Literature DB >> 15963890

Predicting protein function from sequence and structural data.

James D Watson1, Roman A Laskowski, Janet M Thornton.   

Abstract

When a protein's function cannot be experimentally determined, it can often be inferred from sequence similarity. Should this process fail, analysis of the protein structure can provide functional clues or confirm tentative functional assignments inferred from the sequence. Many structure-based approaches exist (e.g. fold similarity, three-dimensional templates), but as no single method can be expected to be successful in all cases, a more prudent approach involves combining multiple methods. Several automated servers that integrate evidence from multiple sources have been released this year and particular improvements have been seen with methods utilizing the Gene Ontology functional annotation schema.

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Year:  2005        PMID: 15963890     DOI: 10.1016/j.sbi.2005.04.003

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   6.809


  121 in total

1.  Real-time ligand binding pocket database search using local surface descriptors.

Authors:  Rayan Chikhi; Lee Sael; Daisuke Kihara
Journal:  Proteins       Date:  2010-07

Review 2.  Proteins: form and function.

Authors:  Roy D Sleator
Journal:  Bioeng Bugs       Date:  2012-03-01

3.  Topological network alignment uncovers biological function and phylogeny.

Authors:  Oleksii Kuchaiev; Tijana Milenkovic; Vesna Memisevic; Wayne Hayes; Natasa Przulj
Journal:  J R Soc Interface       Date:  2010-03-17       Impact factor: 4.118

4.  Structure-based prediction of DNA-binding proteins by structural alignment and a volume-fraction corrected DFIRE-based energy function.

Authors:  Huiying Zhao; Yuedong Yang; Yaoqi Zhou
Journal:  Bioinformatics       Date:  2010-06-04       Impact factor: 6.937

5.  Detecting local ligand-binding site similarity in nonhomologous proteins by surface patch comparison.

Authors:  Lee Sael; Daisuke Kihara
Journal:  Proteins       Date:  2012-01-24

6.  Solution structure of the Escherichia coli protein ydhR: a putative mono-oxygenase.

Authors:  Matthew Revington; Anthony Semesi; Adelinda Yee; Gary S Shaw
Journal:  Protein Sci       Date:  2005-10-31       Impact factor: 6.725

7.  Enhanced automated function prediction using distantly related sequences and contextual association by PFP.

Authors:  Troy Hawkins; Stanislav Luban; Daisuke Kihara
Journal:  Protein Sci       Date:  2006-05-02       Impact factor: 6.725

8.  Towards fully automated structure-based function prediction in structural genomics: a case study.

Authors:  James D Watson; Steve Sanderson; Alexandra Ezersky; Alexei Savchenko; Aled Edwards; Christine Orengo; Andrzej Joachimiak; Roman A Laskowski; Janet M Thornton
Journal:  J Mol Biol       Date:  2007-01-30       Impact factor: 5.469

9.  Targeting the ubiquitin-conjugating enzyme E2D4 for cancer drug discovery-a structure-based approach.

Authors:  Vishwanath Ramatenki; Ramakrishna Dumpati; Rajender Vadija; Santhiprada Vellanki; Sarita Rajender Potlapally; Rohini Rondla; Uma Vuruputuri
Journal:  J Chem Biol       Date:  2016-12-24

10.  The evolutionary origin of epithelial cell-cell adhesion mechanisms.

Authors:  Phillip W Miller; Donald N Clarke; William I Weis; Christopher J Lowe; W James Nelson
Journal:  Curr Top Membr       Date:  2013       Impact factor: 3.049

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