UniProtKB  •  The UniProt Knowledgebase (UniProtKB) is produced by the UniProt consortium composed of EBI (Rolf Apweiler), PIR (Cathy Wu) and SIB (Swiss-Prot group, Ioannis Xenarios). It is the central hub for the collection of functional information on proteins with accurate, consistent and rich annotation. It consists of: UniProtKB/Swiss-Prot (manually-annotated records and curator-evaluated computational analysis) and UniProtKB/TrEMBL (computationally analyzed records awaiting manual annotation). [less]

UniProtKB/Swiss-Prot  •  UniProtKB/Swiss-Prot is the manually annotated component of UniProtKB. It contains manually-annotated (reviewed) records with information extracted from the literature and curator-evaluated computational analysis. [less]

STRING  •  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. [less]

SWISS-MODEL Repository  •  SWISS-MODEL Repository is a database of protein structure homology models generated by the fully automated SWISS-MODEL modeling pipeline. [less]

PROSITE  •  PROSITE consists of documentation entries describing protein domains, families and functional sites as well as associated patterns and profiles to identify them. [less]

ViralZone  •  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. [less]

neXtProt  •  neXtProt is an innovative knowledge platform dedicated to human proteins. This resource contains a wealth of high-quality data on all the human proteins that are produced by the 20'000 protein-coding genes found in the human genome. The content of neXtProt is continuously extended so as to provide many more carefully selected data sets and analysis tools. [less]

ENZYME  •  ENZYME is a repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided. [less]

GlycoSuiteDB  •  GlycoSuiteDB is a curated and annotated glycan database [less]

GPSDB  •  GPSDB (Gene and Protein Synonym DataBase) collects gene/protein names, in a species specific way, from several biological resources. A web-based search interface gives access to the database: given a gene/protein name, it retrieves all synonyms for this entity and queries Medline with a set of user-selected terms. [less]

HAMAP  •  HAMAP is a system, based on manual protein annotation, that identifies and semi-automatically annotates proteins that are part of well-conserved families or subfamilies: the HAMAP families. HAMAP is based on manually created family rules and is applied to bacterial, archaeal and plastid-encoded proteins. [less]

MIAPEGelDB  •  MIAPEGelDB helps end-users to write MIAPE documents (minimum information to report when describing or publishing a proteomics experiment), through a self-documenting web interface. The produced documents are stored in a database, and thus remain easily accessible by anybody through a stable URL unique for each document. [less]

MyHits  •  Hits is a free database devoted to protein domains. It is also a collection of tools for the investigation of the relationships between protein sequences and motifs described on them. These motifs are defined by an heterogeneous collection of predictors, which currently includes regular expressions, generalized profiles and hidden Markov models. [less]

PANDITplus  •  Along with sequence data for Pfam gene families and protein domains, PANDITplus provides access to data on protein interactions, functional and chemical pathway annotation, gene expression, and association with disease, and pre-computed estimates from evolutionary codon models. [less]

PaxDb  •  PaxDb contains estimated abundance values for a large number of proteins in several different species (12 in version 2.0). Furthermore, it contains information about inter-species variation of protein abundances.  [less]

Prolune  •  Publication ??lectronique (en fran??ais) de vulgarisation scientifique du groupe Swiss-Prot de l'Institut Suisse de Bioinformatique d??di??e aux prot??ines qui font parler d'elles dans l'actualit??. [less]

Protein Model Portal  •  The Protein Model Portal has been developed to foster effective usage of molecular models in biomedical research by providing convenient and comprehensive access to structural information for a protein - both experimental structures and theoretical models. Protein Model Portal is a component of the Nature PSI Structural Biology Knowledgebase. [less]

Protein Spotlight  •  Protein Spotlight is a monthly review written by the Swiss-Prot team of the Swiss Institute of Bioinformatics. Spotlight articles describe a specific protein or family of proteins on an informal tone. [less]

SugarBind  •  This database provides a list of known carbohydrate sequences to which pathogenic organisms specifically adhere. The data were compiled through an exhaustive search of literature published over the past 30 years by glycobiologists, microbiologists, and medical histologists.  [less]

SWISS-2DPAGE  •  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. [less]

SwissVar  •  SwissVar is a portal to search variants 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. [less]

TCS  •  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. [less]

UniPathway  •  UniPathway is a curated resource of metabolic pathways for the UniProtKB/Swiss-Prot knowledgebase. [less]

World-2DPAGE Constellation  •  Entry point to the World-2DPAGE Constellation, formed by the World2D-PAGE Repository, the World-2DPAGE Portal, Swiss-2DPAGE, Make2D-DB II, MiapeGelDB, Melanie Viewer, 2D-PAGE Submission Process and the 2D-PAGE list of resources.  [less]

