Web Tools

Structural Biology Calculations  
A tool for calculating geometric quantities of proteins (accessible surface area, volume, etc).
Submitted: Oct 19, 2000
Compute pI/Mw  
Compute pI/Mw is a tool which allows the computation of the theoretical pI (isoelectric point) and Mw (molecular weight) for a list of SWISS-PROT and/or TrEMBL entries or for a user entered sequence.
Submitted: Oct 22, 2000
PredictProtein  
PredictProtein is a service for sequence analysis, and structure prediction. It does You submit any protein sequence. PredictProtein retrieves similar sequences in the database and predicts aspects of protein structure.
Submitted: Oct 19, 2000
CpG Islands  
Utility to find CpG Islands in a user-entered sequence.
Submitted: Oct 15, 2000
Eukaryotic Promoter Database  
The Eukaryotic Promoter Database is an annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Access to promoter sequences is provided by pointers to positions in nucleotide sequence entries. The annotation part of an entry includes description of the initiation site mapping data, cross-references to other databases, and bibliographic references.
Submitted: Nov 19, 2000
Scanps 2.3  
A fast implementation of the true Smith & Waterman algorithm for protein database searches.
Submitted: Oct 22, 2000
SYSTERS Cluster Set  
SYSTERS (SYSTEmatic Re-Searching) is based on iterative calls of a traditional database search tool like BLASTP or FASTA. The searching algorithm explores the sequence space around a query sequence - called seed - and finds a set of related sequences to this seed - called cluster - which share a strong similarity. The sequences within a cluster are not ranked - a sequence is either in the cluster or it is not. To circumvent problems originating in asymmetric search results, for each pair of sequences identified by a database search a local alignment is computed using LALIGN and a symmetric E-value is recomputed.
Submitted: Nov 18, 2000
ParAlign  
You may search a number of sequence databases for sequences similar to your amino acid query sequence using two very sensitive algorithms. You can choose between a fast implementation of the well-known Smith-Waterman optimal local alignment algorithm or a new algorithm called ParAlign, which is much faster but still almost as sensitive. Both algorithms are implemented using bit-parallelism on a single Pentium III microprocessor, exploiting the MMX and SSE instruction sets. The current implementation of the affine Smith-Waterman algorithm has a speed of about 220 million cells per second (on a 500MHz CPU), which is a nine-fold speed-up relative to SSEARCH.
Submitted: Nov 18, 2000
ProtParam  
ProtParam is a tool which allows the computation of various physical and chemical parameters for a given protein stored in SWISS-PROT or TrEMBL or for a user entered sequence. The computed parameters include the molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (GRAVY).
Submitted: Oct 22, 2000
BioInfo.PL Meta Server  
The Structure Prediction Meta Server offers a single gateway to various structure prediction tools. The user can submit an amino acid sequence as input. The sequence will be first analysed for close homologs in the Protein Data Bank, using Blast. If no close homologs (cutoff 0.1) are detected the sequence will be submitted to the structure prediction servers. The results of the prediction will be stored localy.
Submitted: Sep 26, 2000
Edinburgh Biocomputing Systems Limited  
EBS, a spin out company from the University of Edinburgh formed to develop and market MPSRCH. The software, which implements the full Smith and Waterman algorithm on reasonably priced general purpose hardware, can be accessed free of charge upon registration at the site.
Submitted: Sep 26, 2000
GlycoMod  
GlycoMod is a tool that can predict the 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.
Submitted: Dec 18, 2000
ISREC PatternFind  
This server allows you to search the nonredundant or SwissProt protein database with a user-defined pattern. The pattern can either be a PERL-supported regular expression or a pattern in PROSITE format. The output is either a report on the matches, a multiple sequence file containing all matching patterns (in Pearson format), or a multiple sequence file containing all matching pattern instances.
Submitted: Dec 02, 2000
Multalin  
Graphical version for alignment of multiple sequences using the MultAlin algorithm.
Submitted: Oct 20, 2000
SIM Alignment Tool  
SIM is a program which finds a user-defined number of best non-intersecting alignments between two protein sequences or within a sequence.
