Pharmacoinformatics Lab

Journal Links Bioinformatics Links Molecular Graphics Links

BLAST home page

http://www.ncbi.nlm.nih.gov/BLAST/

Washington University BLAST (WU-BLAST)

http://blast.wustl.edu/

GSC BLAST Search Service

http://genome.wustl.edu/blast/client.pl

Washington University Genome Sequence Center

http://www.genome.wustl.edu

Sanger Institute Sequencing Projects Blast Search Services

http://www.sanger.ac.uk/DataSearch

ProFound, Protein Identification by Comparison of a Peptide Map to NCBI’s NR Database

http://prowl.rockefeller.edu/cgi-bin/ProFound

ExPASy Proteomics Tools

http://www.expasy.ch/tools/

Protein Information Resource

http://pir.georgetown.edu/

ClustalW, General Purpose Multiple Sequence Alignment Program for DNA or Proteins

http://www.ebi.ac.uk/clustalw

TreeView for Displaying Phylogenies

http://taxonomy.zoology.gla.ac.uk/rod/treeview.html

PHYLIP for Inferring Phylogenies

http://evolution.genetics.washington.edu/phylip.html

Web Version of PHYLIP

http://biocore.unl.edu/WEBPHYLIP/

PAUP, Tools for Inferring and Interpreting Phylogenetic Trees

http://paup.csit.fsu.edu/

Genome of Prominent Organisms

http://www.ncbi.nlm.nih.gov/PMGifs/Genomes/org.html.

Complete Genome of Escherichia coli K12

http://www.ncbi.nlm.nih.gov/genomes//framik.cgi?db=G&gi=115

ProSAL, Protein Sequence Analysis Launcher

http://xray.bmc.uu.se/sbnet/prosal.html

META-PP, Meta Server for Protein Prediction

http://maple.bioc.columbia.edu/pp/submit_meta.html

JPred, Consensus Protein Secondary Structure Prediction

http://www.compbio.dundee.ac.uk/~www-jpred/

PSI-pred, Protein Structure Prediction Server

http://bioinf.cs.ucl.ac.uk/psipred/psiform.html

PHD, The Predict Protein Server, Service for Sequence Analysis and Structure Prediction

http://cubic.bioc.columbia.edu/pp

Sspro, Server for Protein Secondary Structure Prediction based on en ensemble of 11 BRNNs (bidirectional recurrent neural networks)

http://www.igb.uci.edu/tools/scratch/

PROF, Secondary Structure Prediction

http://www.aber.ac.uk/~phiwww/prof/index.html

SDSC1, SDSC Protein Structure Homology Modeling Server

http://cl.sdsc.edu/hm.html

CPHmodels, Prediction of Protein Structure

http://www.cbs.dtu.dk/services/CPHmodels/

SWISS-MODEL, Automated Comparative Protein Modeling Server

http://www.expasy.ch/swissmod/SWISS-MODEL.html

ModBase, Database of Comparative Protein Structure Models

http://alto.compbio.ucsf.edu/modbase-cgi/index.cgi

LOOPP (Learning, Observing and Outputting, Protein Patterns), Program for Potential Optimization and Alignment

http://ser-loopp.tc.cornell.edu/loopp.html

Superfamily, Hidden Markov Model Library and Genome Assignments Server

http://supfam.mrc-lmb.cam.ac.uk/SUPERFAMILY/

The Sausage Machine (server currently not available)

http://www.zbh.uni-hamburg.de/mitarbeiter/torda.htm

Meta Server, Protein Structure Prediction

http://bioinfo.pl/Meta/

UCLA/DOE Fold Server, Protein Structure Assignment Based on Sequence-Derived Properties (SDP)

http://fold.doe-mbi.ucla.edu/

DAS (Dense Alignment Surface method), Transmembrane Alpha-helices Prediction Server

