BLAST is a set of similarity search programs designed to explore all of the available sequence databases regardless of whether the query is protein or DNA. It uses a heuristic algorithm which seeks local as opposed to global alignments, and is therefore able to detect relationships among sequences which share only isolated regions of similarity. It can be run locally as a full executable, and can be used to run BLAST searches against private, local databases, or downloaded copies of the NCBI databases. It runs on Mac OS, Win32, LINUX, Solaris, IBM AIX, SGI, Compaq OSF, and HP- UX systems.
Visualization of Protein Ligand Graphs (VPLG) uses a graph-based model to describe the structure of proteins on the super-secondary structure level. A protein-ligand graph is computed from the atomic coordinates in a PDB file and the secondary structure assignments of the DSSP algorithm. In this graph, vertices represent secondary structure elements (SSEs, usually alpha helices and beta strands) or ligand molecules, while the edges model contacts and relative orientations between them. The graphs can be visualized, written to a database, and saved in a text-based file format.