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ECS 289L
Computational Structural Biology
Protein Structure Modeling
Instructor: Patrice Koehl
e-mail: koehl@cs.ucdavis.edu
Web page: www.cs.ucdavis.edu/~koehl
Some useful programs you might want to download
| Program |
Description |
| ParsePDB |
ParsePDB is a simple program that reads in a PDB file, a standard force field file, add polar hydrogens if they are
missing, and generate a flat file summarizing these information in a way that they are easy to use. |
| Volume |
Volume computes the volume and surface area of a union of balls analytically, using the Alpha Shape formalism. If n
eeded, it can also compute the derivatives of these quantities with respect to the position of the ball centers. It is designed to
work on the output of ParsePDB |
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