UCSF Laboratory of Andrej Sali QB3

Programs and World Wide Web servers useful in comparative modeling

  Typea URLb

DATABASES
CATH S http://www.biochem.ucl.ac.uk/bsm/cath/
DBAli S http://www.salilab.org/DBAli/
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/
PSI S http://www.nigms.nih.gov/psi/
Sacch3D 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
UniProtKB S http://www.uniprot.org/

FOLD ASSIGNMENT
123D S http://123d.ncifcrf.gov/
3D-PSSM S http://www.sbg.bio.ic.ac.uk/~3dpssm/
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://fold.doe-mbi.ucla.edu/
FUGUE S http://www-cryst.bioc.cam.ac.uk/~fugue/
LOOPP S http://ser-loopp.tc.cornell.edu/cbsu/loopp.htm
PDB-BLast/FASS S http://bioinformatics.ljcrf.edu/pdb_blast/
PHD, TOPITS S http://www.predictprotein.org/
PROFIT P http://www.came.sbg.ac.at/
SAM-T99/T98 S http://www.cse.ucsc.edu/research/compbio/HMM-apps/
THREADER S http://bioinf.cs.ucl.ac.uk/threader/
UCLA-DOE FRSVR S http://fold.doe-mbi.ucla.edu/

SEQUENCE ALIGNMENT
BCM SERVER S http://searchlauncher.bcm.tmc.edu
BLAST2 S http://www.ncbi.nlm.nih.gov/blast/bl2seq/wblast2.cgi
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://prodes.toulouse.inra.fr/multalin/multalin.html

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
TIGERFAMS S http://www.tigr.org/TIGRFAMs/index.shtml
ICM (a) P http://www.molsoft.com/
InsightII (b) P http://www.accelrys.com/
MODELLER P http://salilab.org/modeller/modeller.html
ModWeb S http://salilab.org/modweb
QUANTA (b) P http://www.accelrys.com/
SYBYL (c) P http://www.tripos.com/
SCWRL P http://dunbrack.fccc.edu/SCWRL3.php
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://protein.bio.puc.cl/cardex/servers/index.html
BIOTECHd S http://biotech.embl-ebi.ac.uk:8400/
CAFASP S http://bioinfo.pl/cafasp/
ERRAT S http://www.doe-mbi.ucla.edu/Services/ERRATv2/
EVA S http://cubic.bioc.columbia.edu/eva/
LiveBench S http://bioinfo.pl/LiveBench/
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
VERIFY3D S http://www.doe-mbi.ucla.edu/Services/Verify_3D/
WHATCHECK P http://www.sander.embl-heidelberg.de/whatcheck/

COMPARATIVE AND DOCKING MODEL ASSESSMENT
CLUSPRO S http://nrc.bu.edu/cluster/cluspro_v1.cgi
COMBINATORIAL_EXTENSION S http://cl.sdsc.edu/ce.html
DFIRE S http://sparks.informatics.iupui.edu/hzhou/dfire.html
FASTCONTACT S http://structure.pitt.edu/servers/fastcontact/
FIBERDOCK S http://bioinfo3d.cs.tau.ac.il/FiberDock/
METAMQAPII S https://genesilico.pl/toolkit/unimod?method=MetaMQAPII
MODFOLD S http://www.reading.ac.uk/bioinf/ModFOLD/ModFOLD_form_2_0.html
GENTHREADER S http://bioinf4.cs.ucl.ac.uk:3000/psipred/
PCONS S http://pcons.net/
PROQ S http://www.sbc.su.se/~bjornw/ProQ/ProQ.html
PROSA-WEB S https://prosa.services.came.sbg.ac.at/prosa.php
QMEAN S http://swissmodel.expasy.org/qmean/cgi/index.cgi
RAMPAGE S http://mordred.bioc.cam.ac.uk/~rapper/rampage.php
TASSER S http://zhanglab.ccmb.med.umich.edu/I-TASSER/
TM-SCORE S http://zhanglab.ccmb.med.umich.edu/TM-score/
VERIFY3D S http://nihserver.mbi.ucla.edu/Verify_3D/

OTHERS...
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 software package that includes PROSAII, PROFIT and PROSUP, a structure comparison program.

Andrej Sali, PhD, Professor, Department of Bioengineering and Therapeutic Sciences; Department of Pharmaceutical Chemistry; School of Pharmacy, University of California at San Francisco, UCSF MC 2552, Mission Bay, Byers Hall, 1700 4th Street, Suite 503B, San Francisco, CA 94158-2330, Tel +1 (415) 514-4227, Fax +1 (415) 514-4231, 4234, , Web http://www.salilab.org, Assistant: Ms. Hilary Mahon, Email: , Tel +1 (415) 514-4228, Lab +1 (415) 514-4258, 4233