Programs and World Wide Web servers useful in comparative modeling.

Original links collection at: http://guitar.rockefeller.edu/tools/

Name	Type^a	World Wide Web address^b
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://guitar.rockefeller.edu/modbase/`
PDB	S	`http://www.rcsb.org/pdb/`
PRESAGE	S	`http://presage.berkeley.edu/`
PSI	S	`http://www.structuralgenomics.org/`
SCOP	S	`http://scop.mrc-lmb.cam.ac.uk/scop/`
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/`
FastA	S	`http://www.ebi.ac.uk/fasta3/`
FUGUE	S	`http://www-cryst.bioc.cam.ac.uk/~fugue`
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`
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/`
MULTALIN	S	`http://pbil.ibcp.fr/`
MODELING
3D-JIGSAW	S	`http://www.bmm.icnet.uk/people/paulb/3dj/form.html`
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.msi.com`
MODELLER	P	`http://guitar.rockefeller.edu/modeller/modeller.html`
LOOK	P	`http://www.mag.com`
QUANTA (b)	P	`http://www.msi.com`
SYBYL (c)	P	`http://www.tripos.com`
SCWRL	P	`http://www.cmpharm.ucsf.edu/~bower/scwrl/scwrl.html`
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/pub/ANOLEA.html`
AQUA	P	`http://www-nmr.chem.ruu.nl/users/rull/aqua.html`
BIOTECH^d	S	`http://biotech.embl-ebi.ac.uk:8400/`
ERRAT	S	`http://www.doe-mbi.ucla.edu/errat_server.html`
PROCHECK	P	`http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html`
ProsaII^e	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/`
META-PP	S	`http://cubic.bioc.columbia.edu/pp/doc/meta_intro.html`
SearchLauncher	S	`http://www.hgsc.bcm.tmc.edu/SearchLauncher/`
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.