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Resources and tools

Dr Norman Davey, Short Linear Motif Team

PSSMSearch

PSSMSearch is a PSSM-based short, linear motif (SLiMs, mORFs, miniMotifs) and PTM sites discovery tool. PSSMSearch analyses proteomes for regions with significant similarity to a specificity determinant model built from a set of aligned functional peptides. Multiple scoring methods are available to build a position-specific scoring matrix (PSSM) describing the specificity determinant model and users can modify the model to add prior knowledge of specificity determinants through an interactive PSSM heatmap. 

SLiMSearch

SLiMSearch is a consensus-based short, linear motif (SLiMs, mORFs, miniMotifs) and PTM sites discovery tool. Motif attributes known to be strong discriminators of motif functionality, such as accessibility and conservation, are calculated for each instance. Instances are also annotated with experimental, proteomic and genomic data. The tool also allows instance filtering based on keyword, interaction, localisation information. In-depth ontology enrichment and conservation analysis tools are also available. 

ProViz 

ProViz (Protein Vizualisation) is an interactive exploration tool for investigating the functional and evolutionary features of proteins. The tool is designed to be an intuitive and accessible resource to allow users with limited bioinformatic skills to rapidly access and visualise data pertinent to their research. 

The switches.ELM Resource 

The switches.ELM resource consists of a database that curates experimentally validated motif-based molecular switches and a prediction tool to identify possible switching mechanisms that might regulate a user-submitted motif of interest. This tool helps to extend knowledge and direct research on how motifs mediate cooperative decision-making in a context-dependent manner and direct reliable and robust cell regulation.

 

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