Submitted: Oct 20, 2000
2DWG Image Meta-Database  
The 2DWG meta-database of 2D-PAGE protein gel images found on the Web. A meta-database contains information about data in other databases. The 2DWG database is a organized as a spreadsheet table with each gel image represented by a row. Data for each gel entry includes tissue, species, cell-line, image URL, database URL, gel protocol, organization URL, image properties, map URL if it exists, etc. It uses a simple database search engine dbEngine to access selected rows of gels in the full 2DWG table.
Submitted: Dec 03, 2000
AGADIR  
An algorithm to predict the helical content of peptides.
Submitted: Oct 22, 2000
DAS  
The DAS server will predict transmembrane regions of a query sequence. Enter your query protein sequence into the text area below and submit it to the server. The sequence should be in one letter code.
Submitted: Oct 19, 2000
GeneStream II  
Sequence comparision and search programs, including the rigorous Smith-Waterman algorithm (in FastA and Ssearch).
Submitted: Nov 10, 2000
MaxSprout  
MaxSprout is a fast database algorithm for generating protein backbone and side chain co-ordinates from a C(alpha) trace. The backbone is assembled from fragments taken from known structures. Side chain conformations are optimized in rotamer space using a rough potential energy function to avoid clashes.
Submitted: Oct 08, 2000
NetChop  
The NetChop WWW server produces neural network predictions for cleavage sites of the human proteasome.
Submitted: Dec 02, 2000
PeptideMass  
PeptideMass cleaves one or more protein sequences from the SWISS-PROT and/or TrEMBL databases or a user-entered protein sequence with a chosen enzyme, and computes the masses of the generated peptides. The tool also returns theoretical isoelectric point and mass values for the proteins of interest. If desired, PeptideMass can return the mass of peptides known to carry posttranslational modifications, and can highlight peptides whose masses may be affected by database conflicts, isoforms or splicing variants.
Submitted: Oct 22, 2000
PhosphoBase  
PhosphoBase is a revised database of phosphorylation sites in proteins. Information about the position of phosphorylated serines, threonines, or tyrosines and relevant kinetic parameters are presented.
Submitted: Oct 22, 2000
Phosphoprotein Database (PPDB)  
The purpose of a Phosphoprotein Database (PPDB) is to promote a systematic approach to the study of cellular protein phosphorylation. PPDBs have the potential to transform 2DE images from mere collections of spots on gels into images that convey information about cell lineage, the activation state of the cell, the ligands that the cell has encountered, the kinases, phosphatases and substrates present in the cell, and the activation state of these enzymes.
Submitted: Nov 19, 2000
Protein Domain Profile Analysis  
This tool allows you to search our library of functional diagnostic profiles with a protein sequence. A match to one or more of these profiles provides you with an effective multi-alignment of your query sequence to the best-matched profile's defining set of proteins along with its annotations. This in turn allows one to propose that the matching sequence contains a domain of similar structure and function.
Submitted: Oct 22, 2000
PSA Structure Prediction  
The Protein Sequence Analysis (PSA) server predicts probable secondary structures and folding classes for a given amino acid sequence.
Submitted: Oct 22, 2000
Quick Protein Translator  
Translate DNA sequences in all 6 reading frames.
Submitted: Oct 15, 2000
SDSC Biology Workbench  
The Biology WorkBench is a revolutionary web-based tool for biologists. The WorkBench allows biologists to search many popular protein and nucleic acid sequence databases. Database searching is integrated with access to a wide variety of analysis and modeling tools, all within a point and click interface that eliminates file format compatibility problems.
Submitted: Sep 26, 2000
SSCP  
The program SSCP computes predictions for the content of helix, strand, and coil for a given protein using the amino acid composition as the only input information. The basic idea of the method consists in the application of analytic vector decomposition methods applied on the composition vector of the query protein. Both sequences and composition data are allowed as program input.
Submitted: Oct 22, 2000
TMAP  
TMAP multiple sequence alignment form.
