BioC++ library This is a library mainly used to process structure bioinformatics stuff, like PDB structure input, output, bond generation and sequence generation etc. It's a pity that I haven't had much time to improve it lately, e.g., RMSD calculations. Java applet to generate the phylogenetic tree of a sequence family Basically, it reads a multiple sequence alignment in CLUSTAL format, and draws a graph of phylogenetic tree of the sequence family in a web browser using UPGMA algorithm. If you want to see how this applet works, please look at an example or visit genome3d server. A fast and efficient C++ program for modeling protein loops This is a high speed and efficient Monte Carlo Simulated Annealing (MCSA) program for modeling protein loops, which I wrote for my Ph.D. thesis. I made some revision later for the competition in CASP3. Reference: A Fast and Efficient Program for Modeling Protein Loops" Zhang H., Lai L., Wang L., Han Y. and Tang Y. Biopolymers, Vol.41, P61-72, 1997