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Databases

  • UniProtKB  •  The UniProt Knowledgebase (UniProtKB) 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]
  • EMBnet services  •  Set of bioinformatics tools, databases and courses [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]
  • 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 for the classification and annotation of protein sequences. It consists of a collection of manually curated family profiles for protein classification, and associated, manually created annotation rules that specify annotations that apply to family members. HAMAP is applied to bacterial, archaeal and eukaryotic proteins and used to annotate records in UniProtKB via UniProt's automatic annotation pipeline. [less]
  • MetaNetX  •  MetaNetX.org allows to access, analyse and manipulate genome-scale metabolic networks as well as biochemical pathways. It consistently integrates data from various public resources and makes the data accessible in a standardized format using a common namespace. Models can be interactively compared, analysed (e.g. detection of dead-end metabolites/reactions, flux balance analysis or simulation of reaction/gene knockouts), manipulated and exported. Users can upload their own metabolic models. [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. Furthermore, it contains information about inter-species variation of protein abundances.  [less]
  • Prolune  •  Publication électronique (en français) de vulgarisation scientifique du groupe Swiss-Prot de l'Institut Suisse de Bioinformatique dédiée aux protéines qui font parler d'elles dans l'actualité. [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 via lectins or adhesins. 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]
  • SwissBioIsostere  •  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. [less]
  • SwissSidechain  •  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.  [less]
  • SwissVar  •  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. [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]
  • UniCarbKB  •  UniCarbKB is a curated and annotated glycan database which curates information from the scientific literature on glycoprotein derived glycan structures. It includes data previously available from GlycoSuiteDB. [less]
  • UniMES (UniProt metagenomic samples)  •  The UniProt Metagenomic and Environmental Sequences (UniMES) database is a repository specifically developed for metagenomic and environmental data. Currently, unimes.fasta.gz contains only data from the Global Ocean Sampling Expedition (GOS). Clustered sets (unimes_cluster100 and unimes_cluster90) of UniMEs sequences at two resolutions (100% and >90%) are also available. [less]
  • UniParc (UniProt sequence archive)  •  UniParc is a comprehensive and non-redundant database provided by the UniProt Consortium that contains most of the publicly available protein sequences. Proteins may exist in different source databases and in multiple copies in the same database. UniParc avoids such redundancy by storing each unique sequence only once and giving it a stable and unique identifier allowing to identify the same protein from different source databases. UniParc contains only protein sequences.  [less]
  • UniPathway  •  UniPathway is a curated resource of metabolic pathways for the UniProtKB/Swiss-Prot knowledgebase. [less]
  • UniRef (UniProt sequence clusters)  •  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. [less]
  • World-2DPAGE Constellation  •  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.  [less]
  • World-2DPAGE Repository  •  World-2DPAGE is a public repository, standards compliant, for gel-based proteomics data published in the literature [less]

Tools

  • 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]
  • 2ZIP  •  The leucine zipper is a dimerisation domain occurring mostly in regulatory and thus in many oncogenic proteins. 2ZIP combines a standard coiled coil prediction algorithm with an approximate search for the characteristic leucine repeat. No further information from homologues is required for prediction. This approach improves significantly over existing methods, especially in that the coiled coil prediction turns out to be highly informative and avoids large numbers of false positives [less]
  • 3of5  •  The 3of5 application aims at the analysis of protein sequences to find user-defined patterns, described via complex regular expressions-like terms, e.g. to search for a motif with 3 basic AAs in 5 positions.  [less]
  • AACompIdent  •  Protein identification by amino acid composition, and optionally pI, Mw, species, UniProtKB keyword and calibration protein. Several constellations are available, corresponding to various amino acid analysis techniques. [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]
  • Agadir  •  Agadir predicts the helical behaviour of monomeric peptides. It only considers short range interactions. Conditions such as pH, temperature and ionic strength are used in the calculation. Modifications of the termini are also allowed. Keep in mind that Agadir is not a program to predict secondary structure of proteins.  [less]
  • ALF  •  ALF simulates a wide range of evolutionary forces that act on genomes, such as character substitutions, indels, gene duplication, gene loss, lateral gene transfer and genome rearrangement. [less]
  • Alignment tools  •  Four tools for multiple alignments. [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]
  • APSSP  •  Advanced Protein Secondary Structure Prediction Server  [less]
  • Ascalaph  •  Ascalaph is a general purpose molecular modeling software that performs quantum mechanics calculations for initial molecular model development, molecular mechanics and dynamics simulations in the gas or in condensed phase. It can interact with external molecular modeling packages (MDynaMix, NWChem, CP2K and PC GAMESS/Firefly). [less]
  • big-PI  •  GPI modification site prediction  [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]
