BIOINFORMATIC WEBSITE LINKS
By S.Sivakumar
- NCBI - National Centre for Biotechnology Information - (
www.ncbi.nlm.nih.gov/Genbank )
- TIGR
Database - ( www.tigr.org/tdb/mdb/mdbcomplete.html )
- BLAST
- ( www.ncbi.nlm.gov/BLAST/ )
-
FASTA Program - ( www.ebi.ac.uk/fasta33/
)
- Pubmed - (
www.ncbi.nlm.gov/PubMed/ )
- Text Searches - (
http://chaos.swmed.edu/etblast/index.html )
- Linkage Tools - (
http://linkage.rockefeller.edu )
-
Phylip - (
http://evolution.genetocs.washington.edu/phylip.html )
- Tree of Life - (
http://tolweb.org/tree/phylogeny.html
- Array Express - (
http://www.ebi.ac.uk/arrayexpress/ )
-
Shotgun sequencing - ( www.phrap.org )
-
Single Nucleotide Substitution - (
http://droog.mht.washington.edu/PolyPhred.html )
- Genome Annotation - (
http://compbio.ornl.gov/gac/ )
-
Genie - Locate Genes - (
www.fruitfly.org/seq_tools/genie.html )
- Software List - (
www.softberry.com )
- Genetic Variation
- ( www.genome.gov )
- Virtual Cell - (
www.nrcam.uchc.edu )
- SWISS-PROT - (
http://us.expasy.org )
- PIR - (
http://pir.georgetown.edu )
- OWL
Database - (
www.hgmp.mrc.ac.uk/Bioinformatics/Databases/owl-help.html )
- PROSITE - (
www.expasy.ch/prosite )
- Protein
Family Database (Pfam) - (
www.sanger.ac.uk/software/pfam )
- Protein Data Bank - (
www.pdb.org )
- PDBSum - (
http://www.ebi.ac.uk/thornton-srv/databases/pdbsum/ )
- CATH - (
www.biochem.ucl.ac.uk/bsm/cath/
)
- SCOP - (
http://scop.mrc-lmb.cam.ac.uk/scop/ )
- EMBL - (
www.ebi.ac.uk/embl )
- UniGene - (
www.ncbi.nlm.nih.gov/UniGene/
)
- Sacchromyces Genome Database (SGD) - ( genome-www.standford.edu/Sacchromyces/
)
- Genome Databases - (
www.ebi.ac.uk/genomes/ )
- Eukaryotic Genome Annotations - Ensembl - (
www.ensembl.org )
- Genome Analysis - (
http://bioinfo.mbby.yale.edu/genome )
- Cluster of Orthologous Group
Databases - ( www.ncbi.nlm.nih.gov/COG
)
- Tumor Expression Data base - (
http://llmpp.nih.gov/lymphoma/ )
- Human Gene Data base - GeneCards - (
http://bioinformatics.weizmann.ac.il/cards/ )
- KEGG - Kyoto Encyclopedia
of Genes and Genomes - (
www.genome.ad.jp/kegg/ )
- Protein Sequencing - SAPS - (
http://www.isrec.isb-sib.ch/software/SAPS_form.html )
- DotPlot - (
www.accelrys.com/gcg )
- Codon Usage
analysis - (
www.hgmp.mrc.ac.uk/Registered/Option/codonw.html )
- ProteinProspector - (
http://prospector.ucsf.edu/ )
-
Signal Scan - Pattern searches - (
http://bimas.dcrt.nih.gov/molbio/signal/ )
- Search engine - Biological,
Agricultural and Medical Sciences - (
http://infomine.ucr.edu/cgi-bin/search?bioag )
- Search engine - Biolinks -
( www.biolinks.com )
- Searcg engine list
- ( www.searchengineguide.com )
-
Database retrieval system - DBGET - (
www.genome.ad.jp/dbget )
- Biology workbench - (
http://workbench.sdsc.edu/ )
- BioRs -
Biological data retrieval system - (
http://mips.gsf.de/projects/biors )
