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Showing 20 records out of 363 total
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Categories: genomics, (characterisation/annotation) - Software type(s): website - tool
SSA is a software package for the analysis of nucleic acid sequence motifs that are positionally correlated with a functional site such as a transcription initiation site. The programs provided by this web server are the following: generation of a constraint profile (Cpr); generation of a signal list (SList); generation of a signal occurrence profile (OProf); pattern optimization tool (PatOp); find motifs around functional sites (FindM), and extract sequences around functional sites (FromFPS).
Categories: proteomics, (protein structure) - Software type(s): website - tool
Java-based software for structural alignments of proteins
keywords: sequence alignment
Categories: proteomics, (protein interactions) - Software type(s): website - database
STRING is a database of known and predicted protein-protein interactions. The database contains information from numerous sources, including experimental repositories, computational prediction methods and public text collections. STRING is regularly updated and gives a comprehensive view on protein-protein interactions currently available.
keywords: network
Categories: proteomics, (protein modifications), glycomics - Software type(s): website - database
SugarBind covers knowledge of glycan binding of human pathogen lectins and adhesins. Information is collected by experts from articles published in peer-reviewed scientific journals. The data were compiled through an exhaustive search of literature published over the past 30 years by glycobiologists, microbiologists, and medical histologists.
Categories: proteomics, glycomics - Software type(s): website - tool
SugarSketcher was designed to provide users with a simple and efficient interface for drawing glycan molecules with the logos defined in the Symbol Nomenclature for Glycans (SNFG) . The tool operates in a quick mode in which the top menu shows a limited set of logos or in a normal mode in which the top menu is comprehensive. In either cases, a structure can be drawn from scratch or from a core structure. Structures are exportable as .svg images or in the GlycoCT format.
Categories: proteomics, (protein modifications) - Software type(s): website - tool
The Sulfinator is a software tool able to predict tyrosine sulfation sites in protein sequences. It employs four different Hidden Markov Models that were built to recognise sulfated tyrosine residues located N-terminally, within sequence windows of more than 25 amino acids and C-terminally, as well as sulfated tyrosines clustered within 25 amino acid windows, respectively. All four HMMs contain the distilled information from one multiple sequence alignment.
Categories: proteomics - Software type(s): website - tool
SulfoSite is to computationally predict sulfation sites within given protein sequences. A representative set of 162 protein tyrosine sulfation sites from the Swiss-Port were used to analyze characteristics and to train and test in SulfoSite. Support Vector Machine (SVM) is applied for learning to each group of sequences and accessible surface area (ASA) value surrounding to the sulfation residues.
Categories: proteomics, (protein modifications) - Software type(s): website - tool
The SUMOplot??? Analysis Program predicts and scores sumoylation sites in your protein. The presence of this post-translational modification may help explain larger MWs than expected on SDS gels due to attachment of SUMO protein (11kDa) at multiple positions in your protein.
Categories: proteomics, (protein modifications) - Software type(s): website - tool
Protein sumoylation plays important roles in a variety of biological processes, such as transcriptional regulation, signaling transduction, cell cycle progression and differentiation. SUMOsp predicts sumoylation sites in proteins.
Categories: proteomics, (sequence sites, features and motifs) - Software type(s): website - tool
Use the SUPERFAMILY database of structural and functional annotation to provide structural (and hence implied functional) assignments to protein sequences primarily at the SCOP superfamily level. A superfamily contains all proteins for which there is structural evidence of a common evolutionary ancestor. This service offers sophisticated and expertly chosen remote homology detection.
Categories: sequence sites, features and motifs - Software type(s): website - tool
Assign SCOP domains to your sequences using the SUPERFAMILY hidden Markov models
Categories: evolutionary biology - Software type(s): GUI - tool
SuperTree is a software to assemble phylogenetic trees into a more comprehensive one, called supertree, using specific algorithms
Categories: proteomics, IT infrastructure - Software type(s): website, CLI - tool
SUSHI (Support Users for SHell script Integration) is a pipeline framework developed in Ruby on Rails in order to share useful pipeline scripts. SUSHI provides both web-based front end and command line interface.
Categories: proteomics, (protein modifications), glycomics - Software type(s): website - tool
Swiss Mass Abacus is a calculator of peptide and glycopeptide masses. It is purposefully kept as simple as a basic calculator executing arithmetic operations.
Categories: proteomics, (proteomics experiment) - Software type(s): website - database
The SWISS-2DPAGE database assembles data on proteins identified on various 2-D PAGE and SDS-PAGE maps. Each SWISS-2DPAGE entry contains textual data on one protein, including mapping procedures, physiological and pathological information, experimental data and bibliographical references. In addition several 2-D PAGE and SDS-PAGE images are provided, showing the experimentally determined location of the protein, as well as a theoretical region where the protein might be found in the gel.
Categories: proteomics, (protein structure), structure analysis, biophysics - Software type(s): website - database
SWISS-MODEL Repository is a database of protein structure homology models generated by the fully automated SWISS-MODEL modeling pipeline.
Categories: proteomics, (protein structure), structure analysis, biophysics - Software type(s): website - tool
SWISS-MODEL is a fully automated web based protein structure homology-modeling expert system. The SWISS-MODEL Workspace is a web-based integrated service which assist and guides the user in building protein homology models at different levels of complexity. A personal working environment (workspace), where several modelling projects can be carried out in parallel, is provided for each user.
Categories: proteomics, (protein structure), structure analysis - Software type(s): website - tool
Swiss-PdbViewer (aka DeepView) is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.
Categories: proteomics, medicinal chemistry - Software type(s): website - tool
SwissADME gives free access to a number of parameters and predictive models in order to compute the physicochemistry and estimate the pharmacokinetics, druglikeness and medicinal chemistry friendliness of one or several small molecules.
Categories: proteomics, structure analysis, medicinal chemistry - Software type(s): website - database
SwissBioisostere is a database containing information on millions of molecular replacements and their performance in biochemical assays. It is meant to provide researchers in drug discovery projects with ideas for bioisosteric modifications of their current lead molecule, and to give access to the details on particular molecular replacements.
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