ArticleJournal of structural and functional genomics2012
Structure- and sequence-based function prediction for non-homologous proteins.
Article in Journal of structural and functional genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- AlphaFun: Structural-Alignment-Based Proteome Annotation Reveals why the Functionally Unknown Proteins (uPE1) Are So Understudied.Journal of proteome research · 2024Article
- Putative Protein Discovery from Microalgal Genomes as a Synthetic Biology Protein Library for Heavy Metal Bio-Removal.Biology · 2022Article
- ContactPFP: Protein function prediction using predicted contact information.Frontiers in bioinformatics · 2022Article
- Evolution of Protein Functional Annotation: Text Mining Study.Journal of personalized medicine · 2022Article
- Romo1 is a mitochondrial nonselective cation channel with viroporin-like characteristics.The Journal of cell biology · 2018Article
- The PFP and ESG protein function prediction methods in 2014: effect of database updates and ensemble approaches.GigaScience · 2015Article
- CAB-Align: A Flexible Protein Structure Alignment Method Based on the Residue-Residue Contact Area.PloS one · 2015Article
- Computational prediction of protein function based on weighted mapping of domains and GO terms.BioMed research international · 2014Article
- Mass spectrometry coupled experiments and protein structure modeling methods.International journal of molecular sciences · 2013Review
- A novel function prediction approach using protein overlap networks.BMC systems biology · 2013Article
- In-depth performance evaluation of PFP and ESG sequence-based function prediction methods in CAFA 2011 experiment.BMC bioinformatics · 2013Article
- Parallel in vivo DNA assembly by recombination: experimental demonstration and theoretical approaches.PloS one · 2013Article
- Evaluation of function predictions by PFP, ESG,and PSI-BLAST for moonlighting proteins.BMC proceedings · 2012Article
- Protein domain recurrence and order can enhance prediction of protein functions.Bioinformatics (Oxford, England) · 2012Article
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Authors and funding
3 authors.
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Abstract
The structural genomics projects have been accumulating an increasing number of protein structures, many of which remain functionally unknown. In parallel effort to experimental methods, computational methods are expected to make a significant contribution for functional elucidation of such proteins. However, conventional computational methods that transfer functions from homologous proteins do not help much for these uncharacterized protein structures because they do not have apparent structural or sequence similarity with the known proteins. Here, we briefly review two avenues of computational function prediction methods, i.e. structure-based methods and sequence-based methods. The focus is on our recent developments of local structure-based and sequence-based methods, which can effectively extract function information from distantly related proteins. Two structure-based methods, Pocket-Surfer and Patch-Surfer, identify similar known ligand binding sites for pocket regions in a query protein without using global protein fold similarity information. Two sequence-based methods, protein function prediction and extended similarity group, make use of weakly similar sequences that are conventionally discarded in homology based function annotation. Combined together with experimental methods we hope that computational methods will make leading contribution in functional elucidation of the protein structures.
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