  • BLAST (UniProt)  •  BLAST sequence similarity search against UniProtKB or taxonomic subdivisions, complete proteomes, UniRef, PDB or UniParc - on the UniProt web site. [less]
  • BLAST - NCBI  •  The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.  [less]
  • BLAST - PBIL  •  BLAST search on protein sequence databases [less]
  • Blast2Fasta  •  Converts BLAST output from NCBI to FASTA format. [less]
  • boxshade  •  Boxshade is a program for creating good looking printouts from multiple-aligned protein or DNA sequences.  [less]
  • CFSSP  •  This server predicts secondary structure of protein from the amino acid sequence. In this server, Chou & Fasman algorithm has been implemented. [less]
  • ChloroP  •  The ChloroP server predicts the presence of chloroplast transit peptides (cTP) in protein sequences and the location of potential cTP cleavage sites.  [less]
  • Click2Drug  •  Directory of computational drug design tools, containing many links to databases, chemical structure representation, molecular modeling, homology modeling, binding site prediction, docking, screening, target prediction, ligand design, binding free energy estimation etc. [less]
  • ClustalO (UniProt)  •  Align two or more protein sequences on the UniProt web site using ClustalOmega. [less]
  • ClustalW  •  Multiple alignment of nucleic acid and protein sequences. [less]
  • ClustalW - PBIL  •  ClustalW is a general purpose multiple sequence alignment program for DNA or proteins [less]
  • ClustalW2  •  ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins. [less]
  • Coiled-Coils prediction  •  This program delineates coiled-coil domains in otherwise globular proteins, such as the leucine zipper domains in transcriptional regulators, and to predict regions of discontinuity within coiled-coil structures, such as the hinge region in myosin. [less]
  • COILS  •  COILS is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. By comparing this score to the distribution of scores in globular and coiled-coil proteins, the program then calculates the probability that the sequence will adopt a coiled-coil conformation. [less]
  • ColorSeq  •  Color Protein Sequence. [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]
  • CPHmodels  •  CPHmodels 3.2 is a protein homology modeling server. The template recognition is based on profile-profile alignment guided by secondary structure and exposure predictions [less]
  • CSS-Palm  •  Palmitoylation will enhance the surface hydrophobicity and membrane affinity of protein substrates, and play important roles in modulating proteins' trafficking and stability. After manual collection of the experimentally verified palmitoylation sites from scientific literature, we could get training data containing 439 palmitoylation sites from 194 distinct proteins, used to train the CSS-Palm program. [less]
  • DAS-TMfilter  •  DAS (Dense Alignment Surface) is based on low-stringency dot-plots of the query sequence against a set of library sequences - non-homologous membrane proteins - using a previously derived, special scoring matrix. The method provides a high precision hyrdophobicity profile for the query from which the location of the potential transmembrane segments can be obtained. The novelty of the DAS-TMfilter algorithm is a second prediction cycle to predict TM segments in the sequences of the TM-library. [less]
  • Decrease redundancy  •  Redundancy reduction in a set of aligned or unaligned sequences [less]
  • DIALIGN  •  While standard alignment methods rely on comparing single residues and imposing gap penalties, DIALIGN constructs pairwise and multiple alignments by comparing entire segments of the sequences. No gap penalty is used. This approach can be used for both global and local alignment, but it is particularly successful in situations where sequences share only local homologies. [less]
  • DictyOGlyc  •  Neural network predictions for GlcNAc O-glycosylation sites in Dictyostelium discoideum proteins. [less]
  • DisEMBL  •  Disordered proteins or protein segments lack a folded tertiary structure. They are thought to be intrinsically disordered regions providing essential biological functions. DisEMBL is a tool for prediction of disordered/unstructured regions within a protein sequence. [less]
  • DLP-SVM  •  DLP-SVM is a domain linker predictor. It is composed of three loop-length dependent SVM predictors of domain linkers (SVM-All, SVM-Long and SVM-Short), and SVM-Joint, which combines the results of SVM-Short and SVM-Long into a single consolidated prediction. [less]
  • Dotlet  •  Diagonal plots to graphically compare of biological sequences and identify regions of close similarity [less]
  • EasyProt  •  EasyProt is a platform for mass spectrometry data processing, protein identification, quantification and unexpected PTM characterization. It provides a graphical interface to perform a large part of the proteomic data analysis workflow. Protein identification is based on OLAV scoring schemes and protein quantification is implemented (isobaric labeling and label-free). Features: peak list processing, isotopic correction, spectra filtering, charge-state deconvolution and spectra merging.  [less]
  • ELM  •  Eukaryotic Linear Motif resource for functional sites in proteins  [less]
  • EMBnet services  •  Set of bioinformatics tools, databases and courses [less]
  • EMBOSS translation tools  •  Sequence Translation (Transeq, Sixpack) is used to translate nucleic acid sequence to corresponding peptide sequences. Back-translation (Backtranseq, Backtranambig) is used to predict the possible nucleic acid sequence that a specified peptide sequence has originated from.  [less]
  • epestfind  •  epestfind allows rapid and objective identification of PEST motifs in protein target sequences. Those proteins share high local concentrations of amino acids proline (P), glutamic acid (E), serine (S), threonine (T) and to a lesser extent aspartic acid (D). It seems that PEST motifs reduce the half-lives of proteins dramatically and hence, that they target proteins for proteolytic degradation [less]
