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.