ArticleProteins2005
Structural characterization of proteins using residue environments.
Article in Proteins, 2005. 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, 27 citations in OpenAlex.
- Protein structure prediction using residue- and fragment-environment potentials in CASP11.Proteins · 2016Article
- Detecting local residue environment similarity for recognizing near-native structure models.Proteins · 2014Article
- A simple method for finding a protein's ligand-binding pockets.BMC structural biology · 2014Article
- Protein structure based prediction of catalytic residues.BMC bioinformatics · 2013Article
- Local functional descriptors for surface comparison based binding prediction.BMC bioinformatics · 2012Article
- Active site prediction using evolutionary and structural information.Bioinformatics (Oxford, England) · 2010Article
- Identification of recurring protein structure microenvironments and discovery of novel functional sites around CYS residues.BMC structural biology · 2010Article
- Graphlet kernels for prediction of functional residues in protein structures.Journal of computational biology : a journal of computational molecular cell biology · 2010Article
- Improving protein structure similarity searches using domain boundaries based on conserved sequence information.BMC structural biology · 2009Article
- Distance matrix-based approach to protein structure prediction.Journal of structural and functional genomics · 2009Article
- The unfoldomics decade: an update on intrinsically disordered proteins.BMC genomics · 2008Article
- Clustering protein environments for function prediction: finding PROSITE motifs in 3D.BMC bioinformatics · 2007Article
- Evaluation of features for catalytic residue prediction in novel folds.Protein science : a publication of the Protein Society · 2007Article
- Identification of similar regions of protein structures using integrated sequence and structure analysis tools.BMC structural biology · 2006Article
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
A primary challenge for structural genomics is the automated functional characterization of protein structures. We have developed a sequence-independent method called S-BLEST (Structure-Based Local Environment Search Tool) for the annotation of previously uncharacterized protein structures. S-BLEST encodes the local environment of an amino acid as a vector of structural property values. It has been applied to all amino acids in a nonredundant database of protein structures to generate a searchable structural resource. Given a query amino acid from an experimentally determined or modeled structure, S-BLEST quickly identifies similar amino acid environments using a K-nearest neighbor search. In addition, the method gives an estimation of the statistical significance of each result. We validated S-BLEST on X-ray crystal structures from the ASTRAL 40 nonredundant dataset. We then applied it to 86 crystallographically determined proteins in the protein data bank (PDB) with unknown function and with no significant sequence neighbors in the PDB. S-BLEST was able to associate 20 proteins with at least one local structural neighbor and identify the amino acid environments that are most similar between those neighbors.
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