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© Research
Publication : Journal of chemical theory and computation

CoMoDo: Identifying Dynamic Protein Domains Based on Covariances of Motion

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Journal of chemical theory and computation - 12 May 2015

Wieninger SA, Ullmann GM

Link to Pubmed [PMID] – 26575576

J Chem Theory Comput 2015 Jun;11(6):2841-54

Most large proteins are built of several domains, compact units which enable functional protein motions. Different domain assignment approaches exist, which mostly rely on concepts of stability, folding, and evolution. We describe the automatic assignment method CoMoDo, which identifies domains based on protein dynamics. Covariances of atomic fluctuations, here calculated by an Elastic Network Model, are used to group residues into domains of different hierarchical levels. The so-called dynamic domains facilitate the study of functional protein motions involved in biological processes like ligand binding and signal transduction. By applying CoMoDo to a large number of proteins, we demonstrate that dynamic domains exhibit features absent in the commonly assigned structural domains, which can deliver insight into the interactions between domains and between subunits of multimeric proteins. CoMoDo is distributed as free open source software at www.bisb.uni-bayreuth.de/CoMoDo.html .

http://www.ncbi.nlm.nih.gov/pubmed/26575576