A C++ Library for modelling and analyzing biochemical networks
EMBOSS is a dynamic and comprehensive Open Source package for bioinformatics (DNA and protein sequence analysis, protein structure, phylogenetics, etc.). EMBOSS is written in C, also compatible with C++, and has a separate Java interface (Jemboss)
mccore is a bioinformatics data structures and tools library for efficient analysis and manipulation of RNA, DNA and protein 3D structures.
The Molecular Modeling Templates, MMT is a C++ class library for molecular simulation applications. MMT serves as a code basis that can be easily extended and modified to perform Monte Carlo and molecular dynamics simulations.