codnasq/. The data can be retrieved from the website. The source code of the database can be downloaded from https://github.com/SfrRonaldo/codnas-q. Contactnpalopoli@unq.edu.ar

bioinformatics↗

bioRxiv2020

CoDNaS-RNA: a database of Conformational Diversity in the Native State of RNA

Conformational changes in RNA native ensembles are central to fulfill many of their biological roles. Systematic knowledge of the extent and possible modulators of this conformational diversity is desirable to better understand the relationship between RNA dynamics and function. We have developed CoDNaS-RNA as the first database of conformational diversity in RNA molecules. Known RNA structures are retrieved and clustered to identify alternative conformers of each molecule. Pairwise structural comparisons within each cluster allows to measure the variability of the molecule. Additional data on structural features, molecular interactions and functional annotations are provided. CoDNaS-RNA is implemented as a public resource that can be of much interest for computational and bench scientists alike. AvailabilityCoDNaS-RNA is freely accessible at http://ufq.unq.edu.ar/codnasrna Contactnpalopoli@unq.edu.ar

bioinformatics↗