- Motif search - Meme/ Mast system - (
http://meme.sdsc.edu/meme/website/intro.html )
- MORGAN - Gene
Finding - (
www.tigr.org/~salzberg/morgan.html )
- Secondary structure Prediction -
nnPredict - (
http://www.cmpharm.ucsf.edu/~nomi/nnpredict-instrucs.html )
- GeneFinder -
(
http://pir.georgetown.edu/gfserver/genefind.html/ )
- Genome Databases -
GOLD - (
http://wit.integratedgenomics.com/GOLD/ )
- Completed Genomes - (
www.ebi.ac.uk/genomes/ )
- Genomic
Biology - (
http://www.ncbi.nlm.nih.gov/Genomes/ )
- Pathogenic and Model Organisms
genomes - (
www.sanger.ac.uk/Projects/Microbes/ )
- Human Genome - (
www.genome.gov )
- Human Genome Project - (
www.ornl.gov/TechResources/Human_Genome/ )
- RESTRICTION MAPS - RFLP - (
http://pgrc.ipk-gastersleben.de/rflp/rflp.html )
- STS - (
www.ncbi.nlm.nih.gov/dbSTS/ )
-
EST - ( www.ncbi.nlm.nih.gov/dbEST
)
- RH MAPPER - (
www.hgmp.mrc.ac.uk/Registered/Option/rhmapper.html )
- SEQUENCE ASSEMBLY
TOOLS - Genome Sequencing - (
www.geospiza.com/products/tools/index.htm)
- Phrap - overlapping identified
- (
www.geospiza.com/products/tools/phrap.htm )
- Phred - (
www.geospiza.com/products/tools/phred.htm )
- overlapping - Assembler 2.0 -
(
www.tigr.org/software/assembler/ )
- CAP3 - (
http://deepc2.zool.iastate.edu/aat/cap/cap.html )
- Sequencer - Sequencing
- ( www.genecodes.com )
- Accelrys
softwares - (
www.accelrys.com/products/gcg_wisconsin_package/ )
- EMBOSS Programms - (
www.hgmp.mrc.ac.uk/Software/EMBOSS/Apps/ )
- Genematcher2 - Gap opening and
penalty analysis - (
www.paracel.com/products/gm2.html )
- Local Alignment - Blitz - (
www.ebi.ac.uk/searches/blitz_input.html )
- Local Alignment - SSearch - (
www.accelrys.com/products/seqweb/program_list.html )
- Multiple Sequence
Alignment - ClustalW - (
www.ebi.ac.uk/clustalw/ )
- MSA Program - (
www.psc.edu/general/software/packages/msa )
- Pileup - (
www.accelrys.com/products/gcg_wisconsin_package/program_list.html#PileUp )
-
Pattern Induced Multiple Alignment (PIMA) - (
http://bioweb.pasteur.fr/seqanal/inter-faces/pima-simple.html )
- Multalign
- (
http://cbrg.inf.ethz.ch/Server/MultAlign.html )
- Dialign - (
www.gsf.de/biodv/dialign.html
)
- Serial Alignment by Genetic Algorithms (SAGA) - (
http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/saga_home_page.html
)
- Parallel Prrn - (
http://prrn.ims.u-tokyo.ac.jp/ )
- Hmmt - (
www.psc.edu/general/software/packages/hmmer/manual/hmmt.html )
- BlockMaker
- (
www.blocks.fhcrc.org/blockmkr/make_blocks.html )
- PHYLOGENETICS - MP -
PHYLIP DNAPARS - (
http://bioweb.pasteur.fr/cgi-bin/seqanal/dnapars.pl )
- ML - FastDNAml - (
http://bioweb.pasteur.fr/seqanal/interfaces/fastdnaml-simple.html )
-
PhyloBLAST - (
www.pathogenomics.bc.ca/phyloBLAST/ )
- PHYLIP - Phylogeny Inference
Package - (
http://evolution.genetics.washington.edu/phylip.html )
- Phylogenetic
