Brief Funct Genomic Proteomic. 2008 Jul;7(4):291-302. Epub 2008 Jul 3.

Structure-based function prediction: approaches and applications.

Source

Department of Biology, Centre for Molecular Bioinformatics, University of Tor Vergata, Rome, Italy. pier.federico.gherardini@uniroma2.it

Abstract

The ever increasing number of protein structures determined by structural genomic projects has spurred much interest in the development of methods for structure-based function prediction. Existing methods can be roughly classified in two groups: some use a comparative approach looking for the presence of structural motifs possibly associated with a known biochemical function. Other methods try to identify functional patches on the surface of a protein using only its physicochemical characteristics. This review will cover both kinds of approaches to structure-based function prediction as well as their use in real-world cases. The main issues and limitations in using protein structure to predict function will also be discussed. These are mainly: the assessment of the statistical significance of structural similarities and the extent to which these methods depend on the accuracy and availability of structural data.

PMID:: 18599513; [PubMed - indexed for MEDLINE]

Free full text

Publication Types, MeSH Terms, Substances

Publication Types

MeSH Terms

Substances

Proteins

LinkOut - more resources

Full Text Sources

Other Literature Sources

Labome Researcher Resource - ExactAntigen/Labome

Supplemental Content

Save items

Related citations in PubMed

Protein structure prediction and analysis as a tool for functional genomics. [Appl Bioinformatics. 2003]
Protein structure prediction and analysis as a tool for functional genomics.
Baker EN, Arcus VL, Lott JS. Appl Bioinformatics. 2003; 2(3 Suppl):S3-10.
A study of statistical methods for function prediction of protein motifs. [Appl Bioinformatics. 2004]
A study of statistical methods for function prediction of protein motifs.
Tao T, Zhai CX, Lu X, Fang H. Appl Bioinformatics. 2004; 3(2-3):115-24.
Review Bioinformatics methods to predict protein structure and function. A practical approach. [Mol Biotechnol. 2003]
Review Bioinformatics methods to predict protein structure and function. A practical approach.
Edwards YJ, Cottage A. Mol Biotechnol. 2003 Feb; 23(2):139-66.
Review Predicting protein function from sequence and structural data. [Curr Opin Struct Biol. 2005]
Review Predicting protein function from sequence and structural data.
Watson JD, Laskowski RA, Thornton JM. Curr Opin Struct Biol. 2005 Jun; 15(3):275-84.
Identification of function-associated loop motifs and application to protein function prediction. [Bioinformatics. 2006]
Identification of function-associated loop motifs and application to protein function prediction.
Espadaler J, Querol E, Aviles FX, Oliva B. Bioinformatics. 2006 Sep 15; 22(18):2237-43. Epub 2006 Jul 26.

See reviews... See all...

Cited by 12 PubMed Central articles

Identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities. [BMC Bioinformatics. 2012]
Identification of binding pockets in protein structures using a knowledge-based potential derived from local structural similarities.
Bianchi V, Gherardini PF, Helmer-Citterich M, Ausiello G. BMC Bioinformatics. 2012 Mar 28; 13 Suppl 4:S17. Epub 2012 Mar 28.
A library of protein surface patches discriminates between native structures and decoys generated by structure prediction servers. [BMC Struct Biol. 2011]
A library of protein surface patches discriminates between native structures and decoys generated by structure prediction servers.
Gamliel R, Kedem K, Kolodny R, Keasar C. BMC Struct Biol. 2011 May 4; 11(1):20. Epub 2011 May 4.
Accurate protein structure annotation through competitive diffusion of enzymatic functions over a network of local evolutionary similarities. [PLoS One. 2010]
Accurate protein structure annotation through competitive diffusion of enzymatic functions over a network of local evolutionary similarities.
Venner E, Lisewski AM, Erdin S, Ward RM, Amin SR, Lichtarge O. PLoS One. 2010 Dec 13; 5(12):e14286. Epub 2010 Dec 13.

See all...

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
Substance (MeSH Keyword)
PubChem chemical substance (submitted) records that are classified under the same Medical Subject Headings (MeSH) controlled vocabulary as the current articles.
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

Structure-based function prediction: approaches and applications.
Structure-based function prediction: approaches and applications.
Brief Funct Genomic Proteomic. 2008 Jul ;7(4):291-302. Epub 2008 Jul 3 .

PubMed
Targeted disruption of beta-catenin in Sf1-expressing cells impairs development ...
Targeted disruption of beta-catenin in Sf1-expressing cells impairs development and maintenance of the adrenal cortex.
Development. 2008 Aug ;135(15):2593-602. Epub 2008 Jul 3 .

PubMed
Lung EC-SOD overexpression attenuates hypoxic induction of Egr-1 and chronic hyp...
Lung EC-SOD overexpression attenuates hypoxic induction of Egr-1 and chronic hypoxic pulmonary vascular remodeling.
Am J Physiol Lung Cell Mol Physiol. 2008 Sep ;295(3):L422-30. Epub 2008 Jul 3 .

PubMed
A 40-year-old woman with diabetes contemplating pregnancy after gastric bypass s...
A 40-year-old woman with diabetes contemplating pregnancy after gastric bypass surgery.
JAMA. 2008 Jun 4 ;299(21):2550-7. Epub 2008 May 6 .

PubMed
The evolution of modularity in bacterial metabolic networks.
The evolution of modularity in bacterial metabolic networks.
Proc Natl Acad Sci U S A. 2008 May 13 ;105(19):6976-81. Epub 2008 May 6 .

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Result Filters

Display Settings:

Send to: