The Experts below are selected from a list of 126 Experts worldwide ranked by ideXlab platform
Norman E Davey - One of the best experts on this subject based on the ideXlab platform.
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discovery of Short Linear Motif mediated interactions through phage display of intrinsically disordered regions of the human proteome
FEBS Journal, 2017Co-Authors: Norman E Davey, Jouhyun Jeon, Izabella Krystkowiak, Debbie Dong, Natalia Markova, Vikash Kumar Yadav, Cecilia Blikstad, Ylva IvarssonAbstract:The intrinsically disordered regions of eukaryotic proteomes are enriched in Short Linear Motifs (SLiMs), which are of crucial relevance for cellular signaling and protein regulation; many mediate ...
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Discovery of Short Linear Motif-mediated interactions through phage display of intrinsically disordered regions of the human proteome
FEBS Journal, 2017Co-Authors: Norman E Davey, Moon Hyeong Seo, Satra Nim, Jouhyun Jeon, Izabella Krystkowiak, Debbie Dong, Natalia Markova, Vikash Kumar Yadav, Cecilia Blikstad, Philip M. KimAbstract:The intrinsically disordered regions of eukaryotic proteomes are enriched in Short Linear Motifs (SLiMs), which are of crucial relevance for cellular signaling and protein regulation; many mediate interactions by providing binding sites for peptide-binding domains. The vast majority of SLiMs remain to be discovered highlighting the need for experimental methods for their large-scale identification. We present a novel proteomic peptide phage display (ProP-PD) library that displays peptides representing the disordered regions of the human proteome, allowing direct large-scale interrogation of most potential binding SLiMs in the proteome. The performance of the ProP-PD library was validated through selections against SLiM-binding bait domains with distinct folds and binding preferences. The vast majority of identified binding peptides contained sequences that matched the known SLiM-binding specificities of the bait proteins. For SHANK1 PDZ, we establish a novel consensus TxF Motif for its non-C-terminal ligands. The binding peptides mostly represented novel target proteins, however, several previously validated protein–protein interactions (PPIs) were also discov-ered. We determined the affinities between the VHS domain of GGA1 and three identified ligands to 40–130 lM through isothermal titration calorime-try, and confirmed interactions through coimmunoprecipitation using full-length proteins. Taken together, we outline a general pipeline for the design and construction of ProP-PD libraries and the analysis of ProP-PD-derived, SLiM-based PPIs. We demonstrated the methods potential to identify low affinity Motif-mediated interactions for modular domains with distinct binding preferences. The approach is a highly useful complement to the current toolbox of methods for PPI discovery.
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SLiMPrints: conservation-based discovery of functional Motif fingerprints in intrinsically disordered protein regions
Nucleic Acids Research, 2012Co-Authors: Norman E Davey, Denis C Shields, Toby J Gibson, Joanne L. Cowan, Mark J. Coldwell, Richard J EdwardsAbstract:Large portions of higher eukaryotic proteomes are intrinsically disordered, and abundant evidence suggests that these unstructured regions of proteins are rich in regulatory interaction interfaces. A major class of disordered interaction interfaces are the compact and degenerate modules known as Short Linear Motifs (SLiMs). As a result of the difficulties associated with the experimental identification and validation of SLiMs, our understanding of these modules is limited, advocating the use of computational methods to focus experimental discovery. This article evaluates the use of evolutionary conservation as a discriminatory technique for Motif discovery. A statistical framework is introduced to assess the significance of relatively conserved residues, quantifying the likelihood a residue will have a particular level of conservation given the conservation of the surrounding residues. The framework is expanded to assess the significance of groupings of conserved residues, a metric that forms the basis of SLiMPrints (Short Linear Motif fingerprints), a de novo Motif discovery tool. SLiMPrints identifies relatively overconstrained proximal groupings of residues within intrinsically disordered regions, indicative of putatively functional Motifs. Finally, the human proteome is analysed to create a set of highly conserved putative Motif instances, including a novel site on translation initiation factor eIF2A that may regulate translation through binding of eIF4E.
