Related Experiment Video
Updated: Sep 29, 2026

A Protocol for Computer-Based Protein Structure and Function Prediction
Published on: November 3, 2011
Protein domain identification and improved sequence similarity searching using PSI-BLAST
Richard A George1, Jaap Heringa
1Division of Mathematical Biology, National Institute for Medical Research, The Ridgeway, Mill Hill, United Kingdom.
Abstract:
Protein sequences containing more than one structural domain are problematic when used in homology searches where they can either stop an iterative database search prematurely or cause an explosion of a search to common domains. We describe a method, DOMAINATION, that infers domains and their boundaries in a query sequence from local gapped alignments generated using PSI-BLAST. Through a new technique to recognize domain insertions and permutations, DOMAINATION submits delineated domains as successive database queries in further iterative steps. Assessed over a set of 452 multidomain proteins, the method predicts structural domain boundaries with an overall accuracy of 50% and improves finding distant homologies by 14% compared with PSI-BLAST. DOMAINATION is available as a web based tool at http://mathbio.nimr.mrc.ac.uk, and the source code is available from the authors upon request.
Related Concept Videos
Conservation of Protein Domains Over Different Proteins
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Protein Families
Conservation of Protein Domains
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to form...
Conserved Binding Sites
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Evolutionary Relationships through Genome Comparisons
Rapid Identification of Pathogens

