./biology/pdbalign, Prediction of Protein Secondary Structure and Active Sites

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Branch: pkgsrc-2012Q3, Version: 20030812, Package name: pdbalign-20030812, Maintainer: hdp

Given a GCG multiple sequence alignment file (a GCG MSF file), which a
includes a sequence of known structure, the program pdbalign maps the
sequence variability onto the known structure. The central premise is
of course, that for a closely related family of proteins (sequence ID
> 40%) the 3-D structures will not be significantly different.pdbdist
calculates the distance from each atom in the pdb file to each atom in
the ligand and records the minimum in the temperature field for that
atom record.distalign reads the output from pdbdist and also the
original GCG MSF file and produces an MSF file annotated with a
measure of sequence variability and the distance of the residue at
that position (of the sequence of known structure) from the ligand.

Master sites:

SHA1: 83f8e393fe98cb877bc90e804911b1819a18c1d3
RMD160: 7cc3f416fd3347628e2f21f48f6243ec51342e98
Filesize: 10.212 KB

Version history: (Expand)