Predicting Protein Function and Structure Using Bioinformatics Protocols: A Case Study of the SAND Protein Family - Essays in Bioinformatics - page 163

Table 1. Tools for sequence similarity searches and the sequence retrieval system
(SRS). The servers permit searches against one or more databases.

Software Reference URL

BLAST [1] http://www.ncbi.nlm.nih.gov/BLAST/

PSI-BLAST [1] http://www.ncbi.nlm.nih.gov/BLAST/

HMMER [2] UK (http://www.sanger.ac.uk/ Software/Pfam/)

USA (http://pfam.wustl.edu/)
France (http://pfam.jouy.inra.fr/)
Sweden (http://Pfam.cgb.ki.se/)

SRS [3] http://srs.ebi.ac.uk/

Table 2. Servers to perform secondary structure, solvent accessibility and fold
prediction.

Software Reference URL

Secondary structure
JPRED [4] http://www.compbio.dundee.ac.uk/~www-jpred/

PHD [5] http://www.embl-heidelberg.de/predictprotein/predictprotein.html

Protein fold prediction
PHD (TOPITS) [5] http://www.embl-heidelberg.de/predictprotein/predictprotein.html

GenThreader [6] http://bioinf.cs.ucl.ac.uk/psipred/psiform.html

FUGUE [7] http://www-cryst.bioc.cam.ac.uk/servers.html

3D-PSSM [8] http://www.sbg.bio.ic.ac.uk/~3dpssm/

PRIDE [9] http://www.icgeb.org/pride/

MetaServer [10] http://bioinfo.pl/meta/

MetaServer [11] http://genesilico.pl/meta/

Table 3. Tools for comparative modelling of protein structures. The key to the
symbols used in the table are as follows; * refers to restraint based molecular
modelling methods and refers to rigid body fragment assembly methods.

Software Reference URL

Academic versions
COMPOSER^

[12,13] http://www-cryst.bioc.cam.ac.uk/

Modeller* [14] http://salilab.org/modeller/

WhatIF ¶

[15] http://www.cmbi.kun.nl/whatif/

SwissModel ¶

[16] http://swissmodel.expasy.org

Commercial
Modeller*

- http://www.accelrys.com/

Homology ¶ - http://www.accelrys.com/

QUANTA - http://www.accelrys.com/

SYBYL - http://www.tripos.com/

COMPOSER^ - http://www.tripos.com/