We found a match
Your institution may have access to this item. Find your institution then sign in to continue.
- Title
Characterization and prediction of residues determining protein functional specificity.
- Authors
John A. Capra; Mona Singh
- Abstract
Motivation: Within a homologous protein family, proteins may be grouped into subtypes that share specific functions that are not common to the entire family. Often, the amino acids present in a small number of sequence positions determine each proteins particular function-al specificity. Knowledge of these specificity determining positions (SDPs) aids in protein function prediction, drug design and experimental analysis. A number of sequence-based computational methods have been introduced for identifying SDPs; however, their further development and evaluation have been hindered by the limited number of known experimentally determined SDPs. Results: We combine several bioinformatics resources to automate a process, typically undertaken manually, to build a dataset of SDPs. The resulting large dataset, which consists of SDPs in enzymes, enables us to characterize SDPs in terms of their physicochemical and evolution-ary properties. It also facilitates the large-scale evaluation of sequence-based SDP prediction methods. We present a simple sequence-based SDP prediction method, GroupSim, and show that, surprisingly, it is competitive with a representative set of current methods. We also describe ConsWin, a heuristic that considers sequence conservation of neighboring amino acids, and demonstrate that it improves the performance of all methods tested on our large dataset of enzyme SDPs. Availability: Datasets and GroupSim code are available online at http://compbio.cs.princeton.edu/specificity/ Contact: msingh@cs.princeton.edu Supplementary information: Supplementary data are available at Bioinformatics online.
- Publication
Bioinformatics, 2008, Vol 24, Issue 13, p1473
- ISSN
1367-4803
- Publication type
Academic Journal
- DOI
10.1093/bioinformatics/btn214