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the identification of Short Linear Motif mediated interfaces within the human interactome
Bioinformatics, 2012Co-Authors: Robert J Weatheritt, Norman E Davey, K Luck, Evangelia Petsalaki, Toby J GibsonAbstract:Motivation: Eukaryotic proteins are highly modular, containing multiple interaction interfaces that mediate binding to a network of regulators and effectors. Recent advances in high-throughput proteomics have rapidly expanded the number of known protein–protein interactions (PPIs); however, the molecular basis for the majority of these interactions remains to be elucidated. There has been a growing appreciation of the importance of a subset of these PPIs, namely those mediated by Short Linear Motifs (SLiMs), particularly the canonical and ubiquitous SH2, SH3 and PDZ domain-binding Motifs. However, these Motif classes represent only a small fraction of known SLiMs and outside these examples little effort has been made, either bioinformatically or experimentally, to discover the full complement of Motif instances. Results: In this article, interaction data are analysed to identify and characterize an important subset of PPIs, those involving SLiMs binding to globular domains. To do this, we introduce iELM, a method to identify interactions mediated by SLiMs and add molecular details of the interaction interfaces to both interacting proteins. The method identifies SLiM-mediated interfaces from PPI data by searching for known SLiM–domain pairs. This approach was applied to the human interactome to identify a set of high-confidence putative SLiM-mediated PPIs. Availability: iELM is freely available at http://elmint.embl.de Contact: toby.gibson@embl.de Supplementary information:Supplementary data are available at Bioinformatics online.
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SLiMSearch 2.0: biological context for Short Linear Motifs in proteins
Nucleic Acids Research, 2011Co-Authors: Norman E Davey, Niall J Haslam, Denis C Shields, Richard J EdwardsAbstract:Short, Linear Motifs (SLiMs) play a critical role in many biological processes. The SLiMSearch 2.0 (Short, Linear Motif Search) web server allows researchers to identify occurrences of a user-defined SLiM in a proteome, using conservation and protein disorder context statistics to rank occurrences. User-friendly output and visualizations of Motif context allow the user to quickly gain insight into the validity of a putatively functional Motif occurrence. For each Motif occurrence, overlapping UniProt features and annotated SLiMs are displayed. Visualization also includes annotated multiple sequence alignments surrounding each occurrence, showing conservation and protein disorder statistics in addition to known and predicted SLiMs, protein domains and known post-translational modifications. In addition, enrichment of Gene Ontology terms and protein interaction partners are provided as indicators of possible Motif function. All web server results are available for download. Users can search Motifs against the human proteome or a subset thereof defined by Uniprot accession numbers or GO term. The SLiMSearch server is available at: http://bioware.ucd.ie/slimsearch2.html.
Denis C Shields - One of the best experts on this subject based on the ideXlab platform.
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slimscape a protein Short Linear Motif analysis plugin for cytoscape
BMC Bioinformatics, 2013Co-Authors: Kevin T Obrien, Niall J Haslam, Denis C ShieldsAbstract:Background Computational protein Short Linear Motif discovery can use protein interaction information to search for Motifs among proteins which share a common interactor. Cytoscape provides a visual interface for protein networks but there is no streamlined way to rapidly visualize Motifs in a network of proteins, or to integrate computational discovery with such visualizations.
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SLiMPrints: conservation-based discovery of functional Motif fingerprints in intrinsically disordered protein regions
Nucleic Acids Research, 2012Co-Authors: Norman E Davey, Denis C Shields, Toby J Gibson, Joanne L. Cowan, Mark J. Coldwell, Richard J EdwardsAbstract:Large portions of higher eukaryotic proteomes are intrinsically disordered, and abundant evidence suggests that these unstructured regions of proteins are rich in regulatory interaction interfaces. A major class of disordered interaction interfaces are the compact and degenerate modules known as Short Linear Motifs (SLiMs). As a result of the difficulties associated with the experimental identification and validation of SLiMs, our understanding of these modules is limited, advocating the use of computational methods to focus experimental discovery. This article evaluates the use of evolutionary conservation as a discriminatory technique for Motif discovery. A statistical framework is introduced to assess the significance of relatively conserved residues, quantifying the likelihood a residue will have a particular level of conservation given the conservation of the surrounding residues. The framework is expanded to assess the significance of groupings of conserved residues, a metric that forms the basis of SLiMPrints (Short Linear Motif fingerprints), a de novo Motif discovery tool. SLiMPrints identifies relatively overconstrained proximal groupings of residues within intrinsically disordered regions, indicative of putatively functional Motifs. Finally, the human proteome is analysed to create a set of highly conserved putative Motif instances, including a novel site on translation initiation factor eIF2A that may regulate translation through binding of eIF4E.
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Prediction of Short Linear Protein Binding Regions
Journal of Molecular Biology, 2011Co-Authors: Catherine Mooney, Denis C Shields, Gianluca Pollastri, Niall J HaslamAbstract:Abstract Short Linear Motifs in proteins (typically 3–12 residues in length) play key roles in protein–protein interactions by frequently binding specifically to peptide binding domains within interacting proteins. Their tendency to be found in disordered segments of proteins has meant that they have often been overlooked. Here we present SLiMPred (Short Linear Motif predictor), the first general de novo method designed to computationally predict such regions in protein primary sequences independent of experimentally defined homologs and interactors. The method applies machine learning techniques to predict new Motifs based on annotated instances from the Eukaryotic Linear Motif database, as well as structural, biophysical, and biochemical features derived from the protein primary sequence. We have integrated these data sources and benchmarked the predictive accuracy of the method, and found that it performs equivalently to a predictor of protein binding regions in disordered regions, in addition to having predictive power for other classes of Motif sites such as polyproline II helix Motifs and Short Linear Motifs lying in ordered regions. It will be useful in predicting peptides involved in potential protein associations and will aid in the functional characterization of proteins, especially of proteins lacking experimental information on structures and interactions. We conclude that, despite the diversity of Motif sequences and structures, SLiMPred is a valuable tool for prioritizing potential interaction Motifs in proteins.
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SLiMSearch 2.0: biological context for Short Linear Motifs in proteins
Nucleic Acids Research, 2011Co-Authors: Norman E Davey, Niall J Haslam, Denis C Shields, Richard J EdwardsAbstract:Short, Linear Motifs (SLiMs) play a critical role in many biological processes. The SLiMSearch 2.0 (Short, Linear Motif Search) web server allows researchers to identify occurrences of a user-defined SLiM in a proteome, using conservation and protein disorder context statistics to rank occurrences. User-friendly output and visualizations of Motif context allow the user to quickly gain insight into the validity of a putatively functional Motif occurrence. For each Motif occurrence, overlapping UniProt features and annotated SLiMs are displayed. Visualization also includes annotated multiple sequence alignments surrounding each occurrence, showing conservation and protein disorder statistics in addition to known and predicted SLiMs, protein domains and known post-translational modifications. In addition, enrichment of Gene Ontology terms and protein interaction partners are provided as indicators of possible Motif function. All web server results are available for download. Users can search Motifs against the human proteome or a subset thereof defined by Uniprot accession numbers or GO term. The SLiMSearch server is available at: http://bioware.ucd.ie/slimsearch2.html.
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PRIB - SLiMSearch: a webserver for finding novel occurrences of Short Linear Motifs in proteins, incorporating sequence context
Pattern Recognition in Bioinformatics, 2010Co-Authors: Norman E Davey, Niall J Haslam, Denis C Shields, Richard J EdwardsAbstract:Short, Linear Motifs (SLiMs) play a critical role in many biological processes. The SLiMSearch (Short, Linear Motif Search) webserver is a flexible tool that enables researchers to identify novel occurrences of predefined SLiMs in sets of proteins. Numerous masking options give the user great control over the contextual information to be included in the analyses, including evolutionary filtering and protein structural disorder. User-friendly output and visualizations of Motif context allow the user to quickly gain insight into the validity of a putatively functional Motif occurrence. Users can search Motifs against the human proteome, or submit their own datasets of UniProt proteins, in which case Motif support within the dataset is statistically assessed for over- and under-representation, accounting for evolutionary relationships between input proteins. SLiMSearch is freely available as open source Python modules and all webserver results are available for download. The SLiMSearch server is available at: http://bioware.ucd.ie/slimsearch.html.
Toby J Gibson - One of the best experts on this subject based on the ideXlab platform.
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Short Linear Motif candidates in the cell entry system used by sars cov 2 and their potential therapeutic implications
arXiv: Biomolecules, 2020Co-Authors: Balint Meszaros, Lucia B Chemes, Jesus Alvaradovalverde, Jelena Calyseva, Manjeet Kumar, Hugo Samanosanchez, Elizabeth Martinezperez, Renato J Alves, Friedrich Rippmann, Toby J GibsonAbstract:The primary cell surface receptor for SARS-CoV-2 is the angiotensin-converting enzyme 2 (ACE2). Recently it has been noticed that the viral Spike protein has an RGD Motif, suggesting that cell surface integrins may be co-receptors. We examined the sequences of ACE2 and integrins with the Eukaryotic Linear Motif resource, ELM, and were presented with candidate Short Linear Motifs (SLiMs) in their Short, unstructured, cytosolic tails with potential roles in endocytosis, membrane dynamics, autophagy, cytoskeleton and cell signalling. These SLiM candidates are highly conserved in vertebrates. They suggest potential interactions with the AP2 mu2 subunit as well as I-BAR, LC3, PDZ, PTB and SH2 domains found in signalling and regulatory proteins present in epithelial lung cells. Several Motifs overlap in the tail sequences, suggesting that they may act as molecular switches, often involving tyrosine phosphorylation status. Candidate LIR Motifs are present in the tails of ACE2 and integrin beta3, suggesting that these proteins can directly recruit autophagy components. We also noticed that the extracellular part of ACE2 has a conserved MIDAS structural Motif, which are commonly used by beta integrins for ligand binding, potentially supporting the proposal that integrins and ACE2 share common ligands. The findings presented here identify several molecular links and testable hypotheses that might help uncover the mechanisms of SARS-CoV-2 attachment, entry and replication, and strengthen the possibility that it might be possible to develop host-directed therapies to dampen the efficiency of viral entry and hamper disease progression. The strong sequence conservation means that these putative SLiMs are good candidates: Nevertheless, SLiMs must always be validated by experimentation before they can be stated to be functional.
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how to annotate and submit a Short Linear Motif to the eukaryotic Linear Motif resource
Methods of Molecular Biology, 2020Co-Authors: Marc Gouw, Holger Dinkel, Jesus Alvaradovalverde, Jelena Calyseva, Francesca Diella, Manjeet Kumar, Sushama Michael, Kim Van Roey, Toby J GibsonAbstract:Over the past few years, it has become apparent that approximately 35% of the human proteome consists of intrinsically disordered regions. Many of these disordered regions are rich in Short Linear Motifs (SLiMs) which mediate protein-protein interactions. Although these Motifs are Short and often partially conserved, they are involved in many important aspects of protein function, including cleavage, targeting, degradation, docking, phosphorylation, and other posttranslational modifications. The Eukaryotic Linear Motif resource (ELM) was established over 15 years ago as a repository to store and catalogue the scientific discoveries of Motifs. Each Motif in the database is annotated and curated manually, based on the experimental evidence gathered from publications. The entries themselves are submitted to ELM by filling in two annotation templates designed for Motif class and Motif instance annotation. In this protocol, we describe the steps involved in annotating new Motifs and how to submit them to ELM.
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Short Linear Motif core and flanking regions modulate retinoblastoma protein binding affinity and specificity
Protein Engineering Design & Selection, 2018Co-Authors: Nicolas Palopoli, Toby J Gibson, Nicolas Gonzalez S Foutel, Lucia B ChemesAbstract:: Pocket proteins retinoblastoma (pRb), p107 and p130 are negative regulators of cellular proliferation and multifunctional proteins regulating development, differentiation and chromatin structure. The retinoblastoma protein is a potent tumor suppressor mutated in a wide range of human cancers, and oncogenic viruses often interfere with cell cycle regulation by inactivating pRb. The LxCxE and pRb AB groove Short Linear Motifs (SLiMs) are key to many pocket protein mediated interactions including host and viral partners. A review of available experimental evidence reveals that several core residues composing each Motif instance are determinants for binding. In the LxCxE Motif, a fourth hydrophobic position that might allow variable spacing is required for binding. In both Motifs, flanking regions including charged stretches and phosphorylation sites can fine-tune the binding affinity and specificity of pocket protein SLiM-mediated interactions. Flanking regions can modulate pocket protein binding specificity, or tune the high affinity interactions of viral proteins that hijack the pRb network. The location of SLiMs within intrinsically disordered regions allows faster evolutionary rates that enable viruses to acquire a functional variant of the core Motif by convergent evolution, and subsequently test numerous combinations of flanking regions towards maximizing interaction specificity and affinity. This knowledge can guide future efforts directed at the design of peptide-based compounds that can target pocket proteins to regulate the G1/S cell cycle checkpoint or impair viral mediated pRb inactivation.