  • FASTA/SSEARCH/GGSEARCH/GLSEARCH  •  This tool provides sequence similarity searching against protein databases using the FASTA suite of programs. FASTA provides a heuristic search with a protein query. FASTX and FASTY translate a DNA query. Optimal searches are available with SSEARCH (local), GGSEARCH (global) and GLSEARCH (global query, local database).  [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]
  • FingerPRINTScan  •  The program scans a protein sequence against the PRINTS Protein Fingerprint Database. [less]
  • FUGUE  •  FUGUE is a program for recognizing distant homologues by sequence-structure comparison. It utilizes environment-specific substitution tables and structure-dependent gap penalties, where scores for amino acid matching and insertions/deletions are evaluated depending on the local environment of each amino acid residue in a known structure [less]
  • GENIO/logo  •  Positional dependent information contents of aligned RNA/DNA or amino acid sequences are useful for the display of consensus sequences and for finding optimal search windows used in sequence analysis. The program calculates the positional information content of mono or poly nucleotides/amino acids from a FASTA file of aligned sequences and writes a Postscript (or encapsulated Postscript, EPS) file that can be viewed and included in text processors [less]
  • Geno3D  •  Geno3D is an automatic web server for protein molecular modelling [less]
  • GlobPlot  •  GlobPlot is a web service that allows the user to plot the tendency within the query protein for order/globularity and disorder [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]
  • Glycoviewer  •  Visualisation tool for representing a set of glycan structures as a summary figure of all structural features using icons and colours recommended by the Consortium for Functional Glycomics (CFG).  [less]
  • GOR  •  Protein secondary structure prediction [less]
  • GPI-SOM  •  Identification of GPI-anchor signals by a Kohonen self organizing map [less]
  • GPMAW lite  •  GPMAW lite is a protein bioinformatics tool to perform basic bioinformatics calculations on any protein amino acid sequence, including predicted molecular weight, molar absorbance and extinction coefficient, isoelectric point and hydrophobicity index, as well as amino acid composition and protease digest. [less]
  • GPS  •  Computational prediction of phosphorylation sites with their cognate protein kinases (PKs) is greatly helpful for further experimental design. GPS could predict kinase-specific phosphorylation sites for 408 human PKs in hierarchy. [less]
  • Graphical Codon Usage Analyser  •  Differences in codon usage preference among organisms lead to a variety of problems concerning heterologous gene expression but can be overcome by rational gene design and gene synthesis. The gcua tool displays the codon quality either in codon usage frequency values or relative adaptiveness values [less]
  • HAMAP  •  HAMAP is a system for the classification and annotation of protein sequences. It consists of a collection of manually curated family profiles for protein classification, and associated, manually created annotation rules that specify annotations that apply to family members. HAMAP is applied to bacterial, archaeal and eukaryotic proteins and used to annotate records in UniProtKB via UniProt's automatic annotation pipeline. [less]
  • HAMAP-Scan  •  Scan several protein sequences or a whole genome (all ORFs) against HAMAP family profiles. Sequences that match HAMAP profiles will be annotated in the UniProtKB format by the associated annotation rules.  [less]
  • HCA (hydrophobic cluster analysis)  •  The HCA method is based on the use of a bidimensional plot, called the HCA plot. The bidimensional plot is associated with an alpha helicoidal pitch (3.6 residue/turn, connectivity distance of 4) which has been shown to offer the best correspondence between clusters and regular secondary structures. Examination of the HCA plot of a protein sequence allow to easily identify globular regions from non globular ones and, in globular regions, to identify secondary structures. [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]
  • HeliQuest  •  HeliQuest calculates from the amino acid sequence of a helix (??-helix, 3-10 helix, 3-11 helix or ?? helix) its physicochemical properties and amino acid composition and uses the results to screen any databank in order to identify protein segments possessing similar features.  [less]
  • HHpred  •  Homology detection & structure prediction by HMM-HMM comparison [less]
  • HMMTOP  •  Prediction of transmembranes helices and topology of proteins. [less]
  • HTMSRAP  •  Helical TransMembrane Segment Rotational Angle Prediction [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]
  • InsPecT  •  InsPecT is an MS/MS database search tool, with an emphasis on efficiently and confidently identifying modified peptides. It includes special scoring models for phosphorylation which allow for increased accuracy. In addition, InsPecT implements the MS-Alignment algorithm for discovery of unanticipated modifications in blind mode.  [less]
  • InterProScan  •  InterProScan is a tool that combines different protein signature recognition methods into one resource. The number of signature databases and their associated scanning tools, as well as the further refinement procedures, increases the complexity of the problem. [less]
  • ISMARA  •  MARA models genome-wide expression data in terms of our genome-wide annotations of regulatory sites. For a given expression data-set it infers the key transcription regulators, their sample-dependent activities, and their genome-wide targets. [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]
  • Jmol  •  Jmol is an open-source Java viewer for chemical structures in 3D. [less]
  • Jpred  •  Secondary Structure Prediction Server [less]
  • Kalign - EBI  •  Kalign is a fast and accurate multiple sequence alignment algorithm. [less]
