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pdbalign
Prediction of Protein Secondary Structure and Active Sites
/Main/NetBSD/current-packages/NetBSD/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.Homepage:
Info:
Homepage: - Package version: - Architecture: NetBSD Distribution: NetBSD current-packages Filename: pdbalign-20030812.tgz Browse inside pdbalign-20030812.tgz:
pkg://pdbalign-20030812.tgz:19681/ downloads[DIR]bin/ 65535+ twin directories
6 B 2007-04-17+SIZE_PKG view 25016+ mirrors
2 B 2007-04-17+SIZE_ALL view 26917+ mirrors
767 B 2007-04-17+DESC view 219+ mirrors
464 B 2007-04-17+CONTENTS view 326+ mirrors
59 B 2007-04-17+COMMENT view 6916+ mirrors
638 B 2007-04-17+BUILD_VERSION view 30 mirrors
814 B 2007-04-17+BUILD_INFO view 60 mirrorsDownload pdbalign-20030812.tgz:
2007-09-12 ftp://ftp.uni-hannover.de/pub/mirror/bsd/NetBSD/packages/current-packages/NetBSD/x86_64/4.99.x/All/pdbalign-20030812.tgz
2007-09-12 ftp://ftp.free.fr/.mirrors1/ftp.netbsd.org/packages/current-packages/NetBSD/x86_64/4.99.x/All/pdbalign-20030812.tgz
2007-10-12 ftp://ftp.estpak.ee/pub/pkgsrc/packages/NetBSD/powerpc/3.1_2007Q3/All/pdbalign-20030812.tgz
2007-10-12 ftp://ftp.estpak.ee/pub/pkgsrc/packages/NetBSD/powerpc/3.1_2007Q4/All/pdbalign-20030812.tgz
2007-10-12 ftp://ftp.esat.net/mirrors/.3/ftp.netbsd.org/pub/NetBSD/packages/current-packages/NetBSD/powerpc/3.1_2007Q4/All/pdbalign-20030812.tgz
2007-10-12 ftp://ftp.esat.net/mirrors/.3/ftp.netbsd.org/pub/NetBSD/packages/current-packages/NetBSD/powerpc/3.1_2007Q3/All/pdbalign-20030812.tgz
2008-09-10 ftp://ftp.funet.fi/.m/mirrors5/ftp.netbsd.org/pub/NetBSD/packages/current-packages/NetBSD/x86_64/4.99.x/All/pdbalign-20030812.tgz
2007-10-13 ftp://ftp.jp.xemacs.org/pub/NetBSD/packages/current-packages/NetBSD/powerpc/3.1_2007Q3/All/pdbalign-20030812.tgz
2007-10-12 ftp://ftp.netbsd.org/pub/pkgsrc/packages/NetBSD/powerpc/3.1_2007Q4/All/pdbalign-20030812.tgz
2007-10-12 ftp://ftp.netbsd.org/pub/pkgsrc/packages/NetBSD/powerpc/3.1_2007Q3/All/pdbalign-20030812.tgz
2008-09-10 ftp://ftp.netbsd.org/pub/NetBSD/packages/current-packages/NetBSD/x86_64/4.99.x/All/pdbalign-20030812.tgz
2008-09-10 ftp://ftp.ticklers.org/pub/NetBSD/packages/current-packages/NetBSD/x86_64/4.99.x/All/pdbalign-20030812.tgz
2007-10-12 ftp://ftp.fr.netbsd.org/pub/pkgsrc/packages/NetBSD/powerpc/3.1_2007Q4/All/pdbalign-20030812.tgz
2007-10-12 ftp://ftp.fr.netbsd.org/pub/pkgsrc/packages/NetBSD/powerpc/3.1_2007Q3/All/pdbalign-20030812.tgz
2008-09-10 ftp://core.ring.gr.jp/pub/NetBSD/packages/current-packages/NetBSD/x86_64/4.99.x/All/pdbalign-20030812.tgz
2007-10-13 ftp://202.18.64.24/pub/NetBSD/packages/current-packages/NetBSD/powerpc/3.1_2007Q4/All/pdbalign-20030812.tgz
2007-10-13 ftp://202.18.64.24/pub/NetBSD/packages/current-packages/NetBSD/powerpc/3.1_2007Q3/All/pdbalign-20030812.tgz
2007-10-13 ftp://ftp.aist-nara.ac.jp/0/NetBSD/packages/current-packages/NetBSD/powerpc/3.1_2007Q3/All/pdbalign-20030812.tgz
2007-10-13 ftp://ftp.aist-nara.ac.jp/0/NetBSD/packages/current-packages/NetBSD/powerpc/3.1_2007Q4/All/pdbalign-20030812.tgz
2007-10-12 ftp://192.87.102.42/vol/1/netbsd/packages/current-packages/NetBSD/powerpc/3.1_2007Q3/All/pdbalign-20030812.tgz
2007-10-12 ftp://192.87.102.42/vol/1/netbsd/packages/current-packages/NetBSD/powerpc/3.1_2007Q4/All/pdbalign-20030812.tgz
2007-10-12 ftp://ftp.twaren.net/pub/BSD/NetBSD/packages/current-packages/NetBSD/powerpc/3.1_2007Q3/All/pdbalign-20030812.tgz
2007-10-12 ftp://ftp.twaren.net/pub/BSD/NetBSD/packages/current-packages/NetBSD/powerpc/3.1_2007Q4/All/pdbalign-20030812.tgz
2007-10-12 ftp://ftp.au.freebsd.org/disks/la3/.p/netbsd/packages/current-packages/NetBSD/powerpc/3.1_2007Q4/All/pdbalign-20030812.tgz
2007-10-12 ftp://ftp.au.freebsd.org/disks/la3/.p/netbsd/packages/current-packages/NetBSD/powerpc/3.1_2007Q3/All/pdbalign-20030812.tgz
2008-09-10 ftp://ftp.esat.net/mirrors/.3/ftp.netbsd.org/pub/NetBSD/packages/current-packages/NetBSD/x86_64/4.99.x/All/pdbalign-20030812.tgz
2008-09-10 ftp://ftp.jp.netbsd.org/pub/NetBSD/packages/current-packages/NetBSD/x86_64/4.99.x/All/pdbalign-20030812.tgz
2008-09-10 ftp://192.87.102.43/vol/1/netbsd/packages/current-packages/NetBSD/x86_64/4.99.x/All/pdbalign-20030812.tgz
2008-09-10 ftp://ftp.netbsd.org/pub/pkgsrc/packages/NetBSD/x86_64/4.99.x/All/pdbalign-20030812.tgz
2008-09-10 ftp://ftp2.nl.freebsd.org/netbsd/packages/current-packages/NetBSD/x86_64/4.99.x/All/pdbalign-20030812.tgz
2008-09-30 ftp://133.24.255.161/mirror3/NetBSD/packages/current-packages/NetBSD/x86_64/4.99.x/All/pdbalign-20030812.tgz
2008-09-10 ftp://ftp.nrc.ca/pub/systems/bsd/netbsd/packages/current-packages/NetBSD/x86_64/4.99.x/All/pdbalign-20030812.tgz
2008-09-10 ftp://192.87.102.42/vol/1/netbsd/packages/current-packages/NetBSD/x86_64/4.99.x/All/pdbalign-20030812.tgz
2008-09-10 ftp://ftp.estpak.ee/pub/pkgsrc/packages/NetBSD/x86_64/4.99.x/All/pdbalign-20030812.tgz
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