Table 4. Software for protein sequence and tertiary structure analysis.

Software	Portable Version	Description	URL
BLASTp	Yes	Pairwise sequence alignment comparing a query protein sequence with a database of protein sequences	http://blast.ncbi.nlm.nih.gov/Blast.cgi
CLUSTALW	Yes	Multiple sequence alignment comparing a number of protein sequences	http://www.ebi.ac.uk/Tools/msa/clustalw2/
AL2CO	Yes	Quantification of conservation index at each aligned position in a multiple sequence alignment	http://prodata.swmed.edu/al2co/al2co.php
VMD	Yes	Molecular visualization for displaying, animating, and analyzing large biomolecular systems using 3D graphics	http://www.ks.uiuc.edu/Research/vmd/
PSI-PRED	Yes	Prediction secondary structure from amino acid sequence	http://bioinf.cs.ucl.ac.uk/psipred/
MODELLER	Free for academics, but commercial versions are also available.	Homology modeling of protein 3D structures. An option to introduce single point mutations in the target protein to obtain its 3D model is also included.	http://www.salilab.org/modeller/
SWISS-MODEL	No	Automated comparative modeling of 3D protein structures	http://swissmodel.expasy.org/
GROMACS	Yes	Molecular dynamics simulations	http://www.gromacs.org/

3D, three-dimensional.