OpenScience / Software / Chemistry

A Java-based, on-line biomolecular modeling package. It should be useful in generating initial structures of biopolymers and small organic molecules. Simple force-field energy minimizations can be carried out in addition to simulated annealing with molecular dynamics. Find B at: http://www.scripps.edu/case/Biomer/index.html

ChemSol is designed for the calculations of solvation free energies using the Langevin Dipoles (LD) solvation model, in which the solvent is approximated by polarizable dipoles fixed on a cubic grid. Find ChemSol at: http://laetro.usc.edu/chemsol/index.html

Fungimol is an extensible system for designing atomic-scale objects. The intent is to eventually extend it to be a useful system for doing molecular nanotechnology design work. At the moment it’s a PDB file viewer and Buckminsterfullerine editor. Find Fungimol … Continue reading →