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MODELLER WORKSHOP LINKS

Name Typea World Wide Web addressb
DATABASES
CATH S http://www.biochem.ucl.ac.uk/bsm/cath/
GenBank S http://www.ncbi.nlm.nih.gov/Genbank/GenbankSearch.html
GeneCensus S http://bioinfo.mbb.yale.edu/genome
MODBASE S http://salilab.org/modbase/ 
MSD S http://www.rcsb.org/databases.html
NCBI S http://www.ncbi.nlm.nih.gov/
PDB S http://www.rcsb.org/pdb/
PRESAGE S http://presage.berkeley.edu/
PS S http://www.structuralgenomics.org/
Sacch3 S http://genome-www.stanford.edu/Sacch3D/
SCOP S http://scop.mrc-lmb.cam.ac.uk/scop/
TIGR S http://www.tigr.org/tdb/mdb/mdbcomplete.html
TrEMBL S http://srs.ebi.ac.uk/
FOLD ASSIGNMENT
123D S http://www.lecb.ncifcrf.gov/~nicka/123D.html
3D-PSSM S http://www.bmm.icnet.uk/~3dpssm/html/ffrecog.html
BIOINBGU S http://www.cs.bgu.ac.il/~bioinbgu/
BLAST S http://www.ncbi.nlm.nih.gov/BLAST/
DALI S http://www2.ebi.ac.uk/dali/
FASS S http://bioinformatics.burnham-inst.org/FFAS/index.html
FastA S http://www.ebi.ac.uk/fasta3/
FRSVR S http://www.doe-mbi.ucla.edu/~frsvr/preds/MG/MG.html
FUGUE S http://www-cryst.bioc.cam.ac.uk/~fugue
Koonin Group S ftp://ncbi.nlm.nih.gov/pub/koonin/FOLDS/index.html
LOOPP S http://www.tc.cornell.edu/reports/NIH/resource/CompBiologyTools/loopp/
PDB-BLast/FASS S http://bioinformatics.ljcrf.edu/pdb_blast/
PHD, TOPITS S http://www.embl-heidelberg.de/predictprotein/predictprotein.html
PROFIT P http://www.came.sbg.ac.at
SAM-T99/T98 S http://www.cse.ucsc.edu/research/compbio/HMM-apps/
THREADER S http://insulin.brunel.ac.uk/threader/threader.html
ToPLign/123D S http://cartan.gmd.de/Genome/
UCLA-DOE FRSVR S http://www.doe-mbi.ucla.edu/people/frsvr/frsvr.html
SEQUENCE ALIGNMENT
BCM SERVER S http://dot.imgen.bcm.tmc.edu:9331/multi-align/multi-align.html
BLAST2 S http://www.ncbi.nlm.nih.gov/gorf/bl2.html
BLOCK MAKER S http://blocks.fhcrc.org/blocks/blockmkr/make_blocks.html
CLUSTALW S http://www2.ebi.ac.uk/clustalw/
FASTA3 S http://www2.ebi.ac.uk/fasta3/
Gerstein Group S http://bioinfo.mbb.yale.edu/Align/
MULTALIN S http://pbil.ibcp.fr/
MODELING
3D-JIGSAW S http://www.bmm.icnet.uk/servers/3djigsaw/
CPH-Models S http://www.cbs.dtu.dk/services/CPHmodels/
COMPOSER P http://www-cryst.bioc.cam.ac.uk/
CONGEN P http://www.congenomics.com/congen/congen.html
DRAGON P http://mathbio.nimr.mrc.ac.uk/aaszodi/ug.html
FAMS S http://physchem.pharm.kitasato-u.ac.jp/FAMS/fams.html
ICM (a) P http://www.molsoft.com
InsightII (b) P http://www.accelrys.com/
MODELLER P http://salilab.org/modeller/modeller.html
QUANTA (b) P http://www.accelrys.com/
SYBYL (c) P http://www.tripos.com
SCWRL P http://www.fccc.edu/research/labs/dunbrack/scwrl/
SDSC1 S http://cl.sdsc.edu/hm.html
SWISS-MODEL S http://www.expasy.ch/swissmod/SWISS-MODEL.html
WHAT IF P http://www.cmbi.kun.nl/whatif/
MODEL EVALUATION
ANOLEA S http://www.fundp.ac.be/sciences/biologie/bms/CGI/anolea.html
AQUA P http://urchin.bmrb.wisc.edu/~jurgen/aqua/
BIOTECHd S http://biotech.embl-ebi.ac.uk:8400/
CAFASP1 S http://www.cs.bgu.ac.il/~dfischer/cafasp1/cafasp1.html
ERRAT S http://www.doe-mbi.ucla.edu/errat_server.html
PROCHECK P http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html
ProsaIIe P http://www.came.sbg.ac.at
PROVE S http://www.ucmb.ulb.ac.be/UCMB/PROVE
SQUID P http://www.yorvic.york.ac.uk/~oldfield/squid
VERIFY3D S http://www.doe-mbi.ucla.edu/verify3d.html
WHATCHECK P http://www.sander.embl-heidelberg.de/whatcheck/
META SERVERS
BioInfo S http://BioInfo.PL/meta/
Bork Group S http://dove.embl-heidelberg.de/3D/
CASP S http://predictioncenter.llnl.gov/
GeneQuiz II S http://columba.ebi.ac.uk:8765/ext-genequiz/
Gerstein Group S http://bioinfo.mbb.yale.edu/genome/
META-PP S http://cubic.bioc.columbia.edu/pp/doc/meta_intro.html
PEDANT S http://pedant.gsf.de/
SearchLauncher S http://searchlauncher.bcm.tmc.edu/
WorkBench S http://workbench.sdsc.edu/

aS, server; P, program.
bSome of the sites are mirrored on additional computers.
c(a) MolSoft Inc., San Diego. (b) Molecular Simulations Inc., San Diego. (c) Tripos Inc., St Louis.
dThe BIOTECH server uses PROCHECK and WHATCHECK for structure evaluation.
eProCyon is a new software package that includes PROSAII, PROFIT and PROSUP, a structure comparison program.

 

Last modified: June 2004