  • Kalign - SBC  •  Kalign is a fast and accurate multiple sequence alignment algorithm.  [less]
  • LALIGN  •  LALIGN, from the FASTA package, finds multiple matching subsegments in two sequences, locally or globally. [less]
  • LipoP  •  The LipoP 1.0 server produces predictions of lipoproteins and discriminates between lipoprotein signal peptides, other signal peptides and N-terminal membrane helices in Gram-negative bacteria, with a good performance on sequences from Gram-positive bacteria also. [less]
  • LiveBench  •  LiveBench provides simple evaluation of the structure prediction servers from the point of view of a potential user. The evaluation of sensitivity and specificity of the available servers can help the user develop sequence analysis strategies and assess the confidence of the obtained predictions. [less]
  • MAFFT - CBRC  •  MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. [less]
  • MAFFT - EBI  •  MAFFT (Multiple Alignment using Fast Fourier Transform) is a high speed multiple sequence alignment program. [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]
  • MakeMultimer.py  •  Macromolecular structure pdb files that represent multimeric molecules often do not contain the coordinates of all multimer subunits. For such files, MakeMultimer.py calculates the coordinates of the missing subunits from the BIOMT transformation matrices contained in the pdb file.  [less]
  • MALDIPepQuant  •  A tool to quantify MALDI peptides (SILAC) from Phenyx output [less]
  • MARCOIL  •  predicting coiled-coils in protein sequences [less]
  • MarvinSpace  •  MarvinSpace is a Java-based software for visualization, modeling and interactive rendering [less]
  • Mascot  •  Mascot is a powerful search engine which uses mass spectrometry data to identify proteins from primary sequence databases. Mascot integrates all of the proven methods of searching: Peptide Mass Fingerprint (the only experimental data are peptide mass values), Sequence Query (peptide mass data are combined with amino acid sequence and composition information), MS/MS Ion Search using uninterpreted MS/MS data from one or more peptides.  [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]
  • MaxAlign  •  The presence of gaps in an alignment of nucleotide or protein sequences is often an inconvenience for bioinformatical studies. MaxAlign maximizes the number of characters that are present in gap-free columns. It can be used prior to any phylogenetic analysis as well as in other situations where this form of alignment clean up is useful, such as the presence of badly aligned or truncated sequences.  [less]
  • Medline Ranker  •  Ranking the biomedical literature according to a selected topic. [less]
  • MeDor  •  Disordered proteins or protein segments lack a folded tertiary structure. They are thought to be intrinsically disordered regions providing essential biological functions. MeDor is a metaserver for predicting protein disorder [less]
  • MetaNetX  •  MetaNetX.org allows to access, analyse and manipulate genome-scale metabolic networks as well as biochemical pathways. It consistently integrates data from various public resources and makes the data accessible in a standardized format using a common namespace. Models can be interactively compared, analysed (e.g. detection of dead-end metabolites/reactions, flux balance analysis or simulation of reaction/gene knockouts), manipulated and exported. Users can upload their own metabolic models. [less]
  • MITOPROT  •  MitoProt calculates the N-terminal protein region that can support a Mitochondrial Targeting Sequence and the cleavage site. [less]
  • MolTalk  •  MolTalk is a computational environment (programming library with an integrated scripting language) for doing structural bioinformatics. It interprets PDB formatted files and creates an object representation of the structure-chain-residue-atom hierarchy. [less]
  • MovieMaker  •  MovieMaker is a web server that allows short (~10 sec), downloadable movies to be generated of protein dynamics. It accepts PDB files or PDB accession numbers as input and automatically outputs colorful animations covering a wide range of protein motions and other dynamic processes. [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]
  • Multialin  •  Multiple sequence alignment with hierarchical clustering [less]
  • Multicoil  •  The MultiCoil program predicts the location of coiled-coil regions in amino acid sequences and classifies the predictions as dimeric or trimeric. The method is based on the PairCoil algorithm. To analyze your own sequences with MultiCoil, you can either use the web interface or download the program.  [less]
  • MUSCLE  •  Multiple alignment server [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]
  • MzJava  •  MzJava is an open-source Java library for the analysis of mass spectrometry data. It provides algorithms and data structures for processing mass spectra and their associated biological molecules, such as small molecules, glycans, proteins, and peptides with post-translational modifications. MzJava includes methods to perform mass calculation, protein digestion, peptide and glycan fragmentation, MS/MS signal processing, and scoring for spectra-spectra and peptide/glycan-spectra matches.  [less]
  • NetAcet  •  NetAcet predicts substrates of N-acetyltransferase A (NatA). The method was trained on yeast data but it obtains similar performance values on mammalian substrates acetylated by NatA orthologs.  [less]
  • NetCGlyc  •  Neural network predictions of C-mannosylation sites in mammalian proteins.  [less]
  • NetCorona  •  NetCorona predicts coronavirus 3C-like proteinase (or protease) cleavage sites using artificial neural networks on amino acid sequences. Every potential site is scored and a list is compiled in addition to a graphical representation. [less]
  • NetGlycate  •  Predicts glycation of epsilon amino groups of lysines in mammalian proteins.  [less]
