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Showing 19 records out of 359 total
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Categories: proteomics, (protein sequences and identification, function analysis, protein modifications, protein interactions) - Software type(s): website - database
UniProtKB/Swiss-Prot is the manually annotated component of UniProtKB (produced by the UniProt consortium). It contains manually-annotated (reviewed) records with information extracted from the literature and curator-evaluated computational analysis.
Categories: proteomics, (protein sequences and identification) - Software type(s): website, databases files - database
The UniRef databases provide clustered sets of sequences from UniProt Knowledgebase (including splice variants and isoforms) and selected UniParc records, in order to obtain complete coverage of sequence space at several resolutions while hiding redundant sequences (but not their descriptions) from view.
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Categories: proteomics, (protein sequences and identification) - Software type(s): website - database
VenomZone is a free web resource that provides information on venoms from six animal taxa (snakes, scorpions, spiders, cone snails, sea anemones and insects), as well as on their targets. Information can be browsed through pages on taxonomy, activity and venom protein families and all these pages link to related venom/toxin protein information from the manually curated UniProtKB/Swiss-Prot database.
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Categories: proteomics, (protein sequences and identification) - Software type(s): website - database
ViralZone is a web resource for all viral genus and families, providing general molecular and epidemiological informations, along with virion and genome figures. Each virus or family page gives an easy access to UniProtKB/Swiss-Prot viral protein entries.
keywords: pathogen
Categories: proteomics, IT infrastructure - Software type(s): website, CLI - tool
Vital-IT is an innovative life science informatics initiative providing computational resources, consultancy and training to connect fundamental and applied research.
Categories: proteomics, (protein structure), imaging - Software type(s): GUI - tool
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code.
Categories: proteomics, (sequence sites, features and motifs, similarity search/alignment), genomics, (sequence alignment) - Software type(s): website - tool
Sequence logos are a graphical representation of an amino acid or nucleic acid multiple sequence alignment. Each logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each amino or nucleic acid at that position.
Categories: proteomics, (protein structure) - Software type(s): website - tool
WHAT IF is a versatile molecular modelling package that is specialized on working with proteins and the molecules in their environment like water, ligands, nucleic acids, etc.
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Categories: proteomics, genomics - Software type(s): website - tool
The Wise2 form compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors.
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Categories: proteomics, (proteomics experiment) - Software type(s): website - database
Entry point to the World2D-PAGE Repository, the World-2DPAGE Portal (a dynamic portal to simultaneously query world-wide gel-based proteomics databases), Swiss-2DPAGE, Make2D-DB II, MiapeGelDB, Melanie Viewer, 2D-PAGE Submission Process and the 2D-PAGE list of resources.
Categories: proteomics, (proteomics experiment) - Software type(s): website - database
World-2DPAGE is a public repository, standards compliant, for gel-based proteomics data published in the literature
Categories: proteomics, (similarity search/alignment), genomics, (similarity search) - Software type(s): website - tool
Protein databases query to find regions of sequence similarity quickly, with minimum loss of sensitivity.
keywords: sequence alignment
Categories: proteomics, (proteomics experiment) - Software type(s): website - tool
Computes all possible crosslinks based on proteins of interest (max. 30 proteins) for further interrogation using standard search engine (e.g. Phenyx, Mascot, Sequest, OMSSA, X!Tandem)
Categories: proteomics - Software type(s): website - tool
The XplorMed server allows you to explore a set of abstracts derived from a MEDLINE search. The system gives you the main associations between the words in groups of abstracts. Then, you can select a subset of your abstracts based on selected groups of related words and iterate your analysis on them.
Categories: proteomics, (proteomics experiment) - Software type(s): website - tool
xQuest is a search engine for cross-linked peptides from complex samples. xQuest works with small and large protein databases and features flexible fragment ion assignment, advanced scoring, and interactive evaluation tools.
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
XSTREAM is a rapid and powerful algorithm for identifying perfect and degenerate tandem repeat motifs in protein (and nucleotide) sequence data. XSTREAM also effectively models the architecture of repetitive domains in tandem repeat proteins and eliminates motif redundancy to identify "fundamental" tandem repeat patterns.
Categories: proteomics, (protein structure) - Software type(s): GUI - tool
YASARA is a molecular-graphics, -modeling and -simulation program for Windows, Linux and Mac OS X
Categories: proteomics, (protein modifications), glycomics - Software type(s): website - tool
The YinOYang WWW server produces neural network predictions for O-beta-GlcNAc attachment sites in eukaryotic protein sequences. This server can also use NetPhos, to mark possible phosphorylated sites and hence identify "Yin-Yang" sites.
Categories: genomics - Software type(s): website - tool
ZFN-Site is intended to search genomes for specific target sites and off-target sites, such as for pairs of zinc finger proteins (ZFPs), zinc finger nucleases (ZFNs) and modified homing endonucleases. This can either define a zinc finger nucleases (hetero-dimer) or allow for homo-dimers depending on the status of the checkbox in the input form.
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