ArticleBMC bioinformatics2011
StralSV: assessment of sequence variability within similar 3D structures and application to polio RNA-dependent RNA polymerase.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Design of cross-reactive antigens with machine learning and high-throughput experimental evaluation.Frontiers in bioinformatics · 2025Article
- Design of immunogens for eliciting antibody responses that may protect against SARS-CoV-2 variants.PLoS computational biology · 2022Article
- Rational Control of Poliovirus RNA-Dependent RNA Polymerase Fidelity by Modulating Motif-D Loop Conformational Dynamics.Biochemistry · 2019Article
- Multiscale analysis for patterns of Zika virus genotype emergence, spread, and consequence.PloS one · 2019Article
- Microbial mercury methylation in Antarctic sea ice.Nature microbiology · 2016Article
- Sendai virus intra-host population dynamics and host immunocompetence influence viral virulence duringVirus evolution · 2016Article
- GeneSV - an Approach to Help Characterize Possible Variations in Genomic and Protein Sequences.Bioinformatics and biology insights · 2014Article
- Identification of a novel drug lead that inhibits HCV infection and cell-to-cell transmission by targeting the HCV E2 glycoprotein.PloS one · 2014Article
- Vaccine-derived mutation in motif D of poliovirus RNA-dependent RNA polymerase lowers nucleotide incorporation fidelity.The Journal of biological chemistry · 2013Article
- Highly similar structural frames link the template tunnel and NTP entry tunnel to the exterior surface in RNA-dependent RNA polymerases.Nucleic acids research · 2013Article
- Computational analysis of pathogen-borne metallo β-lactamases reveals discriminating structural features between B1 types.BMC research notes · 2012Article
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5 authors.
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Abstract
backgroundMost of the currently used methods for protein function prediction rely on sequence-based comparisons between a query protein and those for which a functional annotation is provided. A serious limitation of sequence similarity-based approaches for identifying residue conservation among proteins is the low confidence in assigning residue-residue correspondences among proteins when the level of sequence identity between the compared proteins is poor. Multiple sequence alignment methods are more satisfactory--still, they cannot provide reliable results at low levels of sequence identity. Our goal in the current work was to develop an algorithm that could help overcome these difficulties by facilitating the identification of structurally (and possibly functionally) relevant residue-residue correspondences between compared protein structures.
resultsHere we present StralSV (structure-alignment sequence variability), a new algorithm for detecting closely related structure fragments and quantifying residue frequency from tight local structure alignments. We apply StralSV in a study of the RNA-dependent RNA polymerase of poliovirus, and we demonstrate that the algorithm can be used to determine regions of the protein that are relatively unique, or that share structural similarity with proteins that would be considered distantly related. By quantifying residue frequencies among many residue-residue pairs extracted from local structural alignments, one can infer potential structural or functional importance of specific residues that are determined to be highly conserved or that deviate from a consensus. We further demonstrate that considerable detailed structural and phylogenetic information can be derived from StralSV analyses.
conclusionsStralSV is a new structure-based algorithm for identifying and aligning structure fragments that have similarity to a reference protein. StralSV analysis can be used to quantify residue-residue correspondences and identify residues that may be of particular structural or functional importance, as well as unusual or unexpected residues at a given sequence position. StralSV is provided as a web service at http://proteinmodel.org/AS2TS/STRALSV/.
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