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SLiMPrints: conservation-based discovery of functional Motif fingerprints in intrinsically disordered protein regions
Nucleic Acids Research, 2012Co-Authors: Norman E Davey, Denis C Shields, Toby J Gibson, Joanne L. Cowan, Mark J. Coldwell, Richard J EdwardsAbstract:Large portions of higher eukaryotic proteomes are intrinsically disordered, and abundant evidence suggests that these unstructured regions of proteins are rich in regulatory interaction interfaces. A major class of disordered interaction interfaces are the compact and degenerate modules known as Short Linear Motifs (SLiMs). As a result of the difficulties associated with the experimental identification and validation of SLiMs, our understanding of these modules is limited, advocating the use of computational methods to focus experimental discovery. This article evaluates the use of evolutionary conservation as a discriminatory technique for Motif discovery. A statistical framework is introduced to assess the significance of relatively conserved residues, quantifying the likelihood a residue will have a particular level of conservation given the conservation of the surrounding residues. The framework is expanded to assess the significance of groupings of conserved residues, a metric that forms the basis of SLiMPrints (Short Linear Motif fingerprints), a de novo Motif discovery tool. SLiMPrints identifies relatively overconstrained proximal groupings of residues within intrinsically disordered regions, indicative of putatively functional Motifs. Finally, the human proteome is analysed to create a set of highly conserved putative Motif instances, including a novel site on translation initiation factor eIF2A that may regulate translation through binding of eIF4E.
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ielm a web server to explore Short Linear Motif mediated interactions
Nucleic Acids Research, 2012Co-Authors: Robert J Weatheritt, Peter Jehl, Holger Dinkel, Toby J GibsonAbstract:The recent expansion in our knowledge of protein–protein interactions (PPIs) has allowed the annotation and prediction of hundreds of thousands of interactions. However, the function of many of these interactions remains elusive. The interactions of Eukaryotic Linear Motif (iELM) web server provides a resource for predicting the function and positional interface for a subset of interactions mediated by Short Linear Motifs (SLiMs). The iELM prediction algorithm is based on the annotated SLiM classes from the Eukaryotic Linear Motif (ELM) resource and allows users to explore both annotated and user-generated PPI networks for SLiM-mediated interactions. By incorporating the annotated information from the ELM resource, iELM provides functional details of PPIs. This can be used in proteomic analysis, for example, to infer whether an interaction promotes complex formation or degradation. Furthermore, details of the molecular interface of the SLiM-mediated interactions are also predicted. This information is displayed in a fully searchable table, as well as graphically with the modular architecture of the participating proteins extracted from the UniProt and Phospho.ELM resources. A network figure is also presented to aid the interpretation of results. The iELM server supports single protein queries as well as large-scale proteomic submissions and is freely available at http://i.elm.eu.org.
Richard J Edwards - One of the best experts on this subject based on the ideXlab platform.
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qslimfinder improved Short Linear Motif prediction using specific query protein data
Bioinformatics, 2015Co-Authors: Nicolas Palopoli, Richard J Edwards, Kieren T LythgowAbstract:MOTIVATION: The sensitivity of de novo Short Linear Motif (SLiM) prediction is limited by the number of patterns (the Motif space) being assessed for enrichment. QSLiMFinder uses specific query protein information to restrict the Motif space and thereby increase the sensitivity and specificity of predictions. RESULTS: QSLiMFinder was extensively benchmarked using known SLiM-containing proteins and simulated protein interaction datasets of real human proteins. Exploiting prior knowledge of a query protein likely to be involved in a SLiM-mediated interaction increased the proportion of true positives correctly returned and reduced the proportion of datasets returning a false positive prediction. The biggest improvement was seen if a Short region of the query protein flanking the interaction site was known. AVAILABILITY AND IMPLEMENTATION: All the tools and data used in this study, including QSLiMFinder and the SLiMBench benchmarking software, are freely available under a GNU license as part of SLiMSuite, at: http://bioware.soton.ac.uk. CONTACT: richard.edwards@unsw.edu.au Supplementary information: Supplementary data are available at Bioinformatics online.
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SLiMPrints: conservation-based discovery of functional Motif fingerprints in intrinsically disordered protein regions
Nucleic Acids Research, 2012Co-Authors: Norman E Davey, Denis C Shields, Toby J Gibson, Joanne L. Cowan, Mark J. Coldwell, Richard J EdwardsAbstract:Large portions of higher eukaryotic proteomes are intrinsically disordered, and abundant evidence suggests that these unstructured regions of proteins are rich in regulatory interaction interfaces. A major class of disordered interaction interfaces are the compact and degenerate modules known as Short Linear Motifs (SLiMs). As a result of the difficulties associated with the experimental identification and validation of SLiMs, our understanding of these modules is limited, advocating the use of computational methods to focus experimental discovery. This article evaluates the use of evolutionary conservation as a discriminatory technique for Motif discovery. A statistical framework is introduced to assess the significance of relatively conserved residues, quantifying the likelihood a residue will have a particular level of conservation given the conservation of the surrounding residues. The framework is expanded to assess the significance of groupings of conserved residues, a metric that forms the basis of SLiMPrints (Short Linear Motif fingerprints), a de novo Motif discovery tool. SLiMPrints identifies relatively overconstrained proximal groupings of residues within intrinsically disordered regions, indicative of putatively functional Motifs. Finally, the human proteome is analysed to create a set of highly conserved putative Motif instances, including a novel site on translation initiation factor eIF2A that may regulate translation through binding of eIF4E.
