CoDNaS: a database of Conformational Diversity in the Native State of proteins

MONZON, ALEXANDER; EZEQUIEL JURITZ; FORNASARI, MS; GUSTAVO PARISI

BIOINFORMATICS (OXFORD, ENGLAND)

OXFORD UNIV PRESS

Lugar: Oxford; Año: 2013

1367-4803

Conformational diversity is a key concept in the under-standing of different issues related with protein function such as the study of catalytic processes in enzymes, protein-protein recognition, protein evolution and the origins of new biological functions. Here we present a database of proteins with different degrees of confor-mational diversity. CoDNaS (from Conformational Diversity of Native Sate) is a redundant collection of tridimensional structures for the same protein derived from Protein Data Bank. Structures for the same protein obtained under different crystallographic conditions have been associated with snapshots of protein dynamism and consequently could characterize protein conformers. CoDNaS al-lows the user to explore global and local structural differences among conformers as a function of different parameters such as presence of ligand, post-translational modifications, changes in oligomeric states, differences in pH and temperature. Additionally CoDNaS contains information about protein taxonomy and function, disorder level and structural classification offering useful information to explore the underlying mechanism of conformational diversity and its close relationship with protein function. Currently CoDNaS has 54,364 structures integrating 9398 entries, with an average of 6.14 conformers per protein.