|\/| () |-| ! T: database and tool 4 modeling

Table 1: Common uses of comparative protein structure models. A list of our papers using MODELLER to address practical problems in collaboration with experimentalists can be obtained at URL http://guitar.rockefeller.edu/publications/ref/ref.html.

Designing (site-directed) mutants to test hypotheses about function

Identifying active and binding sites

Searching for ligands of a given binding site

Designing and improving ligands of a given binding site

Modeling substrate specificity

Predicting antigenic epitopes

Protein-protein docking simulations

Inferring function from calculated electrostatic potential around the protein

Molecular replacement in X-ray structure refinement

Refining models against NMR dipolar coupling data

Testing a given sequence - structure alignment

Rationalizing known experimental observations

Planning new experiments

Table 2: Web sites useful for comparative modeling.

Databases
NCBI	www.ncbi.nlm.nih.gov/
PDB	www.rcsb.org/
MSD	www.rcsb.org/databases.html
CATH	www.biochem.ucl.ac.uk/bsm/cath/
TrEMBL	srs.ebi.ac.uk/
SCOP	scop.mrc-lmb.cam.ac.uk/scop/
PRESAGE	presage.stanford.edu
MODBASE	guitar.rockefeller.edu/modbase/
GeneCensus	bioinfo.mbb.yale.edu/genome
GeneBank	www.ncbi.nlm.nih.gov/Genbank/GenbankSearch.html
PSI	www.structuralgenomics.org
Template search, fold assignment
PDB-Blast	bioinformatics.burnham-inst.orgpdb_blast
BLAST	www.ncbi.nlm.nih.gov/BLAST/
FastA	www.dna.affrc.go.jp/htdocs/Blast/fasta.html
DALI	www2.ebi.ac.uk/dali/
PhD, TOPITS	www.embl-heidelberg.de/predictprotein/predictprotein.html
THREADER	insulin.brunel.ac.uk/
123D	genomic.sanger.ac.uk/123D/run123D.html
UCLA-DOE	www.doe-mbi.ucla.edu/people/frsvr/frsvr.html
PROFIT	lore.came.sbg.ac.at/
MATCHMAKER	www.tripos.com/software/mm.html
3D-PSSM	www.bmm.icnet.uk/ 3dpssm/html/ffrecog.html
BIOINGBGU	www.cs.bgu.ac.il/ bioinbgu/
FUGUE	www-cryst.bioc.cam.ac.uk/ fugue
LOOPP	ser-loopp.tc.cornell.edu/loopp.html
FASS	bioinformatics.burnham-inst.org/FFAS/index.html
SAM-T99/T98	www.cse.ucsc.edu/research/compbio/sam.html

Comparative modeling
3D-JIGSAW	www.bmm.icnet.uk/servers/3djigsaw/
CPH-Models	www.cbs.dtu.dk/services/CPHmodels/
COMPOSER	www-cryst.bioc.cam.ac.uk/
FAMS	physchem.pharm.kitasato-u.ac.jp/FAMS/fams.html
MODELLER	guitar.rockefeller.edu/modeller/modeller.html
PrISM	honiglab.cpmc.columbia.edu/
SWISS-MODEL	www.expasy.ch/swissmod/SWISS-MODEL.html
SDSC1	cl.sdsc.edu/hm.html
WHAT IF	www.cmbi.kun.nl/bioinf/predictprotein/
ICM	www.molsoft.com/
SCWRL	www.fccc.edu/research/labs/dunbrack/scwrl/
InsightII	www.accelrys.com
SYBYL	www.tripos.com
Model evaluation
PROCHECK	www.biochem.ucl.ac.uk/~roman/procheck/procheck.html
WHATCHECK	www.cmbi.kun.nl/swift/whatcheck/
ProsaII	www.came.sbg.ac.at
BIOTECH	biotech.embl-ebi.ac.uk:8400/
VERIFY3D	www.doe-mbi.ucla.edu/Services/Verify_3D/
ERRAT	www.doe-mbi.ucla.edu/Services/Errat.html
ANOLEA	guitar.rockefeller.edu/ fmelo/anolea/anolea.html
AQUA	urchin.bmrb.wisc.edu/ jurgen/Aqua/server/
SQUID	www.yorvic.york.ac.uk/~oldfield/squid
PROVE	www.ucmb.ulb.ac.be/UCMB/PROVE/