http://www.sbc.su.se/~miklos/DAS/

TMHMM Server, Prediction of Transmembrane Helices in Proteins

http://www.cbs.dtu.dk/services/TMHMM-2.0/

TopPred2, Topology Prediction of Membrane Proteins

http://www.sbc.su.se/~erikw/toppred2/

MOMENT, Transmembrane Helix Prediction

http://www.doe-mbi.ucla.edu/Services/moment/

Pfam, Sequence Analysis Server

http://pfam.wustl.edu/hmmsearch.shtml

InterProScan, Protein Function and Structure Prediction

http://www.ebi.ac.uk/interpro/scan.html

ProDom, Protein Domain Database

http://prodes.toulouse.inra.fr/prodom/current/html/home.php

BLOCKS, Block Searcher

http://blocks.fhcrc.org/blocks_search.html

SMART (Simple Modular Architecture Research Tool), Sequence and Architecture Analyses

http://smart.embl-heidelberg.de/

DomFish (Domain Fishing), Finding Domains in Protein Sequences and Analysis

http://www.bmm.icnet.uk/~3djigsaw/dom_fish/

Database of Protein Family and Domains

http://tw.expasy.ch/prosite/

eMOTIF, Database of Highly Specific and Sensitive Protein Sequence Motifs Representing Conserved Biochemical Properties and Biological Functions

http://dna.stanford.edu/identify

GeneQuiz, Highly Automated Analysis of Biological Sequences

http://jura.ebi.ac.uk:8765/ext-genequiz/

PRINTS, Compendium of Protein Fingerprints, Conserved Motifs Used to Characterise a Protein Family

http://bioinf.man.ac.uk/dbbrowser/PRINTS/PRINTS.html

P-val FPScan, Scan PRINTS with a query sequence

http://bioinf.man.ac.uk/cgi-bin/dbbrowser/fingerPRINTScan/muppet/FPScan.cgi

SignalP, Server Predicting the Presence and Location of Signal Peptide Cleavage Sites in Amino Acid Sequences

http://www.cbs.dtu.dk/services/SignalP/

PsortII, Prediction of Protein Localization Sites in Cells

http://psort.nibb.ac.jp/form2.html

ChloroP, Server Predicting the Presence of Chloroplast Transit Peptides (cTP) in Protein Sequences and the Location of Potential cTP Cleavage Sites.

http://www.cbs.dtu.dk/services/ChloroP/

ExPASy (Expert Protein Analysis System), Proteomic Server

http://www.expasy.ch/

NetPhos, Neural Network Predictions for Serine, Threonine and Tyrosine Phosphorylation Sites in Eukaryotic Proteins

http://www.cbs.dtu.dk/services/NetPhos/

NetPicoRNA, Prediction of Picornavirus Protease Sites

http://www.cbs.dtu.dk/services/NetPicoRNA/

CASP (Critical Assessment of Techniques for Protein Structure Prediction), Protein Structure Prediction Center

http://predictioncenter.llnl.gov/

CAFASP (Critical Assessment of Fully Automated Structure Prediction), Main Data Management Site for Tertiary Structure Prediction

http://bioinfo.pl/cafasp/

LiveBench, Continuous Benchmarking of Structure Prediction Servers

http://bioinfo.pl/LiveBench/

SCOP ( Structural Classification of Proteins)

http://scop.berkeley.edu

BIND (The Biomolecular Interaction Network Database)

http://www.bind.ca/

BRITE (Biomolecular Relations in Information Transmission and Expression)

http://www.genome.ad.jp/brite/

DIP (Database of Interacting Proteins), Database cataloging Experimentally Determined Interactions Between Proteins

http://dip.doe-mbi.ucla.edu/

DPInteract, Database on DNA-Protein Interactions

http://arep.med.harvard.edu/dpinteract/

UMBER (University of Manchester Bioinformatics Education and Research), Visualisation representing All of the Proteins in the Database and Their Interactions

http://www.bioinf.man.ac.uk/resources/interact.shtml

LIGAND, Database of Chemical Compounds and Reactions in Biological Pathways

http://www.genome.ad.jp/dbget/ligand.html

MINT (Molecular Interaction Database), Database Designed to Store Functional Interactions between Biological Molecules

http://cbm.bio.uniroma2.it./mint/

CYGD (Comprehensive Yeast Genome Database), Genome for the budding Yeast Saccharomyces cerevisiae

