LPFC: Code and Documentation

The core-find package is a collection of tools that facilitates calculation and analysis of the cores of families of structurally related molecules. In order to compute a core structure, the user need only specify a multiple alignment of known PDB structures. The program will compute (1) the average core structure, (2) the cutoff between high and low spatial variance residues, (3) the rank order of spatial variability (the 'throwout order'), and (4) all supporting data and coordinates.

Extensive documentation in the form of a README file for the code can be obtained here.


The corefinding process unfolds as follows:

  1. CorePrepare - obtain structural data from the Brookhaven PDB and combine it into a single file.

  2. CoreFind - produce a throwout order in order of decreasing spatial variability of aligned atoms.

  3. CoreCut - determine the core cutoff that separates high variance atoms from low variance atoms.

  4. CoreResult - generate a result file containing structural data about the core.

  5. CoreImage, ViewStructures - produce image files that can be displayed with proteanD and vrml viewers.


Code for computing average core structures is available here. This code has been compiled and tested on a Silicon Graphics Indigo-2 machine under Irix 5.3 using the cc compiler.

ProteanD, a program to display .mvp and .mv files for SGI machines with GL, Motif, or X, is available here.

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Russ B. Altman, Mark B. Gerstein, Bob Schmidt
Stanford University School of Medicine
Contact: russ.altman@stanford.edu
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Revised: Friday 23 February 96
URL: http://helix-web.stanford.edu/LPFC/documentation.html
Copyright © 1996, Stanford University. All rights reserved.