Table 1 Useful servers and programs for protein comparive modeling.

Template Selection

PSI-BLAST

http://www.ncbi.nlm.nih.gov/BLAST/

[20]

HMMER (HMM search)

http://bio.ifom-firc.it/HMMSEARCH/

[35]

TOPITS

http://www.embl-heidelberg.de/predictprotein/submit_adv.html

[17]

FUGUE

http://www-cryst.bioc.cam.ac.uk/~fugue/prfsearch.html

[26]

Threader

http://bioinf.cs.ucl.ac.uk/threader/

[27]

3D-PSSM

http://www.sbg.bio.ic.ac.uk/~3dpssm/

[28]

PFAM

http://www.sanger.ac.uk/Software/Pfam/

[25]

PHYLIP

http://evolution.genetics.washington.edu/phylip.html

[31]

Target-Template alignment

CLUSTALW

http://www.ebi.ac.uk/clustalw/

[34]

HMMER (HMM align)

http://bio.ifom-firc.it/HMMSEARCH/

[35]

STAMP

http://bioinfo.ucr.edu/pise/stamp.html

[36]

CE

http://cl.sdsc.edu

[37]

DSSP

http://bioweb.pasteur.fr/seqanal/interfaces/dssp-simple.html

[38]

Model Building

COMPOSER

http://www-cryst.bioc.cam.ac.uk

[39]

SwissModel

http://swissmodel.expasy.org/

[41]

3D-JIGSAW

http://www.bmm.icnet.uk/servers/3djigsaw/

[44]

MODELLER

http://salilab.org/modeller/

[46]

Loop Modeling

MODLOOP

http://alto.compbio.ucsf.edu/modloop//modloop.html

[50]

ARCHDB

http://sbi.imim.es/cgi-bin/archdb/loops.pl

[51]

Sloop

http://www-cryst.bioc.cam.ac.uk/~sloop/Browse.html

[52]

Sidechain Modeling

WHAT IF

http://swift.cmbi.kun.nl/whatif/

[55]

SCWRL

http://dunbrack.fccc.edu/SCWRL3.php

[56]

Evaluation of the model

PROCHECK

http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html

[67]

PROSA II

http://www.came.sbg.ac.at/

[70]

Biotech

http://biotech.ebi.ac.uk:8400/

Refinement

GROMOS

http://www.igc.ethz.ch/gromos/

[74]

CHARMM

http://www.charmm.org/

[75]

AMBER

http://amber.scripps.edu/

[76]