  • NetNES  •  NetNES 1.1 server predicts leucine-rich nuclear export signals (NES) in eukaryotic proteins using a combination of neural networks and hidden Markov models.  [less]
  • NetNGlyc  •  NetNGlyc predicts N-Glycosylation sites in human proteins using artificial neural networks that examine the sequence context of Asn-Xaa-Ser/Thr sequons.  [less]
  • NetOGlyc  •  Neural network predictions of mucin type GalNAc O-glycosylation sites in mammalian proteins. [less]
  • NetPhos  •  NetPhos produces neural network predictions for serine, threonine and tyrosine phosphorylation sites in eukaryotic proteins.  [less]
  • NetPhosK  •  The NetPhosK 1.0 server produces neural network predictions of kinase specific eukaryotic protein phosphorylation sites. Currently NetPhosK covers the following kinases: PKA, PKC, PKG, CKII, Cdc2, CaM-II, ATM, DNA PK, Cdk5, p38 MAPK, GSK3, CKI, PKB, RSK, INSR, EGFR and Src.  [less]
  • NetPhosYeast  •  predict serine and threonine phosphorylation sites in yeast proteins [less]
  • NetPicoRNA  •  The NetPicoRNA 1.0 server produces neural network predictions of cleavage sites of picornaviral proteases. [less]
  • NetSurfP  •  NetSurfP server predicts the surface accessibility and secondary structure of amino acids in an amino acid sequence. The method also simultaneously predicts the reliability for each prediction, in the form of a Z-score. The Z-score is related to the surface prediction, and not the secondary structure.  [less]
  • NetTurnP  •  NetTurnP predicts if an amino acid is located in a Beta-turn or not. Optional, NetTurnP is also able to predict the nine Beta-turn subtypes.  [less]
  • NMT  •  Prediction of N-terminal N-myristoylation of proteins [less]
  • NQ-Flipper  •  NQ-Flipper recognizes unfavorable rotamers of Asn and Gln residues in protein structures and corrects them. [less]
  • One to Three  •  One to Three converts single letter translations to three letter translations. [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]
  • Paircoil  •  The Paircoil program predicts the location of coiled-coil regions in amino acid sequences. [less]
  • Paircoil2  •  Paircoil2 predicts the parallel coiled coil fold from sequence using pairwise residue probabilities with the Paircoil algorithm and an updated coiled coil database. Paircoil2 shows improved performance over Paircoil and other coiled-coil prediction algorithms.  [less]
  • PATS  •  PATS identifies amino acid sequences that are potentially targeted to the apicoplast matrix of Plasmodium falciparum. Secondary analysis of candidate sequences is required for confirmation. [less]
  • PattInProt  •  PattInProt allows to scan a protein database of one or several sequences for one or several patterns written in PROSITE syntax. The tool allows to specify an allowed number of mismatches or a similarity threshold towards the pattern. [less]
  • PDBePISA  •  PDBePISA is an interactive tool for the exploration of macromolecular (protein, DNA/RNA and ligand) interfaces, prediction of probable quaternary structures (assemblies), database searches of structurally similar interfaces and assemblies, as well as searches on various assembly and PDB entry parameters. [less]
  • PepDraw  •  PepDraw is a tool to draw peptide primary structure and calculate theoretical properties. [less]
  • PepFrag  •  PepFrag is a tool for identifying proteins from a collection of sequences that matches a single tandem mass spectrum.  [less]
  • PepPepSearch  •  PepPepSearch takes as input a sequence and searches this sequence against a variety of databases and returns the highest scoring matches. [less]
  • Peptide Builder  •  The peptide Builder constructs text representations for simple peptides and proteins from a library of 20 standard amino acids. This program support on-the-fly calculation of Molecular Weight and Molecular Formula [less]
  • PeptideCutter  •  PeptideCutter predicts potential substrate cleavage sites, cleaved by proteases or chemicals in a given protein sequence. The tool 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/protease, 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]
  • PEPVAC  •  PEPVAC is a tool aimed to the development of fully covering multi-epitope vaccines against pathogenic organisms based on genome wide predictions of promiscous MHCI-restricted epitopes. [less]
  • Pfam HMM Search  •  Scans a sequence against the Pfam protein families database. [less]
  • pftools  •  The pftools are a collection of programs to build, calibrate, and search biological sequences with generalized profiles. Generalized profiles are an extension of position specific scoring matrices by including position specific scores for insertions and deletions. They correspond to a matrix representation of a multiple sequence alignment that can be used to search distant homologous sequences and precisely align sequences to the model. [less]
  • Phobius  •  Prediction of transmembrane topology and signal peptides from the amino acid sequence of a protein. [less]
  • Phyre2  •  As with Phyre, the new system is designed around the idea that you have a protein sequence/gene and want to predict its three-dimensional (3D) structure. Whereas Phyre used a profile-profile alignment algorithm, Phyre2 uses the alignment of hidden Markov models via HHsearch to significantly improve accuracy of alignment and detection rate. [less]
  • pIcarver  •  A tool to visualize theoretical distributions of peptide pI on a given pH range and generate fractions with similar peptide frequencies [less]
  • PLOGO  •  Protein sequence logos using relative entropy. [less]
  • Poodle  •  Disordered proteins or protein segments lack a folded tertiary structure. They are thought to be intrinsically disordered regions providing essential biological functions, so predicting such disorder should help understand protein functions. [less]
  • PoPMuSiC  •  The PoPMuSiC program is a tool for the computer-aided design of mutant proteins with controlled stability properties. It evaluates the changes in stability of a given protein or peptide under single-site mutations, on the basis of the protein's structure. [less]
