ArticleNucleic acids research2018
PSSMSearch: a server for modeling, visualization, proteome-wide discovery and annotation of protein motif specificity determinants.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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38 citing papers in PubMed.
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- Integrating AlphaFold2 models and clinical data to improve the assessment of Short Linear Motifs (SLiMs) and their variants' pathogenicity.PLoS computational biology · 2025Article
- Uncovering protein prenylation in Th1 cells: novel prenylation sites and insights into statin and farnesyltransferase inhibition.BMC biology · 2025Article
- Hierarchy in regulator interactions with distant transcriptional activation domains empowers rheostatic regulation.Protein science : a publication of the Protein Society · 2025Article
- Defining short linear motif binding determinants by phage display-based deep mutational scanning.Protein science : a publication of the Protein Society · 2025Article
- High resolution profiling of cell cycle-dependent protein and phosphorylation abundance changes in non-transformed cells.Nature communications · 2025Article
- FaSTPACE: a fast and scalable tool for peptide alignment and consensus extraction.NAR genomics and bioinformatics · 2024Article
- Proteome-scale characterisation of motif-based interactome rewiring by disease mutations.Molecular systems biology · 2024Article
- Linear motifs regulating protein secretion, sorting and autophagy in Leishmania parasites are diverged with respect to their host equivalents.PLoS computational biology · 2024Article
- LIRcentral: a manually curated online database of experimentally validated functional LIR motifs.Autophagy · 2023Article
- Proteome-wide screening for mitogen-activated protein kinase docking motifs and interactors.Science signaling · 2023Article
- Des3PI: a fragment-based approach to design cyclic peptides targeting protein-protein interactions.Journal of computer-aided molecular design · 2022Article
- Accurate, high-coverage assignment of in vivo protein kinases to phosphosites from in vitro phosphoproteomic specificity data.PLoS computational biology · 2022Article
- The structural context of posttranslational modifications at a proteome-wide scale.PLoS biology · 2022Article
- N-terminome analyses underscore the prevalence of SPPL3-mediated intramembrane proteolysis among Golgi-resident enzymes and its role in Golgi enzyme secretion.Cellular and molecular life sciences : CMLS · 2022Article
- Structure-based prediction of HDAC6 substrates validated by enzymatic assay reveals determinants of promiscuity and detects new potential substrates.Scientific reports · 2022Article
- Proteome-scale mapping of binding sites in the unstructured regions of the human proteome.Molecular systems biology · 2022Article
- Large scale discovery of coronavirus-host factor protein interaction motifs reveals SARS-CoV-2 specific mechanisms and vulnerabilities.Nature communications · 2021Article
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3 authors.
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Abstract
There is a pressing need for in silico tools that can aid in the identification of the complete repertoire of protein binding (SLiMs, MoRFs, miniMotifs) and modification (moiety attachment/removal, isomerization, cleavage) motifs. We have created PSSMSearch, an interactive web-based tool for rapid statistical modeling, visualization, discovery and annotation of protein motif specificity determinants to discover novel motifs in a proteome-wide manner. PSSMSearch analyses proteomes for regions with significant similarity to a motif specificity determinant model built from a set of aligned motif-containing peptides. Multiple scoring methods are available to build a position-specific scoring matrix (PSSM) describing the motif specificity determinant model. This model can then be modified by a user to add prior knowledge of specificity determinants through an interactive PSSM heatmap. PSSMSearch includes a statistical framework to calculate the significance of specificity determinant model matches against a proteome of interest. PSSMSearch also includes the SLiMSearch framework's annotation, motif functional analysis and filtering tools to highlight relevant discriminatory information. Additional tools to annotate statistically significant shared keywords and GO terms, or experimental evidence of interaction with a motif-recognizing protein have been added. Finally, PSSM-based conservation metrics have been created for taxonomic range analyses. The PSSMSearch web server is available at http://slim.ucd.ie/pssmsearch/.
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