biology/pdbalign - The NetBSD Packages Collection

Prediction of Protein Secondary Structure and Active Sites

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.

Build dependencies

pkgtools/cwrappers

Runtime dependencies

(none)

Binary packages

OSArchitectureVersion
NetBSD 8.0earmv7hfpdbalign-20030812.tgz
NetBSD 8.0earmv7hfpdbalign-20030812.tgz
NetBSD 8.0earmv7hfpdbalign-20030812.tgz
NetBSD 8.0i386pdbalign-20030812.tgz
NetBSD 8.0i386pdbalign-20030812.tgz
NetBSD 8.0i386pdbalign-20030812.tgz
NetBSD 8.0powerpcpdbalign-20030812.tgz
NetBSD 8.0powerpcpdbalign-20030812.tgz
NetBSD 8.0powerpcpdbalign-20030812.tgz
NetBSD 8.0x86_64pdbalign-20030812.tgz
NetBSD 8.0x86_64pdbalign-20030812.tgz
NetBSD 8.0x86_64pdbalign-20030812.tgz
NetBSD 9.0aarch64pdbalign-20030812.tgz
NetBSD 9.0aarch64pdbalign-20030812.tgz
NetBSD 9.0aarch64pdbalign-20030812.tgz
NetBSD 9.0alphapdbalign-20030812.tgz
NetBSD 9.0alphapdbalign-20030812.tgz
NetBSD 9.0alphapdbalign-20030812.tgz
NetBSD 9.0earmpdbalign-20030812.tgz
NetBSD 9.0earmv6hfpdbalign-20030812.tgz
NetBSD 9.0earmv6hfpdbalign-20030812.tgz
NetBSD 9.0earmv6hfpdbalign-20030812.tgz
NetBSD 9.0earmv6hfpdbalign-20030812.tgz
NetBSD 9.0earmv7hfpdbalign-20030812.tgz
NetBSD 9.0earmv7hfpdbalign-20030812.tgz
NetBSD 9.0earmv7hfpdbalign-20030812.tgz
NetBSD 9.0earmv7hfpdbalign-20030812.tgz
NetBSD 9.0i386pdbalign-20030812.tgz
NetBSD 9.0i386pdbalign-20030812.tgz
NetBSD 9.0i386pdbalign-20030812.tgz
NetBSD 9.0mips64ebpdbalign-20030812.tgz
NetBSD 9.0mips64ebpdbalign-20030812.tgz
NetBSD 9.0mips64ebpdbalign-20030812.tgz
NetBSD 9.0powerpcpdbalign-20030812.tgz
NetBSD 9.0powerpcpdbalign-20030812.tgz
NetBSD 9.0sparc64pdbalign-20030812.tgz
NetBSD 9.0sparc64pdbalign-20030812.tgz
NetBSD 9.0sparc64pdbalign-20030812.tgz
NetBSD 9.0sparc64pdbalign-20030812.tgz
NetBSD 9.0sparcpdbalign-20030812.tgz
NetBSD 9.0sparcpdbalign-20030812.tgz
NetBSD 9.0sparcpdbalign-20030812.tgz
NetBSD 9.0x86_64pdbalign-20030812.tgz
NetBSD 9.0x86_64pdbalign-20030812.tgz
NetBSD 9.0x86_64pdbalign-20030812.tgz
NetBSD 9.0x86_64pdbalign-20030812.tgz
NetBSD 9.0x86_64pdbalign-20030812.tgz
NetBSD 9.0x86_64pdbalign-20030812.tgz
NetBSD 9.0x86_64pdbalign-20030812.tgz

Binary packages can be installed with the high-level tool pkgin (which can be installed with pkg_add) or pkg_add(1) (installed by default). The NetBSD packages collection is also designed to permit easy installation from source.

Available build options

(none)

Known vulnerabilities

The pkg_admin audit command locates any installed package which has been mentioned in security advisories as having vulnerabilities.

Please note the vulnerabilities database might not be fully accurate, and not every bug is exploitable with every configuration.


Problem reports, updates or suggestions for this package should be reported with send-pr.