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SLiMSearch 2.0: biological context for Short Linear Motifs in proteins
Nucleic Acids Research, 2011Co-Authors: Norman E Davey, Niall J Haslam, Denis C Shields, Richard J EdwardsAbstract:Short, Linear Motifs (SLiMs) play a critical role in many biological processes. The SLiMSearch 2.0 (Short, Linear Motif Search) web server allows researchers to identify occurrences of a user-defined SLiM in a proteome, using conservation and protein disorder context statistics to rank occurrences. User-friendly output and visualizations of Motif context allow the user to quickly gain insight into the validity of a putatively functional Motif occurrence. For each Motif occurrence, overlapping UniProt features and annotated SLiMs are displayed. Visualization also includes annotated multiple sequence alignments surrounding each occurrence, showing conservation and protein disorder statistics in addition to known and predicted SLiMs, protein domains and known post-translational modifications. In addition, enrichment of Gene Ontology terms and protein interaction partners are provided as indicators of possible Motif function. All web server results are available for download. Users can search Motifs against the human proteome or a subset thereof defined by Uniprot accession numbers or GO term. The SLiMSearch server is available at: http://bioware.ucd.ie/slimsearch2.html.
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PRIB - SLiMSearch: a webserver for finding novel occurrences of Short Linear Motifs in proteins, incorporating sequence context
Pattern Recognition in Bioinformatics, 2010Co-Authors: Norman E Davey, Niall J Haslam, Denis C Shields, Richard J EdwardsAbstract:Short, Linear Motifs (SLiMs) play a critical role in many biological processes. The SLiMSearch (Short, Linear Motif Search) webserver is a flexible tool that enables researchers to identify novel occurrences of predefined SLiMs in sets of proteins. Numerous masking options give the user great control over the contextual information to be included in the analyses, including evolutionary filtering and protein structural disorder. User-friendly output and visualizations of Motif context allow the user to quickly gain insight into the validity of a putatively functional Motif occurrence. Users can search Motifs against the human proteome, or submit their own datasets of UniProt proteins, in which case Motif support within the dataset is statistically assessed for over- and under-representation, accounting for evolutionary relationships between input proteins. SLiMSearch is freely available as open source Python modules and all webserver results are available for download. The SLiMSearch server is available at: http://bioware.ucd.ie/slimsearch.html.
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SLiMFinder: a web server to find novel, significantly over-represented, Short protein Motifs.
Nucleic acids research, 2010Co-Authors: Norman E Davey, Niall J Haslam, Denis C Shields, Richard J EdwardsAbstract:Short, Linear Motifs (SLiMs) play a critical role in many biological processes, particularly in protein-protein interactions. The Short, Linear Motif Finder (SLiMFinder) web server is a de novo Motif discovery tool that identifies statistically over-represented Motifs in a set of protein sequences, accounting for the evolutionary relationships between them. Motifs are returned with an intuitive P-value that greatly reduces the problem of false positives and is accessible to biologists of all disciplines. Input can be uploaded by the user or extracted directly from UniProt. Numerous masking options give the user great control over the contextual information to be included in the analyses. The SLiMFinder server combines these with user-friendly output and visualizations of Motif context to allow the user to quickly gain insight into the validity of a putatively functional Motif. These visualizations include alignments of Motif occurrences, alignments of Motifs and their homologues and a visual schematic of the top-ranked Motifs. Returned Motifs can also be compared with known SLiMs from the literature using CompariMotif. All results are available for download. The SLiMFinder server is available at: http://bioware.ucd.ie/slimfinder.html.
Ylva Ivarsson - One of the best experts on this subject based on the ideXlab platform.
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discovery of Short Linear Motif mediated interactions through phage display of intrinsically disordered regions of the human proteome
FEBS Journal, 2017Co-Authors: Norman E Davey, Jouhyun Jeon, Izabella Krystkowiak, Debbie Dong, Natalia Markova, Vikash Kumar Yadav, Cecilia Blikstad, Ylva IvarssonAbstract:The intrinsically disordered regions of eukaryotic proteomes are enriched in Short Linear Motifs (SLiMs), which are of crucial relevance for cellular signaling and protein regulation; many mediate ...