EMBL News 2013
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SMART

SMART (Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures. » DetailsSMART (Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures. More than 500 domain families found in signalling, extracellular and chromatin-associated proteins are detectable. These domains are extensively annotated with respect to phyletic distributions, functional class, tertiary structures and functionally important residues. Each domain found in a non-redundant protein database as well as search parameters and taxonomic information are stored in a relational database system. User interfaces to this database allow searches for proteins containing specific combinations of domains in defined taxa.

Downloads available:
A - (Commercial) V2.12.1SMART A is the basic version which contains the following features: alignments, profiles, HMMs, "schnipsel" database (i.e. a blastable database of domains), basic, handmade annotations, thresholds SMART A gives a higher sensitivity/selectivity than Pfam and provides some annotation. System requirements: unix Software/DB requirements (public domain tools held locally): HMMER2, searchwise, blast, (SWISSPROT DB in house recommended) Knowledge requirement: for installation and usage of publicly available search software (see above)
A - (Academic) V2.12.1SMART A is the basic version which contains the following features: alignments, profiles, HMMs, "schnipsel" database (i.e. a blastable database of domains), basic, handmade annotations, thresholds SMART A gives a higher sensitivity/selectivity than Pfam and provides some annotation. System requirements: unix Software/DB requirements (public domain tools held locally): HMMER2, searchwise, blast, (SWISSPROT DB in house recommended) Knowledge requirement: for installation and usage of publicly available search software (see above)

STRING

STRING - a comprehensive resource for protein interaction networks - STRING is a database of interactions between proteins - essentially, it is a platform for system-level exploration of cellular machineries. » DetailsSTRING - a comprehensive resource for protein interaction networks - STRING is a database of interactions between proteins - essentially, it is a platform for system-level exploration of cellular machineries. Experimental interaction evidence from a diverse collection of repositories is integrated at a single location for convenient web-based access. Importantly, STRING also includes a large set of predicted interactions extending into the uncharted areas of protein interaction networks, helping to delineate complex systems and to find novel drug targets. The predictions are based on the results of several algorithms that are integrated using a validated scoring scheme. Each predicted interaction is assigned an approximate confidence level. The database covers nearly 2.5 million proteins, many of which can be assigned a putative function even where homology-based analysis fails. STRING includes a web server front-end for intuitive browsing and evidence inspection. STRING is continuously updated and provides the most complete view on protein-protein interactions available. Minimum hardware requirements: Any platform capable of running Linux (x86, PowerPC, Alpha, ...) CPU P4 1GHz 2GB of RAM 250GB free disk space 10Mb ethernet between web server and database

If you want to obtain more information please contact us at info@embl-em.de
Academic users can obtain an academic license by following this link.

Medusa

Medusa is a Java application for visualizing and manipulating graphs of interaction, such as data from the STRING protein interaction database, giving STRING users greater freedom in manipulating STRING data. » DetailsMedusa is a Java application for visualizing and manipulating graphs of interaction, such as data from the STRING protein interaction database, giving STRING users greater freedom in manipulating STRING data. It is also a general graph visualization tool. As a general tool, Medusa is easy to use and flexible. Users can load their own data or interactively add or delete nodes and edges.

If you want to obtain more information please contact us at info@embl-em.de

Gene2disease

Gene2disease is a database of candidate genes for mapped inherited human diseases. Candidate priorities are automatically established by a data mining algorithm that extracts putative genes in the chromosomal region where the disease is mapped, and evaluates their possible relation to the disease based on the phenotype of the disorder. » DetailsGene2disease is a database of candidate genes for mapped inherited human diseases. Candidate priorities are automatically established by a data mining algorithm that extracts putative genes in the chromosomal region where the disease is mapped, and evaluates their possible relation to the disease based on the phenotype of the disorder. The Genes2Diseases server currently presents candidate genes for more than 450 genetically inherited diseases that have been mapped onto chromosomal regions without assignment of a particular gene. Furthermore, users can access two independent benchmarks of the system with known disease-associated genes. The results show that they can be found among the 8 best-scoring genes with a 25% chance, and among the best 30 with a 50% chance, indicating that there is a relationship between the score of a gene and its likelihood of being associated to a particular disease.

If you want to obtain more information please contact us at info@embl-em.de

SNPeffect

SNPeffect is a database of human non-synonymous coding SNPs (nsSNPs) mapping phenotypic effects of allelic variation in human genes. » DetailsSNPeffect is a database of human non-synonymous coding SNPs (nsSNPs) mapping phenotypic effects of allelic variation in human genes. SNPeffect contains 31 659 nsSNPs from 12 480 human proteins. The current release of SNPeffect incorporates data on protein stability, integrity of functional sites, protein phosphorylation and glycosylation, subcellular localization, protein turnover rates, protein aggregation, amyloidosis and chaperone interaction. The SNPeffect software allows to analyse the effect of coding, non-synonymous SNPs on 3 categories of functional and physico-chemical properties of the affected proteins. SNPeffect uses computational tools to predict the effect caused by the mutations on the physico-chemical and biological properties of the affected proteins. It tries to pinpoint the exact effect of a mutation to a specific structural, physico-chemical or biological property.

If you want to obtain more information please contact us at info@embl-em.de