ArticleNucleic acids research2009
INTREPID: a web server for prediction of functionally important residues by evolutionary analysis.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers, 1 of them a synthesis that pooled it.
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Who cites it
23 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- Probing remote residues important for catalysis in Escherichia coli ornithine transcarbamoylase.PloS one · 2020Article
- Adenine Enrichment at the Fourth CDS Residue in Bacterial Genes Is Consistent with Error Proofing for +1 Frameshifts.Molecular biology and evolution · 2017Article
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- ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules.Nucleic acids research · 2016Article
- Type I Interferon Signaling Is Decoupled from Specific Receptor Orientation through Lenient Requirements of the Transmembrane Domain.The Journal of biological chemistry · 2016Article
- Proteins and Their Interacting Partners: An Introduction to Protein-Ligand Binding Site Prediction Methods.International journal of molecular sciences · 2015Review
- Prediction of distal residue participation in enzyme catalysis.Protein science : a publication of the Protein Society · 2015Article
- Biochemical functional predictions for protein structures of unknown or uncertain function.Computational and structural biotechnology journal · 2015Review
- The FunFOLD2 server for the prediction of protein-ligand interactions.Nucleic acids research · 2013Article
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- Protein function annotation with Structurally Aligned Local Sites of Activity (SALSAs).BMC bioinformatics · 2013Article
- POOL server: machine learning application for functional site prediction in proteins.Bioinformatics (Oxford, England) · 2012Article
- CLIPS-1D: analysis of multiple sequence alignments to deduce for residue-positions a role in catalysis, ligand-binding, or protein structure.BMC bioinformatics · 2012Article
- Common and distant structural characteristics of feruloyl esterase families from Aspergillus oryzae.PloS one · 2012Article
- FunFOLDQA: a quality assessment tool for protein-ligand binding site residue predictions.PloS one · 2012Article
- FunFOLD: an improved automated method for the prediction of ligand binding residues using 3D models of proteins.BMC bioinformatics · 2011Article
- Identification of family-determining residues in PHD fingers.Nucleic acids research · 2011Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
We present the INTREPID web server for predicting functionally important residues in proteins. INTREPID has been shown to boost the recall and precision of catalytic residue prediction over other sequence-based methods and can be used to identify other types of functional residues. The web server takes an input protein sequence, gathers homologs, constructs a multiple sequence alignment and phylogenetic tree and finally runs the INTREPID method to assign a score to each position. Residues predicted to be functionally important are displayed on homologous 3D structures (where available), highlighting spatial patterns of conservation at various significance thresholds. The INTREPID web server is available at http://phylogenomics.berkeley.edu/intrepid.
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