Software using PDB file

HBPLUS

http://www.ebi.ac.uk/thornton-srv/software/HBPLUS/

compute all possible van der Waals contacts and hydrogen bonds

MOLMOL

compute the relative solvent-accessible surface area of each amino acid from the protein structure.

SCWRL  

http://dunbrack.fccc.edu/scwrl4/

(http://pages.jh.edu/~fleming/Modeling/SCWRL.html)

identify the most comment side-chain

AMBER

http://ambermd.org/

relieve bad contacts  to minimize energy

ConSurf

http://consurf.tau.ac.il/

compute the conservation score

SURFNET

http://www.ebi.ac.uk/thornton-srv/software/SURFNET/

compute the clefts (cavities and grooves)

Surface Racer

http://pharmacy.mc.uky.edu/faculty/tsodikov/software.php

Surface Racer Caculates  exact accessible surface area, molecular surface area and average curvature of molecular surface for macromolecules.

The program also analyzes cavities in the protein interior inaccessible to solvent from outside.

Outputs: the surface parameters for each residue in addition to those for individual atoms.

CGAL: Computational Geometry Algorithms Library

http://www.cgal.org/

"The Computational Geometry Algorithms Library (CGAL), offers data structures and algorithms liketriangulations (2D constrained triangulations, and Delaunay triangulations and periodic triangulations in 2D and 3D), Voronoi diagrams (for 2D and 3D points, 2D additively weighted Voronoi diagrams, and segment Voronoi diagrams), polygons (Boolean operations, offsets, straight skeleton), polyhedra (Boolean operations), arrangements of curves and their applications (2D and 3D envelopes, Minkowski sums), mesh generation (2D Delaunay mesh generation and 3D surface and volume mesh generation, skin surfaces),geometry processing (surface mesh simplification, subdivision and parameterization, as well as estimation of local differential properties, and approximation of ridges and umbilics), alpha shapes, convex hull algorithms(in 2D, 3D and dD), search structures (kd trees for nearest neighbor search, and range and segment trees),interpolation (natural neighbor interpolation and placement of streamlines), shape analysis, fitting, and distances (smallest enclosing sphere of points or spheres, smallest enclosing ellipsoid of points, principal component analysis), and kinetic data structures."