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.
XDrawChem is a program for drawing chemical structures. Features include fixed length and fixed angle drawing, a ring tool to automatically draw rings, automatic alignment of structures in reactions, 2D structure diagram generation, and 3D structure conversion. It can access structures in the PubChem compound database by name, CAS number, or formula. It can output InChI for structures and search the database by structure. It can predict 1H NMR, 13C NMR, simple IR spectra, and estimated pKa. XDrawChem can work with its native file format, ChemDraw files, and any format supported by OpenBabel (MDL Molfile, CML, etc.).
Jude is a rapid application development tool to develop data management workgroup applications that easy-to-maintain for developers and easy-to-use for end users. It is based on a knowledge base with an object oriented structure on the server side and a compound document agent-based user interface on the client side.