Recognition of Structure Similarities in Proteins

Abstract

Protein fold structure is more conserved than its amino acid sequence and closely associated with biological function, so calculating the similarity of protein structures is a fundamental problem in structural biology and plays a key role in protein fold classification, fold function inference, and protein structure prediction. Large progress has been made in recent years in this field and many methods for considering structural similarity have been proposed, including methods for protein structure comparison, retrieval of protein structures from databases, and ligand binding site comparison. Most of those methods can be available on the World Wide Web, but evaluation of all the methods is still a hard problem. This paper summarizes some popular methods and latest methods for structure similarities, including structure alignment, protein structure retrieval, and ligand binding site alignment.

Non-Gtpase Proteins That Share Common Motifs With G Domains: Convergent or Divergent Evolution or Domain Recombination?

“…As evolution has more conserved structures than sequences (Grishin, 2001;Wang et al, 2008), in a final step, structure superpositions were performed to validate our previous hypotheses. Tertiary structures were all obtained from the PDB (Berman et al, 2008) and their superpositions were carried out with the on line programs MATRAS (Kawabata, 2003) and CE (Shindyalov & Bourne, 1998).…”