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Showing 20 records out of 375 total
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Categories: sequence sites, features and motifs - Software type(s): website - tool
Assign SCOP domains to your sequences using the SUPERFAMILY hidden Markov models
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: 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, 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.
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.
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