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Showing 20 records out of 363 total
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Categories: proteomics, (protein structure), structure analysis, medicinal chemistry - Software type(s): website - tool
SwissDock is a protein ligand docking server, accessible via the ExPASy web server, and based on EADock DSS. The purpose of this server is to make protein-ligand docking accessible to a wide scientific community worldwide.
Categories: proteomics, (function analysis), systems biology - Software type(s): website - database
SwissLipids is a comprehensive reference database that links mass spectrometry-based lipid identifications to curated knowledge of lipid structures, metabolic reactions, enzymes and interacting proteins. It features approximately 500,000 lipid structures from more than 115 lipid classes and over 3,000 enzymatic reactions and 800 proteins.
Categories: proteomics, (protein modifications) - Software type(s): website - database
SwissPalm is an open, comprehensive and manually curated resource to study protein S-palmitoylation. It provides curated information and filters that increase the confidence in true positive hits, and integrates predictions of S-palmitoylated cysteine scores, orthologs and isoform multiple alignments.
Categories: proteomics, (protein structure), structure analysis, biophysics, medicinal chemistry - Software type(s): website - tool
SwissParam is a fully automatic server that provides topology and parameters for small organic molecules, compatible with the CHARMM all atoms force field, for use with CHARMM and GROMACS.
Categories: genomics, (characterisation/annotation), systems biology, transcriptomics - Software type(s): website - database
SwissRegulon is a database of genome-wide annotations of regulatory sites. It contains annotations for 17 prokaryotes and 3 eukaryotes. The database frontend offers an intuitive interface showing genomic information in a clear and comprehensible graphical form.
Categories: proteomics, (protein structure), structure analysis, biophysics, medicinal chemistry - Software type(s): website - database
SwissSidechain is a structural and molecular mechanics database of hundreds of non-natural amino-acid sidechains that can be used to study in silico their insertion into natural peptides or proteins.
Categories: proteomics, medicinal chemistry - Software type(s): website - tool
SwissSimilarity allows the rapid screening of small to very large-scale libraries of drugs, bioactive small molecules, commercially available compounds, and an ultra-large library of virtual compounds readily synthesizable from commercially available reagents. The virtual screening can be performed using molecular fingerprints, as well as superpositional or fast non-superpositional 3D shape similarity approaches.
Categories: proteomics, structure analysis, medicinal chemistry - Software type(s): website - tool
SwissTargetPrediction is an online tool to predict the targets of bioactive small molecules in human and other vertebrates. This is useful to understand the molecular mechanisms underlying a given phenotype or bioactivity, to rationalize possible side-effects or to predict off-targets of known molecules.
Categories: proteomics, genomics, (sequence alignment), evolutionary biology - Software type(s): website - database/tool
The SwissTree project aims to provide a collection of 100 Gold Standard gene phylogenies to the scientific community. This set of reference gene trees is suitable for phylogenomic databases to assess their current quality status, measure changes following new database releases and diagnose improvements subsequent to an upgrade of the analysis procedure. SwissTree is used for benchmarking at the Orthology Benchmarking web service.
Categories: proteomics, (protein sequences and identification) - Software type(s): website - database
SwissVar is a portal to search variants (polymorphism) in UniProt Knowledgebase (UniProtKB) entries, and gives direct access to manual annotation on the genotype-phenotype relationship of each specific variant based on literature, as well as pre-computed information (such as conservation scores and a list of structural features when available) to help assess the effect of the variant.
Categories: proteomics, (protein interactions) - Software type(s): website - tool
This is a tool to find out the ligation strength to a defined HLA type for a sequence of aminoacids. The algorithmus used are based on the book "MHC Ligands and Peptide Motifs" by H.G.Rammensee, J.Bachmann and S.Stevanovic. The probability of being processed and presented is given in order to predict T-cell epitopes.
Categories: proteomics, (similarity search/alignment), genomics, (sequence alignment) - Software type(s): website, CLI - tool
A collection of tools for computing, evaluating and manipulating multiple alignments of DNA, RNA, protein sequences and structures. Includes M-Coffee, R-Coffee, Expresso, PSI-Coffee, iRMSD-APDB.
Categories: similarity search/alignment, sequence alignment - Software type(s): website - tool
T-Coffee is a multiple sequence alignment program. Its main characteristic is that it will allow you to combine results obtained with several alignment methods.
Categories: similarity search/alignment, sequence alignment - Software type(s): website - tool
T-Coffee is a multiple sequence alignment program. Its main characteristic is that it will allow you to combine results obtained with several alignment methods.
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
T-REKS is an algorithm for de novo detection and alignment of repeats in sequences based on K-means algorithm. Minimal length of repeat arrays is 9 for true homorepeats and 14 for other repeats with potential biological meaning.
Categories: proteomics, (protein sequences and identification) - Software type(s): website - tool
Identify proteins with isoelectric point (pI), molecular weight (Mw) and sequence tag, or generate a list of proteins close to a given pI and Mw.
Categories: genomics - Software type(s): website, CLI - tool
TagScan allows searching for exact or near-exact matches between oligonucleotide queries of up to 60 bases and sequence databases comprising entire genomes or mRNA reference sequences. The smallest query allowed is 10 nucleotides long.
Categories: proteomics, (function analysis, protein modifications) - Software type(s): website - tool
TargetP 1.1 predicts the subcellular location of eukaryotic proteins. The location assignment is based on the predicted presence of any of the N-terminal presequences: chloroplast transit peptide (cTP), mitochondrial targeting peptide (mTP) or secretory pathway signal peptide (SP).
Categories: proteomics, (protein modifications) - Software type(s): website - tool
TatP 1.0 server predicts the presence and location of Twin-arginine signal peptide cleavage sites in bacteria. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of two artificial neural networks. A postfiltering of the output based on regular expressions is possible.
Categories: proteomics, (protein interactions), systems biology - Software type(s): website - database
Database show prediction of interaction specificity in two-component systems. These predictions were made with new Bayesian network method that predicts interaction partners using only multiple alignments of amino-acid sequences of interacting protein domains.
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