  • PoPS  •  The PoPS project is a set of computational tools for investigating protease specificity. The main PoPS program allows users to model and profile protease specificity and predict substrate cleavage. Other tools are available to search for substrates within proteomes (protein databases for organisms), and create simple matrix models of specificity from experimental data. [less]
  • PORTER  •  Protein Secondary Structure Prediction [less]
  • PPSearch  •  Search your query sequence for protein motifs, rapidly compare your query protein sequence against all patterns stored in the PROSITE pattern database and determine what the function of an uncharacterised protein is. This tool requires a protein sequence as input, but DNA/RNA may be translated into a protein sequence using transeq and then queried. Allows a graphical output. [less]
  • PRATT  •  An important problem in sequence analysis is to find patterns matching sets or subsets of sequences. This tool allows the user to discover patterns conserved in sets of unaligned protein sequences. The user can specify what kind of patterns should be searched for, and how many sequences should match a pattern to be reported. The patterns are reported using PROSITE syntax. [less]
  • PRATT (EBI)  •  An important problem in sequence analysis is to find patterns matching sets or subsets of sequences.This tool allows the user to search for patterns conserved in sets of unaligned protein sequences. The user can specify what kind of patterns should be searched for, and how many sequences should match a pattern to be reported.  [less]
  • PredictProtein  •  PredictProtein integrates feature prediction for secondary structure, solvent accessibility, transmembrane helices, globular regions, coiled-coil regions, structural switch regions, B-values, disorder regions, intra-residue contacts, protein-protein and protein-DNA binding sites, sub-cellular localization, domain boundaries, beta-barrels, cysteine bonds, metal binding sites and disulphide bridges. [less]
  • Predotar  •  Predotar was designed for systematic screening of large batches of proteins for identifying putative targeting sequences, and recognizes the N-terminal targeting sequences of classically targeted precursor proteins. It provides a probability estimate as to whether the sequence contains a mitochondrial, plastid or ER targeting sequence. [less]
  • PrePS  •  The prenylation prediction suite (PrePS) combines three predictors for protein CaaX farnesylation, CaaX geranylgeranylation and Rab geranylgeranylation in one webinterface. The predictors aim to model the substrate-enzyme interactions based on refinement of the recognition motifs for each of the prenyltransferases.  [less]
  • pROC  •  A package (R, S+) to visualize, smooth and compare receiver operating characteristic (ROC curves) [less]
  • PROCHECK  •  PROCHECK checks the stereochemical quality of a protein structure, producing a number of PostScript plots analysing its overall and residue-by-residue geometry. It includes PROCHECK-NMR for checking the quality of structures solved by NMR.  [less]
  • ProDom  •  ProDom is a protein domain family database constructed automatically by clustering homologous segments. Compare your sequence with ProDom by running a Blast-P or Blast-X search against: the consensus sequence provided with the ProDom families or the multiple alignments provided with each ProDom family. ProDom-CG (Complete Genomes) and ProDom-SG (Structural Genomics Candidate Search) can also be searched. [less]
  • PROF  •  Secondary Structure Prediction System [less]
  • ProFound  •  Tool for searching protein sequence collections with peptide mass maps. A Bayesian algorithm is used to rank the protein sequences in the database according to their probability of producing the peptide map.  [less]
  • ProP  •  ProP 1.0 server predicts arginine and lysine propeptide cleavage sites in eukaryotic protein sequences using an ensemble of neural networks. Furin-specific prediction is the default. It is also possible to perform a general proprotein convertase (PC) prediction.  [less]
  • PROPSEARCH  •  PROPSEARCH was designed to detect functional and / or structural homologs, if the sequence identity is below about 25%. It uses the amino acid physico-chemical properties, content of bulky residues, content of small residues, average hydrophobicity, average charge a.s.o. and are used as query vector. Sequences in the database are transformed into vectors as well, and the euclidian distance between the query and database sequences is calculated. [less]
  • ProSA-web  •  Program of error recognition in 3D structures [less]
  • ProtBud  •  Comparison of asymmetric units and biological units from PDB and PQS [less]
  • Protein Colourer  •  Protein Colourer is a tool for colouring amino acid sequences. The default settings will colour the sequence by the hydrophobicity of the amino acids. You can set the colouring scheme by changing the lists associated with each colour. [less]
  • Protein Disorder Predictors  •  List is a list or Protein Disorder Predictors [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]
  • ProteinProspector  •  Proteomics tools for mining sequence databases in conjunction with mass spectrometry experiments, including MS-Fit, MS-Pattern, MS-Digest, etc. [less]
  • Protein Sequence Logos  •  Protein sequence alignment viewed as sequence logos. The total height of the sequence information part is computed as the relative entropy between the observed fractions of a given symbol and the respective a priori probabilities. [less]
  • ProtParam  •  Compute various physical and chemical parameters for a given protein sequence. The computed parameters include the molecular weight, theoretical pI (isoelectric point), 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]
  • PSIPRED  •  The PSIPRED Protein Structure Prediction Server aggregates several of our structure prediction methods into one location. Users can submit a protein sequence, perform the prediction of their choice and receive the results of the prediction via e-mail. [less]