http://mips.gsf.de/proj/yeast/CYGD/db/index.html

REBASE (The Restriction Enzyme Database), Collection of Information about Restriction Enzymes and Related Proteins

http://rebase.neb.com/rebase/rebase.html

RegulonDB, Database on Transcriptional Regulation and Operon Organization

http://www.cifn.unam.mx/Computational_Genomics/regulondb/

ReLiBase, Web-Based Tool for Searching and Analysing Receptor Ligand Structures in the PDB

http://www.ccdc.cam.ac.uk/prods/relibase

TRANSFAC, The Transcription Factor Database

http://transfac.gbf.de/TRANSFAC/

TRRD, Transcription Regulatory Region Database

http://wwwmgs.bionet.nsc.ru/mgs/dbases/trrd4/

PIMRider®, Hybrigenics' New Functional Proteomics Software Platform, Dedicated to the Exploration of Protein Pathways

http://pim.hybrigenics.com/pimrider/pimriderlobby/PimRiderLobby.jsp

BioCarta, Functional Proteomics Service

http://www.biocarta.com/

BRITE

http://www.genome.ad.jp/brite/

BioCyc, Knowledge Library of Pathways and Genomes

http://biocyc.org/

EMP Project, Enzymes and Metabolic Pathways Database

http://www.empproject.com/

GeneNet, Meta-Search System for the Analysis of Sequence Similarity

http://brac.postech.ac.kr/eng/

KEGG ( Kyoto Encyclopedia of Genes and Genomes), Bioinformatics Resource for Understanding Higher Order Functional Meanings and Utilities of the Cell or the Organism from Its Genome Information

http://www.genome.ad.jp/kegg/

LIGAND

http://www.genome.ad.jp/dbget/ligand.html

CYGD

http://mips.gsf.de/proj/yeast/CYGD/db/index.html

PFBP ( Protein Function and Biochemical Pathways), Comprehensive Resource Containing Information on Organism and Tissue Specific Metabolic and Other Biochemical Pathways

http://www.ebi.ac.uk/research/pfbp/

RegulonDB

http://www.cifn.unam.mx/Computational_Genomics/regulondb/

STKE (Signal Transduction Knowledge Environment)

http://stke.sciencemag.org/

TRRD4

http://wwwmgs.bionet.nsc.ru/mgs/dbases/trrd4/

WIT, Curation of Function Assignments Made to Genes and the Development of Metabolic Models

http://wit.mcs.anl.gov/WIT2/

dbEST, Expressed Sequence Tags database

http://www.ncbi.nlm.nih.gov/dbEST/index.html

SAGE (Serial Analysis of Gene Expression)

http://www.ncbi.nlm.nih.gov/SAGE/

UniGene, Experimental System for Automatically Partitioning GenBank Sequences into a Non-Redundant Set of Gene-Oriented Clusters

http://www.ncbi.nlm.nih.gov/UniGene/

SMD (Stanford Microarray Database), Storing Raw and Normalized Data from Microarray Experiments and Their Corresponding Image Files

http://genome-www5.stanford.edu/MicroArray/SMD/

SWISS-2DPAGE, Two-Dimensional Polyacrylamide Gel Electrophoresis Database

http://tw.expasy.org/ch2d/

SGD (Saccharomyces Genome Database), Scientific Database of the Molecular Biology and Genetics of the Yeast Saccharomyces cerevisiae ( baker's or budding yeast)

http://genome-www.stanford.edu/Saccharomyces/

PLEX (Protein Link Explorer), Constructing Phylogenetic Profiles and Searching for Gene Neighbors of All the Proteins Whose Profiles Match a Given Protein

http://apropos.icmb.utexas.edu/function-prediction.html

CAFASP

http://bioinfo.pl/cafasp/

SWISS-2DPAGE

http://tw.expasy.org/ch2d/

SWISS-PROT, Protein Knowledgebase

http://tw.expasy.org/sprot/

BRENDA, The Comprehensive Enzyme Information System

http://www.brenda.uni-koeln.de/

EVA summary for category sec(1)

http://cubic.bioc.columbia.edu/eva/sec/common.html

EVA (EValuation of Automatic protein structure)