CoDNaS 2.0: a comprehensive database of protein conformational diversity in the native state.

Alexander Miguel Monzon,Cristian Oscar Rohr,Gustavo Parisi,María Silvina Fornasari

doi:10.1093/database/baw038

Abstract

CoDNaS (conformational diversity of the native state) is a protein conformational diversity database. Conformational diversity describes structural differences between conformers that define the native state of proteins. It is a key concept to understand protein function and biological processes related to protein functions. CoDNaS offers a well curated database that is experimentally driven, thoroughly linked, and annotated. CoDNaS facilitates the extraction of key information on small structural differences based on protein movements. CoDNaS enables users to easily relate the degree of conformational diversity with physical, chemical and biological properties derived from experiments on protein structure and biological characteristics. The new version of CoDNaS includes ∼70% of all available protein structures, and new tools have been added that run sequence searches, display structural flexibility profiles and allow users to browse the database for different structural classes. These tools facilitate the exploration of protein conformational diversity and its role in protein function.Database URL: http://ufq.unq.edu.ar/codnas

Highlights

Conformational diversity is a key concept for understanding protein function [1]
The capture of different conformations of the same protein allows key information to be extracted depending on protein movements, and supports the exploration of relationships between protein dynamics, experimental conditions and protein biological properties
CoDNaS includes 70% of all available protein structures presently deposited in Protein Data Bank (PDB), and utilizes PDB updates to maintain current information for our database

Summary

Introduction

Conformational diversity is a key concept for understanding protein function [1]. Conformers are alternative structures that coexist in a dynamic equilibrium that constitutes the native state of proteins. We incorporated new tools for sequence searches, flexibility analyses and structural profiles, which enhance the capacity and use of the database to explore conformational diversity in proteins. The ‘General information’ box (Figure 2a) contains two sub-boxes; ‘Protein overview’ provides a basic description of the protein chain (UniProt ID, name, organism and function) and ‘Structural information’ contains a brief description of the structural alignment data (conformer resolution, experimental method, number of conformers for the protein and global sequence identity between all conformer pairs).

Results

Conclusion