  • PSORT  •  PSORT family of programs for subcellular localization prediction [less]
  • PTS1  •  predict peroxisomal targeting signal 1 containing proteins [less]
  • PVS - Protein Variability Server  •  This server calculates the protein sequence variability within a multiple sequence alignment using several variability metrics. Subsequently, the server can perform several tasks, such as masking the variability in the reference sequence, returning conserved fragments or mapping the sequence variability onto a provided 3D-structure.  [less]
  • PyMOL  •  PyMOL is a user-sponsored molecular visualization system on an open-source foundation.  [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]
  • Radar  •  RADAR stands for Rapid Automatic Detection and Alignment of Repeats in protein sequences. Many large proteins have evolved by internal duplication and many internal sequence repeats correspond to functional and structural units. Radar is uses an automatic algorithm, for segmenting your query sequence into repeats, it identifies short composition biased as well as gapped approximate repeats and complex repeat architectures involving many different types of repeats in your query sequence. [less]
  • RandSeq  •  Random protein sequence generator [less]
  • Rankpep  •  This server predicts peptide binders to MHCI and MHCII molecules from protein sequence/s or sequence alignments using Position Specific Scoring Matrices (PSSMs). In addition, it predicts those MHCI ligands whose C-terminal end is likely to be the result of proteasomal cleavage. A detailed explanation of the method can be found here.  [less]
  • RasMol  •  RasMol is a program for molecular graphics visualization. [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]
  • REP  •  Protein search for repeats, using a collection of repeat families [less]
  • REPRO  •  REPRO is able to recognise distant repeats in a single query sequence. The technique relies on a variation of the Smith-Waterman local alignment strategy to find non-overlapping top-scoring local alignments, followed by a graph-based iterative clustering procedure to delineate the repeat set(s) based on consistency of the pairwise top-alignments. [less]
  • Reverse Transcription and Translation Tool  •  This tool converts DNA to RNA to protein, and reverse transcript RNA to DNA. [less]
  • Reverse Translate  •  Accepts a protein sequence as input and uses a codon usage table to generate a DNA sequence representing the most likely non-degenerate coding sequence. A consensus sequence derived from all the possible codons for each amino acid is also returned.  [less]
  • SAM-T08  •  This server finds similar protein sequences in NR and aligns them, providing sequence logos that show relative conservation of different positions. Local structure predictions are done with neural nets for several different local structure alphabets, and hidden Markov models are created. Fold recognition and alignment to proteins in the Protein Data Bank are done, and a full three-dimensional model is constructed. [less]
  • SAMBA  •  SAMBA is a 128 processor array for speeding up the comparison of biological sequences. The hardware implements a parameterized version of the Smith and Waterman algorithm allowing the computation of local or global alignments with or without gap penalty. [less]
  • SAPS  •  SAPS (Statistical Analysis of Protein Sequences) evaluates a wide variety of protein sequence properties using statistics. Properties considered include compositional biases, clusters and runs of charge and other amino acid types, different kinds and extents of repetitive structures, locally periodic motifs, and anomalous spacings between identical residue types.  [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]
  • Scratch Protein Predictor  •  SCRATCH is a server for predicting protein tertiary structure and structural features. The SCRATCH software suite includes predictors for secondary structure, relative solvent accessibility, disordered regions, domains, disulfide bridges, single mutation stability, residue contacts versus average, individual residue contacts and tertiary structure. [less]
  • SecretomeP  •  The SecretomeP 2.0 server produces ab initio predictions of non-classical i.e. not signal peptide triggered protein secretion. The method queries a large number of other feature prediction servers to obtain information on various post-translational and localizational aspects of the protein, which are integrated into the final secretion prediction.  [less]
  • Seq2Logo  •  Seq2Logo is a web-based sequence logo method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion.  [less]
  • SeqLogos  •  SeqLogos generates sequences logos from amino acid sequence alignment. Sequences logos are useful tools to visualize sequence patterns and represent a more informative alternative to consensus sequence [less]
  • Sequence Similarity Maps (SSM)  •  A data mining solution to map thousands of viral isolates (influenza, dengue and FMDV virus). [less]
  • Sequence Variability Server  •  This server calculates the variability in each column of a multiple sequence alignment using the Shannon entropy (H) function. [less]
  • Sequerome  •  Sequerome is a web based Java tool that acts as a front-end to BLAST queries and provides simplified access to web-distributed resources for protein and nucleic acid analysis. It provides a web-based sequence profiling tool for integrating the results of a BLAST sequence-alignment report with external research tools and servers that perform advanced sequence manipulations, and allowing the user to record the steps of such an analysis. [less]
  • SHOPS  •  SHOPS (SHow OPeron Structures) was developed to analyze the genomic operon context for any group of proteins selected on the basis of a set of sequence or domain identifiers. It uses genome annotations of all available fully sequenced prokaryotes to create a scaled graphical overview of the genomic context around the proteins of interest. [less]
