Software
Alpha shapes
QHull: convex hull, Delaunay triangulatios, Voronoi diagrams, etc.
CGAL: computational geometry library
LEDA: library of efficient data structures and algorithms.
OPT++: nonlinear optimization library.
SWIFT++: collision checking library.
STL: Standard Template Library.
Chimera
EMAN
VMD: Visual Molecular Dynamics.
NAMD: molecular dynamics.
AutoDock: docking of flexible ligands.
FlexX: program for predicting protein-ligand interactions.
SYBYL: molecular dynamics, visualization.
Newmat: a C++ matrix library.
Mathtools.net,
NetLib.org: math software indices.
OpenGL