Wordom is a (simple) command line utility conceived to spare the user some time in manipulating and converting dcd, xtc, pdb, crd and xyz files. Wordom is also a versatile program for a broad range of molecular structure and dynamics analysis. As a plus, it’s easy to use in shell scripts. Due to its simplicity, it is very easy and straightforward to add your own analysis module. Basically, most of what you have to do is write the algorithm – the data are made available by the existing wordom i/o modules.
WebPSN is a webserver to setup and run a procedure based on a mixed Protein Structure Network (PSN) and Elastic Network Model-Normal Mode Analysis (ENM-NMA) approach (i.e. PSN-ENM) to investigate structural communication in biomacromolecules.
Fipd is used to analyse data coming from a ZDOCK run.