World-2DPAGE Portal  •  Dynamic portal to query simultaneously world-wide gel-based proteomics databases. [less]

World-2DPAGE Repository  •  World-2DPAGE is a public repository, standards compliant, for gel-based proteomics data published in the literature [less]

SWISS-MODEL Workspace  •  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. [less]

SwissDock  •  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. [less]

AACompSim  •  Compare amino acid composition of a UniProtKB entry with some or all other UniProtKB entries. Several constellations are available, corresponding to various amino acid analysis techniques. [less]

AllAll  •  The AllAll server takes as input a set of protein sequences and returns various comparisons and visualizations- a distance-based phylogenetic tree, a split tree, some variation indices, some visualizations, the pairwise sequence distances and the most probable ancestral sequence. [less]

Biochemical Pathways  •  Digitized version of the Roche Applied Science "Biochemical Pathways" wall chart. The map, linked to relevant ENZYME database entries, can be browsed online, and keyword searches are available. [less]

BLAST  •  BLAST sequence similarity search (blastp or tblastn) against UniProtKB or taxonomic subdivisions, complete proteomes, UniRef, PDB, EMBL, ESTs [less]

boxshade  •  Boxshade is a program for creating good looking printouts from multiple-aligned protein or DNA sequences.  [less]

Compute pI/MW  •  Compute the theoretical pI (isoelectric point) and Mw (molecular weight) for a list of UniProt Knowledgebase (Swiss-Prot or TrEMBL) entries or for user entered sequences [less]

Decrease redundancy  •  Redundancy reduction in a set of aligned or unaligned sequences [less]

Dotlet  •  Diagonal plots to graphically compare of biological sequences and identify regions of close similarity [less]

EMBnet services  •  Set of bioinformatics tools and databases [less]

FindMod  •  Predict potential protein post-translational modifications (PTM) and find potential single amino acid substitutions in peptides. The experimentally measured peptide masses are compared with the theoretical peptides calculated from a specified Swiss-Prot/TrEMBL entry or from a user-entered sequence, and mass differences are used to better characterise the protein of interest. [less]

FindPept  •  Identify peptides that result from unspecific cleavage of proteins from their experimental masses, taking into account artefactual chemical modifications, post-translational modifications (PTM) and protease autolytic cleavage. [less]

GlycanMass  •  Calculate the mass of an oligosaccharide structure. [less]

GlycoMod  •  Predict possible oligosaccharide structures that occur on proteins from their experimentally determined masses. The program can be used for free or derivatized oligosaccharides and for glycopeptides. [less]

HAMAP  •  HAMAP is a system, based on manual protein annotation, that identifies and semi-automatically annotates proteins that are part of well-conserved families or subfamilies: the HAMAP families. HAMAP is based on manually created family rules and is applied to bacterial, archaeal and plastid-encoded proteins. [less]

HamapScan  •  Scan several sequences or a whole genome (all ORFs) against the HAMAP families, with partial or complete annotation in UniProtKB/Swiss-Prot format. [less]

HCD/CID spectra merger  •  A tool to merge the peptide sequence-ion m/z range from CID spectra and the reporter-ion m/z range from HCD spectra into the appropriate single file, to be further used in identification and quantification search engines [less]

ImageMaster / Melanie  •  Melanie offers a unique and flexible interface for the comprehensive visualization, exploration and analysis of 2D gel data. It provides powerful and innovative solutions to shorten the path from data acquisition to protein information, both for conventional 2-DE and DIGE (Fluorescence Difference Gel Electrophoresis) gels. [less]

IsotopIdent  •  Isotopident can estimate the theoretical isotopic distribution of a peptide or protein, a polynucleotide and a chemical compound from its composition (sequence of amino acids expressed in either 1-letter code, sequence of amino acids expressed in 3-letter code, sequence of nucleotides or its chemical formula). Isotopident can also compute its monoisotopic mass. and predict the most likely isotope combination and the exact mass of the given input.  [less]

Make2D-DB II  •  Make2D-DB II is an environment to create, convert, publish, interconnect and keep up-to-date 2D-PAGE databases. The tool offers the possibility to automatically update data related to numerous external data resources. It is also possible to dynamically interconnect several remote databases or projects to form a virtual global database accessible from one single entry point. This tool can also be used to build up 2D-PAGE repositories, accessible by any one from the Web. [less]

MALDIPepQuant  •  A tool to quantify MALDI peptides (SILAC) from Phenyx output [less]

MARCOIL  •  predicting coiled-coils in protein sequences [less]

MassSearch  •  The MassSearch server takes as input a set of weights determined from a mass spectrometry experiment and uses them to search for the best matching protein in various databases. [less]