Analysis Using Parsimony (PAUP) - (
http://paup.csit.fsu.edu )
- Phylogenetic Analysis by Maximum Likelihood -
PAML - (
http://abacus.gene.ucl.ac.uk/software/paml.html )
- Phylogenetic tree
viewer - Tree View - (
http://taxonomy.zoology.gla.ac.uk/rod/treeview.html )
- NJplot - (
http://pbil.univ-lyon1.fr/software/njplot.html )
- Single Nucleotide
Polymorphisms searches - (
www.ebi.ac.uk/snpfasta3/index.html )
- Prss Program - (
http://fasta.bioch.virginia.edu/fasta/prss.html )
- FASTA - (
http://alpha10.bioch.virginia.edu/fasta/ )
- SWAT - (
http://www.genome.washington.edu/UWGC/analysistools/Swat.cfm )
- BCM search
Launcher - (
http://searchlauncher.bcm.tmc.edu )
- Sequence Alignment and Modeling
system - SAM - (
www.cse.ucsc.edu/research/compbio/sam.html )
- meta-MEME - (
http://metameme.sdsc.edu/ )
- Gene
Prediction - GeneMark - (
www.ebi.ac.uk/genemark/ )
- Genefinding - GRAIL - (
http://compbio.ornl.gov/Grail-1.3/
)
- FindPatterns - (
www.accelrys.com/products/gcg_wisconsin_package/program_list.html#Findpatterns
)
- Frames - (
www.accelrys.com/products/gcg_wisconsin_package/ )
- Mac Vector 6.5 - (
http://www.sxst.it/oxm_mcv.htm )
-
Sequencher - (
http://www.genecodes.com/index.html )
- Testcode - (
http://www.accelrys.com/products/gcg_wisconsin_package/ )
- Procrustes - (
http://hto-13.usc.edu/software/procrustes/ )
- HMMgene - Prediction in
anonymous DNA - (
www.cbs.dtu.dk/services/HMMgene/ )
- Glimmer - (
www.tigr.org/software/glimmer/
)
- Veil System - (
www.tigr.org/~salzberg/veil.html )
- GENSCAN - (
http://genes.mit.edu/GENSCAN.html
)
- Genie - (
http://www.fruitfly.org/seq_tools/genie.html )
- SIGNAL SCAN - (
www.cbs.umn.edu/software/sigscan.html )
- GenLang - (
www.cbil.upenn.edu/genlang/genlang_home.html )
- GeneParser - (
http://beagle.colorado.edu/~eesnyder/GeneParser.html )
- GeneID - (
www1.imim.es/software/geneid/asd.html )
- PolyA Site Prediction - (
http://125.itba.mi.cnr.it/~webgene/wwwHC_polya.html )
- HCtata - (
http://125.itba.mi.cnr.it/~webgene/wwwHC_tata.html )
- MatInspector -
(
www.genomatrix.de/cgi-bin/matinspector/matinspector.pl )
- Signal sequence
search - (
http://bimas.dcrt.nih.gov/molbio/signal/ )
- Tfsitescan - (
www.ifti.org/cgi-bin/ifti/Tfsitescan.pl )
- FramePlot - (
http://watson.nih.go.jp/~jun/cgi-bin/frameplot-3.0b.pl )
- ORF Finder - (
www.ncbi.nlm.nih.gov/gorf/gorf.html )
- Exon Prediction Program - Perceval
- (
http://compbio.ornl.gov/grailexp/gxpfaq2.html )
- Repetitive Elements
Identification - RepeatMasker - (
http://ftp.genome.washington.edu/cgi-bin/RepeatMasker )
- tRNA gene
Prediction - (
www.genetics.wustl.edu/eddy/tRNAscan-SE/ )
- Microarray - Image processing
tool - (
www.scanalytics.com/product/microarray/index.html )
- Image processing tool
- Genepix - (
www.axon.com/GN_GenePixSoftware.html )
- NetAffx - (
www.affymetrix.com/analysis/index.affx )
