Weblinks

General

Protein Sequence Analysis - A www tutorial by T. Attwood (University of Manchester)
http://www.bioinf.man.ac.uk/dbbrowser/bioactivity/prefacefrm.html

Manchester Bioinformatics Education and Research Resources
http://www.bioinf.man.ac.uk/resources/

NCBI, National Center for Biotechnology information (USA)
http://www.ncbi.nih.gov/Sitemap/index.html

Entrez - Search and retrieval system at NCBI
http://www.ncbi.nih.gov/Entrez/

MIPS, Munich Information Center for Protein Sequences
http://mips.gsf.de/

Sanger Centre, Cambridge (UK)
http://www.sanger.ac.uk/Info/

EMBL, European Molecular Biology Laboratory (Germany)
http://www.embl-heidelberg.de

Overview of cheminformatics tools
http://www.msg.ku.edu/~msg/mgm.html

UK-QSAR Homepage
http://www.iainm.demon.co.uk/indexnew.htm

Glossary of Terms used in Medicinal Chemistry
http://www.chem.qmul.ac.uk/iupac/medchem/

IUPAC Compendium of Chemical Terminology - the Gold Book
http://goldbook.iupac.org

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Major Sequence Repositories

Ensembl Genome Browser
http://www.ensembl.org/

NCBI Reference Sequences
http://www.ncbi.nlm.nih.gov/RefSeq/

UCSC Genome Browser
http://genome.ucsc.edu/cgi-bin/hgGateway/

UniGene: An Organized View of the Transcriptome
http://www.ncbi.nlm.nih.gov/UniGene/

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Prediction Tools

PredictProtein Service
http://www.predictprotein.org/

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

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

SigPred - Signal Peptide Prediction
http://bioinformatics.leeds.ac.uk/prot_analysis/Signal.html

Helical Wheel Plot
http://cti.itc.virginia.edu/~cmg/Demo/wheel/wheelApp.html

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Cheminformatics Tools

CDK, Chemistry Development Kit
http://cdk.sourceforge.net

MEQI, Molecular Scaffold Analysis
http://www.pannanugget.com

PowerMV, Cheminformatics Toolkit
http://www.niss.org/PowerMV/

Rweb
http://www.math.montana.edu/Rweb/Rweb.general.html

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QSAR and molecular descriptor programs

Molinspiration toolkits - Java Based software and online calculations of fragments and basic properties/descriptors
http://www.molinspiration.com/

PEST - Shape/Property hybrid descriptor technology, representation of intermolecular interactions
http://www.chem.rpi.edu/chemweb/recondoc/pest.html

QSAR Builder - generate and evaluate QSAR and QSPR models
http://ap-algorithms.com/qsar_builder.htm

ShapeSig - Shape descriptors and statistical analysis
http://histidine.umdnj.edu/~shape/

Virtual Computational Chemistry Laboratory
http://www.vcclab.org

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Molecular Viewers

ACD/3D Viewer
http://www.acdlabs.com/products/chem_dsn_lab/chemsketch/3d/

Chem3D
http://www.cambridgesoft.com

Chime
http://www.mdlchime.com

MOE
http://www.chemcomp.com

MolMol
http://www.mol.biol.ethz.ch/wuthrich/software/molmol/

JME Molecular Editor
http://www.molinspiration.com/jme/

Jmol
http://jmol.sourceforge.net

Ortep-3
http://www.chem.gla.ac.uk/~louis/software/ortep3/index.html

RasMol - OpenRasMol
http://www.umass.edu/microbio/rasmol/
http://openrasmol.org/

Swiss-PdbViewer
http://www.expasy.org/spdbv/index.html

UltraMol
http://www.compuchem.com/ultra1.htm

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Databases

CATH - classification of proteins based on structural similarity
http://cathwww.biochem.ucl.ac.uk/latest/

FingerPRINTScan - Sequence fingerprint search (in PRINTS)
http://bioinf.man.ac.uk/dbbrowser/fingerPRINTScan/

IUPHAR Receptor Database
http://www.iuphar-db.org/latest.jsp

Macromolecular Structure Database (MSD) Search at EBI
http://www.ebi.ac.uk/msd/Services.html

