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

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Branch: CURRENT, Version: 20030812, Package name: pdbalign-20030812, Maintainer: pkgsrc-users

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:

Filesize: 10.212 KB

Version history: (Expand)

CVS history: (Expand)


   2024-08-22 19:06:00 by Greg Troxel | Files touched by this commit (14) 
Log message:
various: Typos in MAINTAINER addresses
   2024-08-22 19:01:18 by Greg Troxel | Files touched by this commit (13) 
Log message:
various: Reset MAINTAINER

Email fails, and someone still at the same domain confirmed they are no
longer there.
   2021-10-26 12:03:45 by Nia Alarie | Files touched by this commit (73) 
Log message:
biology: Replace RMD160 checksums with BLAKE2s checksums

All checksums have been double-checked against existing RMD160 and
SHA512 hashes
   2021-10-07 15:19:44 by Nia Alarie | Files touched by this commit (73) 
Log message:
biology: Remove SHA1 hashes for distfiles
   2015-11-02 19:42:23 by Alistair G. Crooks | Files touched by this commit (38) 
Log message:
Add SHA512 digests for distfiles for biology category.

Existing SHA1 digests verified, all found to be the same on the
machine holding the existing distfiles (morden).  Existing SHA1
digests retained for now as an audit trail.
   2012-09-11 22:32:15 by Aleksej Saushev | Files touched by this commit (31) 
Log message:
"user-destdir" is default these days
   2008-03-03 02:10:06 by Johnny C. Lam | Files touched by this commit (16) 
Log message:
Mechanical changes to add full DESTDIR support to packages that install
their files via a custom do-install target.
   2007-02-22 20:27:30 by Thomas Klausner | Files touched by this commit (721) 
Log message:
Whitespace cleanup, courtesy of pkglint.
Patch provided by Sergey Svishchev in private mail.