- Xcluster - (
www.cbil.upenn.edu/epcondb/servlet/sv?page=xcluster )
- GEPAS - (
http://gepas.bioinfo.cnio.es/tools.html )
- Serial Analysis of Gene
Expression (SAGE) - ( www.sagenet.org )
-
SAGE (NCBI) - (
www.ncbi.nlm.nih.gov/SAGE/ )
- PRIMARY STRUCTURE ANALYSIS - PROWL - (
http://prowl.rockefeller.edu/aainfo/contents.htm )
- PROCHECK - (
www.biochem.ucl.ac.uk/~roman/procheck/procheck.html )
- Calcium Binding
Protein Library - (
http://structbio.vanderbilt.edu/cabp_database/cabp.html )
- Molecular
Modeling Database (MMDB) - (
www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml )
- VIEWERS - Cn3D - (
www.ncbi.nlm.nih.gov/Structure/CN3-D/cn3-D.shtml )
- Rasmol - (
www.umass.edu/micobio/rasmol/
)
- SWISS-PDB Viewer - (
http://us.expasy.org/spdbv/ )
- Kinemages - (
http://kinemage.biochem.duke.edu/kinemage/kinemage.php )
- STRUCTURE
ALIGNMENT - VAST - (
www.ncbi.nlm.nih.gov/Structure/VAST/vastsearch.html )
- DALI - (
www2.ebi.ac.uk/dali/ )
- Conserved Domain Database (CDD) - (
www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml )
- SMART - Simple
Modular Architecture Research Tool ) - (
http://smart.embl-heidelberg.de/
)
- Conserved Domain Archietecture Retrrieval Tool ( CDART) - (
www.ncbi.nlm.nih.gov/Structure/lexington/lexington.cgi?cmd=rps )
- Ligplot
- (
www.biochem.ucl.ac.uk/bsm/ligplot/ligplot.html )
- EXPASY TOOLS - (
www.expasy.org )
- PROTEIN IDENTIFICATION -
AACompIdent - (
http://us.expasy.org/tools/aacomp/ )
- TagIdent - (
http://us.expasy.org/tools/tagident.html )
- PeptIdent - (
http://us.expasy.org/tools/pepident.html )
- MultiIdent - (
http://us.expasy.org/tools/multiident/ )
- AAcompsim - (
http://us.expasy.org/tools/aacsim
)
- FindPept - (
http://ca.expasy.org/tools/findpept.html )
- PROPSEARCH - (
www.infobiosud.univmontp1.fr/SERVEUR/PROPSEARCHpropsearch.html )
- Pepsea -
http://195.41.108.38/PepSeaIntro.html )
- PepMAPPER - (
http://wolf.bms.umist.ac.uk/mapper/ )
- Mascot search - (
www.matrixscience.com/cgi/index.pl?page=/search_form_select.html )
-
Peptide Search - (
www.mann.embl-heidelberg.de/GroupPages/PageLink/peptidesearchpage.html )
-
Transmembrane region Prediction - TMAP - (
www.mbb.ki.se/tmap/ )
- TMHMM - (
www.cbs.dtu.dk/services/TMHMM/
)
- TMPRED - (
www.ch.embnet.org/software/TMPRED_form.html )
- TopPred2 - (
http://bioweb.pasteur.fr/seqanal/interfaces/toppred.html )
- PHDhtm - (
http://www.embl-heidelberg.de/predictprotein/Dtab/phd_htm.html )
- DAS - (
www.sbc.su.se/~miklos/DAS/ )
-
ComputePI/Mw - (
http://ca.expasy.org/tools/pi_tool.html )
- PeptideMass - (
www.expasy.org/tools/peptide-mass.html )
- SAPS - (
www.isrec.isb-sib.ch/software/SAPS_form.html )
- Protparam - (
http://ca.expasy.org/tools/protparam.html )
- Protscale - (
http://ca.expasy.org/cgi-bin/protscale.pl )
- PHD - (
www.embl-heidelberg.de/predictprotein/ )
- PEST - (
