BioJava aims to provide a comprehensive set of Java components for the rapid development of applications in Bioinformatics. It contains interfaces for representing Sequences, Features, and other important bioinformatics concepts. It can also read and write sequence data in a variety of common formats and communicate with Ensembl databases and with DAS and BioCorba servers.
Ghemical is a molecular modelling software package with some nice 3D visualization tools. It supports methods based on both molecular mechanics and quantum mechanics (using MOPAC7, and MPQC for QM). The geometry optimization (for MM and QM) and molecular dynamics (for MM) algorithms are included. Ghemical is written in C++, and hopefully offers a good framework for a generic freeware molecular modelling tool.
Jmol is a Free, Open Source molecule viewer and editor. It is a collaboratively developed visualization and measurement tool for chemical scientists. Jmol is an active project, and there are new features being added to it on a daily basis. Users are encouraged to modify it to fit their needs and to contribute their changes to the project.
Viewmol is a program for building and editing molecules as well as for the visualization of outputs from quantum chemical and molecular mechanics programs. Currently supported are Gaussian 9x, Gamess, Discover, DMol/DSolid/DMol3, Gulp, Mopac, Turbomole, and PDB files. Properties visualized include geometry (with various drawing modes), vibration (animated or with arrows), optimization history/MD trajectories, MO energy level diagram, MOs, basis functions, and electron density. Drawings can be saved as TIFF, HPGL, Postscript, and input files for Rayshade. Viewmol has an embedded Python interpreter for automation. The program is language independent and currently "speaks" English, French, German, Russian, or Spanish.