Biology

Critical Outcome Technologies Critical Outcome Technologies- Offers in silico drug discovery service to the pharmaceutical industry. Based in London, Ontario. Quantum Pharmaceuticals Quantum Pharmaceuticals- Provides drug discovery using computational technology to simulates intermolecular interactions. Scansite Scansite- Scansite searches for motifs within proteins that are likely to be phosphorylated by specific protein kinases or bind to domains such as SH2 domains, 14-3-3 domains or P… ProPred-I ProPred-I- An online service for predicting MHC binding regions in antigens. It also offers the proteasomal and immunoproteasomal filters to improve the applicability of results. EpiC EpiC- Resource for the prediction of antigenicity combined with functional analysis of the target protein. PDBeMotif PDBeMotif- Integrated resource, which provides information about ligands, sequence and structure motifs, their relative position and the neighbour environment. Isoelectric Point Estimator Isoelectric Point Estimator- Calculator with graphical user interface written in Qt library. The ProCKSI Server The ProCKSI Server- A decision support system for protein structure comparison. It provides tools for visualising, analysing, clustering and comparing results. TopMatch: Protein Structure Comparison TopMatch: Protein Structure Comparison- Public web service for the alignment and superposition of protein structures and the instant visualization of structural similarities. DisEMBL DisEMBL- Computational tool for sequence based prediction of intrinsic protein disorder and unstructured regions within a protein. MODBASE MODBASE- A database of annotated comparative protein structure models. The database includes fold assignments and alignments as well as information about putative ligand binding s… TRANSFAC-The Transcription Factor Database TRANSFAC-The Transcription Factor Database- A compilation of transcriptional regulatory protein factors and their cognate gene promoter elements along with DNA sequence search and… SSM SSM- Provides interactive service for matching protein structures in 3D and looking for structural homologues in PDB and SCOP databases, as well as in user-uploaded sets of struct… Phyre- Protein Homology/analogY Recognition Engine Phyre- Protein Homology/analogY Recognition Engine- Phyre is a free for academics service for predicting the 3-dimensional structure of a protein amino acid sequence. ELM - Functional Sites in Proteins ELM - Functional Sites in Proteins- Predicts functional sites (linear motifs) in proteins, such as post-translational modification sites, ligand motifs, and targeting signals. Con… PFP: Automated Function Prediction Server PFP: Automated Function Prediction Server- Accepts a single query protein sequence and returns the most probable Gene Ontology functional annotations in each of the three ontologi… ESyPred3D ESyPred3D- ESyPred3D is an automated homology modeling program getting benefit of the increased alignment performances of a new alignment strategy using neural networks. The final… MultiProt MultiProt- Service for detecting the multiple structural alignments of proteins. Uses the common geometrical cores between the input molecules. Does not require that all the input… ConSurf ConSurf- Identifies functionally important regions on the surface of a protein or domain, of known three-dimensional (3D) structure using the phylogenetic relations between close … UniProt UniProt- UniProt (Universal Protein Resource) is a catalog of information on proteins. It is a central repository of protein sequence and function created by joining the informati… Melanie II 2-D Analysis Software Melanie II 2-D Analysis Software- Powerful, state-of-the-art, 2-D analysis software package with user-friendly interface from the Swiss Institute of Bioinformatics. Proteomics Tools Proteomics Tools- Online software for protein analysis from the Swiss Institute of Bioinformatics (SIB). Jpred Jpred- Secondary protein structure prediction from amino acid sequence; based on a consensus from several methods including DSC, PHD, NNSSP, PREDATOR, ZPRED, and MULPRED. Protein Structure Prediction Server (PSIPRED) Protein Structure Prediction Server (PSIPRED)- 3D protein structure prediction from amino acid sequence. Includes MEMSAT for transmembrane topology prediction, GenTHREADER and mGe… 3D-PSSM Fold Recognition 3D-PSSM Fold Recognition- Combines sequence and structural information for predicting the structure and/or function of your protein sequence, and can detect remote homologies beyo… ProtFun ProtFun- Ab initio predictions of protein function from protein sequence. The method works by integrating various predicted post-translational and localizational aspects of the pr… Molecular Biology Tools Online Molecular Biology Tools Online- Includes WebOligoMelt (Annealing temperature of oligonucleotides), Virtual Ribosome (translate nucleotide sequences into peptides), and SeqScanGrap… Protonet Protonet- Provides automatic hierarchical classification of proteins sequences. Munich Information Center for Protein Sequences (MIPS) Munich Information Center for Protein Sequences (MIPS)- Bioinformatics research group offering organism specific information (Yeast, Cress) as well as search tools for public data… InterPro InterPro- A database built from Pfam, PRINTS and PROSITE. Protein Information Resource Protein Information Resource- PIR is a non-redundant annotated protein sequence database, and analytical tools, maintained by collaboration of MIPS, in Munich and the Japanese Int… SWISS-PROT + TrEMBL SWISS-PROT + TrEMBL- The SWISS-PROT database contains high-quality annotation, is non-redundant and cross-referenced to many other databases. SWISS-PROT is accompanied by TrEMBL, … JAligner JAligner- Open source Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment. TreeGen TreeGen- Tree generation from distance data. [Results by email] MultAlign MultAlign- A multiple-sequence alignment program that also includes distance matrix methods for inferring trees. Vista tools Vista tools- Multiple sequence alignment server and whole genome alignment database. SplitsTree 2 SplitsTree 2- Tool that uses split decomposition method to analyze and visualize distance data from biological sequences. Rare Codon Analysis Rare Codon Analysis- Provides graphical and numerical representation of the codon adaptation index, frequency distribution and GC content of the DNA sequence. Maintained by the Ge… RaCC: Rare Codon Calculator RaCC: Rare Codon Calculator- Determines the number and highlights a rare E. coli codons in a provided DNA sequence. Maintained by UCLA, USA. Silent Silent- Silent mutation restriction enzyme scan. Finds new restriction sites to insert (mutate) with no translation change. TACG TACG- DNA restriction enzyme analysis. Provides a number of hits per enzyme and a list of non-cutters. Allows for selection of the enzymes and parameters. REBsites REBsites- Provides restriction enzyme digest analysis of the input DNA sequence. Results are presented graphically as a "virtual gel". ORF Finder ORF Finder- Identifies all ORFs using the standard or alternative genetic codes. Provides an interactive, graphical interface and allow for saving of a deduced amino acid sequence… StarORF StarORF- A Java application that facilitates the identification of potential ORFs, based on provided DNA sequence and probable ORF length. Primer-BLAST Primer-BLAST- Provides primers specific to the PCR template sequence. Includes primer pair specificity checking against a selected database. Oligo Calc: Oligonucleotide Properties Calculator Oligo Calc: Oligonucleotide Properties Calculator- Provides reverse complement sequence for DNA or RNA primer strands, self complementarity check, physical and thermodynamic const… Readseq Readseq- Converts amino acid and nucleotide sequence data formats including FASTA, GenBank, Phylip and others. Maintained by NIH, USA. NEBcutter NEBcutter- Provides a DNA sequence analysis to find restriction enzymes sites. Finds also non-overlapping open reading frames using the E.coli genetic code. PlasMapper PlasMapper- Offers server generated plasmid maps and image files, from input DNA sequences up to 20,000 bp. Includes citation, and downloadable source code. Maintained by the Univ… Graphical Codon Usage Analyzer Graphical Codon Usage Analyzer- Displays the codon quality in two different ways, codon usage frequency or relative adaptiveness values. FAQ included.