Submitted: Oct 08, 2000
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 occuring transmembrane proteins. The prediction is made using a combination of several weight-matrices for scoring.
Submitted: Oct 22, 2000
Yale Molecular Biophysics Biochemistry Center Structural Biology  
User Guides and worked examples for software applications in structural biology
Submitted: Nov 05, 2000
AbCheck  
This page allows you to test an antibody sequence against the Kabat sequence database. Any unusual residues (occurring in < 1% of chains in the database) will be reported to you. This allows the identification of potential cloning artifacts and sequencing errors.
Submitted: Oct 24, 2000
BLOCK Maker  
The BLOCK MAKER SERVER finds blocks in a group of related protein sequences. Blocks are short multiply aligned ungapped segments corresponding to the most highly conserved regions of proteins. Typically, a group of proteins has more than one region in common and their relationship is represented as a series of blocks separated by unaligned regions.
Submitted: Nov 18, 2000
ChloroP  
The ChloroP WWW-server is able to predict whether or not an amino acid sequence contains an N-terminal chloroplast transit peptide, cTP and the probable site for cleavage of the transit peptide.
Submitted: Oct 22, 2000
DARWIN  
Filling and submitting this form will execute the statements entered as a Darwin program (a tool for peptide and nucleotide sequence analysis).
Submitted: Oct 25, 2000
DictyOGlyc  
The DictyOGlyc WWW server produces neural network predictions for GlcNAc O-glycosylation sites in Dictyostelium discoideum proteins.
Submitted: Dec 02, 2000
EMBL Dali  
The Dali server is a network service for comparing protein structures in 3D. You submit the coordinates of a query protein structure and Dali compares them against those in the Protein Data Bank. A multiple alignment of structural neighbours is mailed back to you. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences.
Submitted: Oct 08, 2000
Expressed Sequence Tags  
dbEST (Expressed Sequence Tag) sequences are 'single pass' partial DNA sequences derived from clones randomly selected from cDNA libraries. dbEST is maintained by NCBI and included in the GenBank database. Because these data differ from traditional GenBank entries and thus require special processing and annotation, NCBI also makes them available in a separate database, dbEST. The full reports contain information on the availability of physical cDNA clones and mapping data in collaboration with the Genome Data Base at Johns Hopkins University.
Submitted: Dec 02, 2000
GeneMatcher  
GeneMatcher programs and databases for your query sequence. Changing the GenMatcher parameters and output parameters is optional.
Submitted: Nov 10, 2000
GlycanMass  
GlycanMass is a tool which allows to calculate the mass of an oligosaccharide structure.
Submitted: Dec 18, 2000
HIV Sequence Database  
The main aim of this website is to provide easy access to our databases, alignments, and the tools and interfaces that The HIV Sequence Database had produced.
Submitted: Dec 02, 2000
ISREC 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.
Submitted: Oct 22, 2000
ISREC ProfileScan  
This server allows you to search one or more sequences against the current release of Amos Bairochs PROSITE database. The server uses an experimental version of a PERL-script that runs a PROSITE database-search using regular expressions. The output of this server is similar to the output of the ppsearch-server running at the EBI.
Submitted: Dec 02, 2000
MassSearch  
Search the SwissProt database for sequences which when digested by the given enzyme will match the given set of masses.
Submitted: Oct 25, 2000
NetOGlyc  
The NetOglyc WWW server produces neural network predictions of mucin type GalNAc O-glycosylation sites in mammalian proteins.
Submitted: Oct 22, 2000
NetPicoRNA  
The NetPicoRNA World Wide Web server produces neural network predictions of cleavage sites of picornaviral proteases.
Submitted: Oct 22, 2000
NHGRI/NCBI Histone Sequence Database  
A comprehensive WWW resource for histones and histone fold-containing proteins.
Submitted: Sep 27, 2000
Nnpredict  
Protein Secondary Structure Prediction.
Submitted: Oct 22, 2000
Peptide Binding Predictions  
Rank potential 8-mer, 9-mer, or 10-mer peptides based on a predicted half-time of dissociation to HLA class I molecules.
