GlyTouCan  •  GlyTouCan is the international glycan structure repository. It is an uncurated registry for glycan structures that assigns globally unique accession numbers to any glycan independent of the level of information provided by the experimental method used to identify the structure(s). [less]

SwissPalm  •  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.  [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]

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]

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]

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]

Alignment tools  •  Four tools for multiple alignments. [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]

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]

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]

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]

ColorSeq  •  Color Protein Sequence. [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]

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]

ELM  •  Eukaryotic Linear Motif resource for functional sites in proteins  [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]

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]

GlycoDomain Viewer  •  The GlycoDomain Viewer is a tool for the visualisation of glycosylation sites in the context of the protein and conserved domains. It contains O-glycoproteomic data from the Clausen lab, and predictions of GalNAc-type glycosylation for the human proteome. [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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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]

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 (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]

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]

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]

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]

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]

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]

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]

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 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]

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]

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]

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 - 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]

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]

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]

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]