www.icnet.uk/LRITu/projects/pest/ )
- PESTfind - (
http://embl1.bcc.univie.ac.at/embnet/tools/bio/PESTfind/ )
- Coils - (
www.ch.embnet.org/software/COILS_form.html )
- Paircoil - (
http://nightingale.lcs.mit.edu/cgi-bin/score )
- MultiCoil - (
http://nightingale.lcs.mit.edu/cgi-bin/multicoil )
- GOR Method - (
http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_gor4.html )
- NNmethod - SIMPA96 - (
http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_simpa96.html )
- nnPredict Method - Neural network method - (
http://www.cmpharm.ucsf.edu/~nomi/nnpredict.html )
- Neural network method
- HNN - (
http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_nn.html )
- PSA - (
http://bmerc-www.bu.edu/psa/request.html )
- PsiPred - (
http://bioinf.cs.ucl.ac.uk/psipred/ )
- Self Optimized Prediction Method -
(SOPMA) - (
http://npsa-pbil.ibcp.fr/cgi-bin/npsa_automat.pl?page=npsa_sopma.html )
-
Profilescan - (
http://hits.isb-sib.ch/cgi-bin/PFSCAN/ )
- FrameProfilescan - (
www.isrec.isb-sib.ch/software/PFRAMESCAN_form.html )
- PileUp - (
http://biobase.dk/gcgmanual/pileup.html )
- LineUp - (
http://biobase.dk/gcgmanual/lineup.html )
- Pretty - (
http://biobase.dk/gcgmanual/pretty.html )
- ProfileMake - (
http://biobase.dk/gcgmanual/profilemake.html )
- ProfileSearch - (
http://biobase.dk/gcgmanual/profilesegments.html )
- ProfileGap - (
http://biobase.dk/gcgmanual/profilegap.html )
- HmmerIndex -
http://biobase.dk/gcgmanual/hmmerindex.html )
- HmmerFetch - (
http://biobase.dk/gcgmanual/hmmerfetch.html )
- Motifs - (
http://biobase.dk/gcgmanual/motifs.html )
- Conserved Pattern search -
Pratt - ( www.ebi.ac.uk/pratt/ )
-
Alignmed Segment Statistical Evaluation (ASSET) - (
http://bip.weizmann.ac.il/software/sg_software/asset.html )
- Motif search
- Hits - ( http://hits.isb-sib.ch/ )
-
MEME - (
http://meme.sdsc.edu/meme/website/intro.html )
- Gibbs - (
http://bayesweb.wadsworth.org/gibbs/gibbs.html )
- ProDom - (
http://prodes.toulouse.inra.fr/prodom/2002.1/html/form.php?typeform=SPTR )
-
PRINTS - (
http://bioin.man.ac.uk/dbbrowser/PRINTS/ )
- Pscan - (
www.hgmp.mrc.ac.uk/Software/EMBOSS/Apps/pscan.html )
- InterPro - (
www.ebi.ac.uk/interpro )
-
STRUCTURE PREDICTION - MaxHom - (
www.embl-heidelberg.de/predictprotein/predictprotein.html )
- Consensus
tool - (
www.bork.embl-heidelberg.de:8080/Alignment/consensus.html )
- MODELLER -
http://guitar.rockefeller.edu/modeller/modeller.html )
- SWISS-MODEL - (
www.expasy.org/swissmod/SWISSMODEL.html )
- 123-D+ - (
http://123-D.ncifcrf.gov/123-D+.html )
- LIBRA I - (
www.ddbj.nig.ac.jp/htmls/E-mail/libra/LIBRA_I.html )
- TOPITS - (
http://cubic.bioc.columbia.edu/predictprotein )
- Threader - (
http://bioinf.cs.ucl.ac.uk/threader/threader.html )
- ROSETTA PREDICTION -
(
www.bioinfo.rpi.edu/~bystrc/hmmstr/server.php )