Submitted: Oct 22, 2000
Pôle Bio-Informatique Lyonnais  
The PBIL (Pôle Bio-Informatique Lyonnais) World Wide Web server - developed at the Laboratory of Biometry and Evolutionary Biology and the Institute of Biology and Chemistry of Proteins - is dedicated to molecular biology and ecology. This server allows to browse through a number of general or specialized sequence databases such as GenBank, NBRF, EMBL, SWISS-PROT/TrEMBL, Hovergen, NRSub and EMGLib. It also allows access to many analytical tools for nucleotide or protein sequence analysis. The PBIL server also offers many documents relevant to these fields of research as well as links with other information sources.
Submitted: Dec 02, 2000
PPSEARCH  
Scans a sequence against PROSITE (with graphical output).
Submitted: Oct 22, 2000
ProtScale  
ProtScale allows you to compute and represent the profile produced by any amino acid scale on a selected protein.
Submitted: Oct 22, 2000
PSA  
The Protein Sequence Analysis (PSA) server predicts probable secondary structures and folding classes for a given amino acid sequence.
Submitted: Oct 22, 2000
PSORT  
PSORT is a computer program for the prediction of protein localization sites in cells. It receives the information of an amino acid sequence and its source orgin, e.g., Gram-negative bacteria, as inputs. Then, it analyzes the input sequence by applying the stored rules for various sequence features of known protein sorting signals. Finally, it reports the possiblity for the input protein to be localized at each candidate site with additional information.
Submitted: Oct 22, 2000
RandSeq  
RandSeq is a tool which generates a random protein sequence.
Submitted: Oct 22, 2000
SAM-T99  
HMM-based Protein Sequence Analysis, SAM-T99.
Submitted: Sep 26, 2000
SAPS  
Statistical analysis of protein sequences.
Submitted: Oct 22, 2000
SDSC Biology Workbench  
The WorkBench allows biologists to search many popular protein and nucleic acid sequence databases. Database searching is integrated with access to a wide variety of analysis and modeling tools, all within a point and click interface that eliminates file format compatibility problems.
Submitted: Nov 10, 2000
SignalP  
The SignalP World Wide Web server 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.
Submitted: Oct 22, 2000
SMART  
SMART (Simple Modular Architecture Research Tool.) identifies and annotates domain sequences known to occur in signalling proteins.
Submitted: Oct 22, 2000
SPIN-PP  
SPIN-PP is a database of all protein-protein interfaces present in the PDB. The program GRASP was used to create molecular surfaces of each half of all 2-chain complexes present in the PDB. A basic set of physico-chemical properties were then mapped on to these surfaces, which were then used to classify the interfaces into a surface property taxonomy. The mapped properties currently include surface curvature , electrostatic potential, based on formal charges, sequence variability , based on the HSSP alignments, and hydrophobicity ,on an atom-based model.
Submitted: Oct 18, 2000
SRSWWW at IUBio  
A list of Data Banks available at IUBio Archive, Indiana, USA.
Submitted: Nov 19, 2000
The Nucleic Acid Database  
The goal of the Nucleic Acid Database Project is to assemble and distribute structural information about nucleic acids. Structures may be selected by making choices based on a large variety of structural and experimental characteristics. The user can then view the structure's coordinates in either NDB or PDB format, view the structure's full NDB entry, view the structure using either a local viewer or the remote viewer (RasMol), or display the structure's atlas entry.
Submitted: Dec 02, 2000
The Protein Colourer  
A tool for colouring your 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. Another scheme could be used to colour the amino acids by size.
Submitted: Oct 23, 2000
The Swiss 7TM Search Tool  
Search the list of known 7TM protein sequences, by using such keywords as NK1, ACETYLCHOLINE, etc...
Submitted: Oct 22, 2000
TMHMM  
Prediction of transmembrane helices in proteins.
Submitted: Oct 22, 2000
WU-BLAST2  
WU-BLAST2 with post-processing of the output integrates multiple biological information resources into a graphical overview.
Submitted: Oct 17, 2000



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