Molecule Pages: A comprehensive signaling database
http://www.signaling-gateway.org/molecule/

PRINTS - Protein motif fingerprint database
http://bioinf.man.ac.uk/dbbrowser/PRINTS/PRINTS.html

PROSITE pattern search
http://www.ebi.ac.uk/ppsearch/

Pfam - multiple sequence alignments & HMM models
http://pfam.cgb.ki.se/

Protein Database (PDB)
http://www.rcsb.org/pdb/

RAPID - DNA database searching tool
http://www.bioinf.man.ac.uk/rapid/index.html

SCOP - classification of proteins based on structural similarity
http://scop.mrc-lmb.cam.ac.uk/scop/

Sequence retrieval system (SRS)
http://srs6.ebi.ac.uk

Summaries and structural analyses of PDB data files
http://www.biochem.ucl.ac.uk/bsm/pdbsum/

Swissprot - protein sequences with good annotations
http://www.expasy.org/sprot/

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Information Retrieval

ChemWeb
http://www.chemweb.com

ChemFinder
http://chemfinder.cambridgesoft.com/

Electronic Journals Library
http://rzblx1.uni-regensburg.de/ezeit/

Elsevier ScienceServer
http://else.hebis.de/

SciFinder Scholar
http://www.chemie.uni-frankfurt.de/OCCB/scifinder/scifinder.html

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Server

European Bioinformatics Institute (EBI)
http://www.ebi.ac.uk/ebi_home.html

Center for Biological Sequence Analysis (CBS), Denmark
http://www.cbs.dtu.dk

Swiss Institute of Bioinformatics (SIB), Switzerland
http://www.isb-sib.ch

EMBL computational services
http://www.embl-heidelberg.de/Services/index.html

GenomeNet, Japan
http://www.genome.ad.jp

Center for Scientific Computing (CSC), Frankfurt
http://www.csc.uni-frankfurt.de

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Alignment

ALIGN - Alignment compendium
http://bioinf.man.ac.uk/dbbrowser/ALIGN/

BLAST - pairwise local sequence alignemt
http://www.ncbi.nlm.nih.gov/BLAST/

CE ALIGN - 3D protein alignment
http://cl.sdsc.edu/ce/ce_align.html

CINEMA - Colour INteractive Editor for Multiple Alignments
http://bioinf.man.ac.uk/dbbrowser/CINEMA2.1/

CLUSTALW - multiple sequence alignemt
http://www.ebi.ac.uk/clustalw/

EMBOSS - basic protein sequence analysis
http://www.ebi.ac.uk/emboss/

FASTA - pairwise local sequence alignemt
http://www.ebi.ac.uk/fasta3/

MPsrch - pairwise sequence alignment implementing the Smith-Waterman algorithm
http://www.ebi.ac.uk/MPsrch/

Phylo_win - molecular phylogenetic inference
http://pbil.univ-lyon1.fr/software/phylowin.html

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Tutorials

Protein Sequence Analysis - A www tutorial by T. Attwood (University of Manchester)
http://www.bioinf.man.ac.uk/dbbrowser/bioactivity/prefacefrm.html

Self-organizing neural networks demo, University of Bochum
http://www.neuroinformatik.ruhr-uni-bochum.de/ini/VDM/research/gsn/DemoGNG/GNG

Principles of protein structure, Birkbeck College
http://pps.cryst.bbk.ac.uk/index.html

Computational biology course, University of Washington
http://www.cs.washington.edu/education/courses/590bi/

Tutorial on Multivariate Techniques (Manchester Metropolitan University)
http://149.170.199.144/multivar/intro.htm

Neural Java (Neural Network Tutorial, EPFL)
http://lcn.epfl.ch/tutorial/english/

"Bioinformatics Tutorial" (University Bielefeld)
http://www.techfak.uni-bielefeld.de/bcd/welcome.html

"UNIMOLIS - Course on Molecular Symmetry and Isomerism" (University Bayreuth)
http://unimolis.uni-bayreuth.de

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