Clote Lab has interests in structural and systems biology, especially relating to RNA. LocalMove is a 5000 line C++ program developed by Peter Clote and Yann Ponty with help from ex-students Radu Istrate and Erik Porcelli, that implements a Monte-Carlo approach to obtain approximate on lattice-models for protein and RNA Protein DataBank (PDB) files. Lattices currently supported are the square 2D lattice, cubic 3D lattice and the face-centered cubic (FCC) lattice. Simulated annealing and greedy descent are additionally featured by the LocalMove program.
Check out our web server for real-time visualizations RNA at http://bioinformatics.bc.edu/clotelab/localmove/index.html.
The cool 3D graphics was built by Yann Ponty from snapshots of the Monte Carlo walk, taken at fixed intervals, rasterized using Pymol and assembled with FFMpeg free software. If you are interested in this kind of research, drop by our lab in Higgins 581.