MSight  •  MSight: An image analysis software for liquid chromatography-mass spectrometry. MSight is a tool specifically developed for the representation of mass spectra along with data from a separation step. It provides simple ways to navigate through very large volumes of data, with the ability to display small regions for closer scrutiny.  [less]

MyDomains  •  Image Creator for linear (multi) domain views [less]

MyHits  •  Hits is a free database devoted to protein domains. It is also a collection of tools for the investigation of the relationships between protein sequences and motifs described on them. These motifs are defined by an heterogeneous collection of predictors, which currently includes regular expressions, generalized profiles and hidden Markov models. [less]

Myristoylator  •  Predict N-terminal myristoylation of proteins by neural networks. Myristoylator uses ensembles of neural networks, in order to learn to discriminate positive and negative sequences for N-myristoylation. [less]

OpenStructure  •  The OpenStructure library project aims to provide an open-source, modular, flexible, molecular modelling and visualization environment. It is targeted at interested users and method developers in the field of structural bioinformatics. Its cleanly designed API available in both Python an C++ provides a command line interface for batch processing as well as a graphical user interface fully scriptable in Python. [less]

PepPepSearch  •  PepPepSearch takes as input a sequence and searches this sequence against a variety of databases and returns the highest scoring matches. [less]

PeptideCutter  •  Predict potential cleavage sites cleaved by proteases or chemicals in a given protein sequence. PeptideCutter returns the query sequence with the possible cleavage sites mapped on it and/or a table of cleavage site positions. [less]

PeptideMass  •  Cleave a protein sequence with a chosen enzyme, and computes the masses of the generated peptides. The tool also returns theoretical isoelectric point and mass values for the protein of interest. If desired, PeptideMass can return the mass of peptides known to carry post-translational modifications, and can highlight peptides whose masses may be affected by database conflicts, polymorphisms or splice variants. [less]

pIcarver  •  A tool to visualize theoretical distributions of peptide pI on a given pH range and generate fractions with similar peptide frequencies [less]

PRATT  •  Tool to discover patterns that are conserved in a set of protein sequences. The patterns are reported using the PROSITE syntax. [less]

pROC  •  A package (R, S+) to visualize, smooth and compare receiver operating characteristic (ROC curves) [less]

Protein Model Portal  •  The Protein Model Portal has been developed to foster effective usage of molecular models in biomedical research by providing convenient and comprehensive access to structural information for a protein - both experimental structures and theoretical models. Protein Model Portal is a component of the Nature PSI Structural Biology Knowledgebase. [less]

ProtParam  •  Compute various physical and chemical parameters for a given protein sequence. The computed parameters include the molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (GRAVY). [less]

ProtScale  •  Compute and represent the profile produced by any amino acid scale on a selected protein sequence. The most frequently used scales are the hydrophobicity or hydrophilicity scales and the secondary structure conformational parameters scales, but ProtScale provides more than 50 predefined scales entered from the literature. [less]

QMEAN  •  Estimating the quality of predicted structural models is a crucial step in homology modeling. Scoring functions analyze different structural features of the protein models in order to generate a quality estimate. QMEAN consists of four statistical potential terms (two non-bonded interaction terms, a torsion angle term and a solvation term) and two components describing the agreement between predicted and observed secondary structure and solvent accessibility. [less]

QuickMod  •  QuickMod is a spectral library search based MSMS data analysis tool, designed to identify modified peptides. The QuickMod algorithm assumes that the precursor mass difference between a query spectrum and a candidate library spectrum can be explained by a modification. Based on this assumption the two spectra are aligned and the fit of the spectral alignment is assigned a similarity score. In a second step the most likely attachment position of the modification is determined.  [less]

RandSeq  •  Random protein sequence generator [less]

RAxML  •  RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It has originally been derived from fastDNAml which in turn was derived from Joe Felsentein's dnaml which is part of the PHYLIP package. [less]

ScanProsite  •  Scan protein sequence(s) against PROSITE, or search for hits by specific motif(s) in protein sequence database(s). ScanProsite may be used alternatively in quick scan mode or advanced scan mode.  [less]

Sequence Similarity Maps (SSM)  •  A data mining solution to map thousands of viral isolates [less]

Sulfinator  •  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. [less]

Swiss-PdbViewer  •  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. [less]

SwissParam  •  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. [less]

T-Coffee  •  A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures [less]

TagIdent  •  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. [less]

TMPred  •  The TMpred program makes a prediction of membrane-spanning regions and their orientation. The algorithm is based on the statistical analysis of TMbase, a database of naturally occurring transmembrane proteins [less]

Translate  •  Translation of a nucleotide (DNA/RNA) sequence to a protein sequence. [less]