  • SignalP  •  SignalP predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks. [less]
  • SIM  •  SIM finds a user-defined number of best non-intersecting alignments between two protein sequences or within a sequence. Results can be viewed with LALNVIEW, a graphical viewer program for pairwise alignments. [less]
  • SMART  •  The Simple Modular Architecture Research Tool allows the identification and annotation of genetically mobile domains and the analysis of domain architectures. Normal SMART, (against UniProtKB and stable Ensembl proteomes), and Genomic SMART, (against complete proteomes) are supported. [less]
  • SmileMS  •  LC-MSMS software for small molecule identification, can search both low and high mass precision libraries. Users can search on multiple libraries simultaneously, including privately built ones. [less]
  • SOPMA  •  Secondary structure prediction. [less]
  • SOSUI  •  Classification and Secondary Structure Prediction of Membrane Proteins. [less]
  • Strap  •  Java-based software for structural alignments of proteins [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]
  • SulfoSite  •  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.  [less]
  • SUMOplot  •  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. [less]
  • SUMOsp  •  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. [less]
  • Superfamily Sequence search  •  Assign SCOP domains to your sequences using the SUPERFAMILY hidden Markov models [less]
  • SUPERFAMILY Sequence Search  •  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. [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]
  • SwissTargetPrediction  •  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.  [less]
  • SYFPEITHI  •  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.  [less]
  • T-Coffee  •  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. [less]
  • T-Coffee - EBI  •  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.  [less]
  • T-Coffee - WUR  •  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. [less]
  • T-REKS  •  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. [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]
  • TargetP  •  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).  [less]
  • TatP  •  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.  [less]
  • TEIRESIAS  •  Pattern discovery on event streams of alphanumeric characters. Possible alphabet sets include nucleic acids, amino acids, etc. [less]
  • TermiNator  •  TermiNator predicts N-terminal methionine excision, N-terminal acetylation, N-terminal myristoylation and S-palmitoylation of either prokaryotic or eukaryotic proteins originating from organellar or nuclear genomes. It also relates the predicted N-terminus to protein half-life (5-220 hours) and relative translation efficiency (relative value 1-5) of eukaryotic proteins. [less]
  • Three- / one-letter code  •  This tool can convert 3-letter amino acid codes to 1-letter amino acid codes and inversely. [less]
  • Three to One  •  Three to One converts three letter translations to single letter translations [less]
  • TLS Motion Determination  •  TLS Motion Determination analyzes a macromolecular crystal structure for evidence of flexibility, e.g. local or inter-domain motions. It does this by partitioning individual chains into multiple segments that are modeled as rigid bodies undergoing TLS (Translation/Libration/Screw) vibrational motion. It generates all possible partitions up to a maximum number of segments.  [less]
  • TMHMM  •  TMHMM is a membrane protein topology prediction method based on a hidden Markov model (HMM). It predicts transmembrane helices in proteins. [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]
  • TopMatch  •  Computational tools for the alignment and superposition of protein structures are essential instruments in structural biology. TopMatch-web provides an easy-to-use interface to a suite of techniques for protein structure alignments. Given a pair of protein structures, TopMatch calculates a list of alignments ordered by structural similarity. The corresponding superpositions can be explored in a 3D molecule viewer which highlights the structurally equivalent parts of the proteins. [less]
  • TopPred  •  Topology prediction of membrane proteins [less]
  • TopSearch  •  TopSearch is a new powerful gateway to protein structures and their structural relationships. Given a query structure the search engine instantly returns a list of known protein structures sorted by structural similarity. TopSearch operates on three structural levels: chains, biological assemblies and quaternary structures, and asymmetric units. [less]
  • Translate  •  Translation of a nucleotide (DNA/RNA) sequence to a protein sequence. [less]
  • TRUST  •  TRUST is a method for ab-initio determination of internal repeats in proteins. The high sensitivity and accuracy of the method is achieved by exploiting the concept of transitivity of alignments.  [less]
  • VMD - Visual Molecular Dynamics  •  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. [less]
  • WebLogo  •  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.  [less]
  • WHAT IF  •  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.  [less]
  • Wise2  •  The Wise2 form compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors. [less]
  • WU BLAST  •  Protein databases query to find regions of sequence similarity quickly, with minimum loss of sensitivity.  [less]
  • xComb  •  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) [less]
  • XplorMed  •  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.  [less]
  • xQuest  •  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.  [less]
  • XSTREAM  •  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. [less]
  • YASARA  •  YASARA is a molecular-graphics, -modeling and -simulation program for Windows, Linux and Mac OS X [less]
  • YinOYang  •  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.  [less]