- Petra - ( www-cryst.bioc.cam.ac.uk/cgi-bin/cgiwrap/charlotte/pet.cgi
)
- Inter residue contact prediction - PDGCON - (
www.pdg.cnb.uam.es:8081/pdg_contact_pred.html )
- CORNET - (
http://prion.biocomp.unibo.it/cornet.html )
- Interstrand contact
prediction - AGADIR - (
http://embl-heidelberg.de/Services/serramp/agador/agador-start.html )
-
PROTEIN FUNCTION - HNB network : (
http://dag.embl-heidelberg.de/hnb_cgi/show_overview_page.pl?MenuPath=%2Ftool_index
)
- GeneQuiz : (
http://bric.postech.ac.kr/seminar/kjh/GeneQuiz_biowave/tsld001.htm )
- EXPASY Translation Tool - (
http://ca.expasy.ch/tools/dna.html )
- Transeq - (
www.ebi.ac.uk/emboss/transeq )
- Backtranslation - (
www.entelechon.com/eng/backtranslation.html )
- TECHNIQUES IN PROTEOMICS -
2D PAGE - ( http://us.expasy.org/ch2d/
)
- HEART- 2D PAGE - (
http://userpage.chemie.fu-berlin.de/~pleiss/dhzb.html )
- Melanie 3 - (
http://us.expasy.org/melanie )
-
Protein Prospector - (
http://prospector.ucsf.edu )
- Database of Interacting Proteins - DIPTM - (
http://dip.doe-mbi.ucla.edu )
- POST
TRANSLATIONAL MODIFICATION - PSORT - (
http://psort.nibb.ac.jp )
- SignalP - (
www.cbs.dtu.dk/services/SignalP/ )
- ChloroP - (
www.cbs.dtu.dk/services/ChloroP/ )
- TargetP - (
www.cbs.dtu.dk/services/TargetP/ )
- Mitochondrial targets - Mitoprot II -
(
http://bioinformer.ebi.ac.uk/newsletter/archieves/2/mitoprotii.html )
-
Predotar - ( www.inra.fr/predotar )
-
NetOGlyc - (
www.cbs.dtu.dk/services/NetOGlyc/ )
- Big-PI Predictor - (
http://mendal.imp.univie.ac.at/sat/gpi/gpi_server.html )
- NetPhos - (
www.cbs.dtu.dk/services/NetPhos/ )
- FindMod - (
http://us.expasy.org/tools/findmod/ )
- GlycoMod - (
http://us.expasy.org/tools/glycomod/ )
- Delta Mass - (
www.abrf.org/index.cfm/dm.home
)
- Scansite - (
http://scansite.mit.edu )
- PATHWAYS - Regulon DB - (
www.cifn.unam.mx/Computational_Genomics/regulondb/ )
- WIT - (
http://wit.mcs.anl.gov/WIT2/ )
- UM
BBD - ( http://umbbd.ahc.umn.edu )
-
EcoCyc - ( www.ecocyc.org )
- MetaCyc - (
http://biocyc.org/metacyc )
- Enzymes
and Metabolic Pathways - (
http://emp.mcs.anl.gov )
- BRITE - (
www.genome.ad.jp/brite )
- GeNet -
(
www.csa.ru/Inst/gorb_dep/inbios/genet/genet.htm )
- GenePath - (
http://magix.fri.uni-lj.si/genepath )
- Cell Signalling Networks Database (
CSNDB) - ( http://geo.nihs.go.jp/csndb/
)
- GenMAPP - ( www.genmapp.org )
-
BioMiner-
www.zbi.uni-saarland.de/chair/projects/BioMiner/index.shtml )
- Signalling
Pathway Database (SPAD) - (
www.grt.kyushu-u.ac.jp/spad/ )
- GSCope - (
http://gscope.gsc.riken.go.jp )
-
Pathway Studio - (
www.ariadnegenomics.com/products/pathway.html )
- Pathtracker - (
http://ocimumbio.com/products/products_pt.htm )
- Metabolic Networks -
Fractal Genomics - (
www.fractalgenomics.com/technology/index.html )
- Metabolic control
Analysis - Gepasi - (
www.gepasi.org/gepasi.html )
- Winscamp - (
