ArticleBioinformatics (Oxford, England)2008
Characterization and prediction of residues determining protein functional specificity.
Article in Bioinformatics (Oxford, England), 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers.
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Who cites it
69 citing papers in PubMed.
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- Leveraging protein language models for accurate multiple sequence alignments.Genome research · 2023Article
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- Exploiting protein family and protein network data to identify novel drug targets for bladder cancer.Oncotarget · 2022Article
- Prediction of Protein Sites and Physicochemical Properties Related to Functional Specificity.Bioengineering (Basel, Switzerland) · 2021Article
- Clustering FunFams using sequence embeddings improves EC purity.Bioinformatics (Oxford, England) · 2021Article
- TwinCons: Conservation score for uncovering deep sequence similarity and divergence.PLoS computational biology · 2021Article
- dSPRINT: predicting DNA, RNA, ion, peptide and small molecule interaction sites within protein domains.Nucleic acids research · 2021Article
- CATH functional families predict functional sites in proteins.Bioinformatics (Oxford, England) · 2021Article
- Analysis of Sequence Divergence in Mammalian ABCGs Predicts a Structural Network of Residues That Underlies Functional Divergence.International journal of molecular sciences · 2021Article
- Predicting the Specificity- Determining Positions of Receptor Tyrosine Kinase Axl.Frontiers in molecular biosciences · 2021Article
- Predicting susceptibility to SARS-CoV-2 infection based on structural differences in ACE2 across species.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2020Article
- DIP/Dpr interactions and the evolutionary design of specificity in protein families.Nature communications · 2020Article
- Deep Analysis of Residue Constraints (DARC): identifying determinants of protein functional specificity.Scientific reports · 2020Article
- Bastion6: a bioinformatics approach for accurate prediction of type VI secreted effectors.Bioinformatics (Oxford, England) · 2018Article
- Expansion and diversification of the gibberellin receptor GIBBERELLIN INSENSITIVE DWARF1 (GID1) family in land plants.Plant molecular biology · 2018Article
- Sequence-based prediction of physicochemical interactions at protein functional sites using a function-and-interaction-annotated domain profile database.BMC bioinformatics · 2018Article
- Effect of the sequence data deluge on the performance of methods for detecting protein functional residues.BMC bioinformatics · 2018Article
- Recognition of sites of functional specialisation in all known eukaryotic protein kinase families.PLoS computational biology · 2018Article
9 more citing papers are in PubMed but not listed here.
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2 authors.
Funding
Abstract
motivationWithin 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 protein's particular functional 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.
resultsWe 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 evolutionary 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/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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