www.cds.caltech.edu/~hsauro/Scamp/scamp.htm )
- SIMULATION OF CELLULAR
ACTIVITIES - E-Cell - ( www.e-cell.org/ )
-
Virtual Cell - (
www.nrcam.uchc.edu/index.html )
- BIOLOGICAL MARKUP LANGUAGES - CellML -
( www.ce..ml.org/ )
- Bioinformatic
Sequence Markup Language (BSML) - (
www.labbook.com/products/xmlbsml.asp )
- Biopolymer Markup Language (BIOML)
- ( www.bioml.com/ )
- Chemical Markup
Language (CML) - ( www.xml-cml.org/ )
-
Gene Expression Markup Language (GEML) - (
www.rosettabio.com/products/conductor/geml/default.htm )
- GeneXML - (
www.ncgr.org/genex/genexml.html
)
- General Feature Format (GFF) - (
www.sanger.ac.uk/Software/formats/GFF/ )
- OMG's Life Sciences Project - (
www.omg.org/homepage/lsr/ )
-
eXtensible Multi Dimensional Simulator ( XMDS) - (
www.physics.uq.edu.au/xmds/ )
-
Extensible Scientific Interchange Language - (
www.cacr.caltech.edu/SDA/xsil/
)
- Ligand Protein Data Base (LPDB) - (
http://lpdb.scripps.edu/ )
- Standard Genetic Code - (
http://micro.nwfsc.noaa.gov/protocols/genecode.html )
- Finding siRNA in
m-RNA - siRNA - (
www.hgmp.mrc.ac.uk/Software/EMBOSS/Apps/sirna.html )
- DOCKING - Biognostik
- (
www.biocan.com/mbio/antisens.htm )
- Soma Logic - (
www.somalogic.com )
- Aptamer database -
( http://aptamer.icmb.utexas.edu/
)
- SELEX - (
www.archemix.com/tech_aptsel.html )
- Affymax - (
www.affymax.com )
- Selectide - (
www.selectide.com )
- Lion Biosciences -
( www.lionbiosciences.com )
-
Available Chemicals Directory (ACD) - ( www.mdl.com
)
- Cambridge Structural Database (CSD) - (
www.ccdc.cam.ac.uk/prods/csd/csd.html )
- Comprehensive Medicinal Chemistry
database (CMC) - (
http://joel.mdli.com/products/knowledge/medicinal_chem/index.jsp )
- World
Drug Index (WDI) - (
www.daylight.com/daycgi/wdi/ )
- PROCHECK - (
www.biochem.ucl.ac.uk/~roman/procheck/procheck.html )
- G-Protein coupled
Receptors - ( www.gpcr.org/7tm/ )
-
ClogP - (
www.biobyte.com/bb/prod/clogp40.html ) or (
www.daylight.com/daycgi/clogp
)
- Conformers - (
www.accelrys.com/cerius2/conformers.html )
- Rubicon - (
www.daylight.com/products/rubicon.html )
- DISCOtech - (
www.tripos.com/sciTech/inSillicoDisc/pharmaPerception/discotech.html )
-
Oxford Molecular tool - oxmol - (
www.accelrys.com/about/oxmol.html )
- Molecular Graphics - (
http://scsg9.unige.ch/fln/eng/toc.html )
- Molecular Modelling toolbox - (
http://webnet.mednet.gu.se/chemistry/molmod/ )
- XED - (
www.ch.cam.ac.uk/SGTL/xed/ )
-
AutoDock - (
www.scripps.edu/pub/olson-web/doc/autodock/ )
- Dock - (
http://dock.compbio.ucsf.edu/ )
-
LUDI - (
http://www.accelrys.com/cerius2/c2ludi.html )
- ADME - (
www.accelrys.com/pharma/cheminformatics/adme.html )
- TOPKAT - (
www.accelrys.com/products/topkat/ )
- DDBJ - (
www.ddbj.nig.ac.jp )
-
MIPS ALERT - (
www.mips.biochem.mpg.de/mips/programs/alert.html)
WHATIF SERVER - ( http://swift.cmbi.kun.nl/WIWWWI/
)