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Install this package:

emerge -a sci-chemistry/panav

If the package is masked, you can unmask it using the autounmask tool or standard emerge options:

autounmask sci-chemistry/panav

Or alternatively:

emerge --autounmask-write -a sci-chemistry/panav

Package Information

Description:

It has been estimated that more than 20% of the proteins in the BMRB are improperly referenced and that about 1% of all chemical shift assignments are mis-assigned. These statistics also reflect the likelihood that any newly assigned protein will have shift assignment or shift referencing errors. The relatively high frequency of these errors continues to be a concern for the biomolecular NMR community. While several programs do exist to detect and/or correct chemical shift mis-referencing or chemical shift mis-assignments, most can only do one, or the other. The one program (SHIFTCOR) that is capable of handling both chemical shift mis-referencing and mis-assignments, requires the 3D structure coordinates of the target protein. Given that chemical shift mis-assignments and chemical shift re-referencing issues should ideally be addressed prior to 3D structure determination, there is a clear need to develop a structure-independent approach. Here, we present a new structure-independent protocol, which is based on using residue-specific and secondary structure-specific chemical shift distributions calculated over small (3–6 residue) fragments to identify mis-assigned resonances. The method is also able to identify and re-reference mis-referenced chemical shift assignments. Comparisons against existing re-referencing or mis-assignment detection programs show that the method is as good or superior to existing approaches.

Homepage:

https://link.springer.com/article/10.1007%2Fs10858-010-9407-y/fulltext.html

License:

all-rights-reserved

Versions

Metadata

Description

• It has been estimated that more than 20% of the proteins in the BMRB are improperly referenced and that about 1% of all chemical shift assignments are mis-assigned. These statistics also reflect the likelihood that any newly assigned protein will have shift assignment or shift referencing errors. The relatively high frequency of these errors continues to be a concern for the biomolecular NMR community. While several programs do exist to detect and/or correct chemical shift mis-referencing or chemical shift mis-assignments, most can only do one, or the other. The one program (SHIFTCOR) that is capable of handling both chemical shift mis-referencing and mis-assignments, requires the 3D structure coordinates of the target protein. Given that chemical shift mis-assignments and chemical shift re-referencing issues should ideally be addressed prior to 3D structure determination, there is a clear need to develop a structure-independent approach. Here, we present a new structure-independent protocol, which is based on using residue-specific and secondary structure-specific chemical shift distributions calculated over small (3–6 residue) fragments to identify mis-assigned resonances. The method is also able to identify and re-reference mis-referenced chemical shift assignments. Comparisons against existing re-referencing or mis-assignment detection programs show that the method is as good or superior to existing approaches.

Maintainers

• Unknown (jlec@gentoo.org) - Type: person
• Gentoo Chemistry Project (sci-chemistry@gentoo.org) - Type: project

<pkgmetadata>
	<maintainer type="person">
		<email>jlec@gentoo.org</email>
	</maintainer>
	<maintainer type="project">
		<email>sci-chemistry@gentoo.org</email>
		<name>Gentoo Chemistry Project</name>
	</maintainer>
	<longdescription>
It has been estimated that more than 20% of the proteins in the BMRB are 
improperly referenced and that about 1% of all chemical shift assignments are 
mis-assigned. These statistics also reflect the likelihood that any newly 
assigned protein will have shift assignment or shift referencing errors. The 
relatively high frequency of these errors continues to be a concern for the 
biomolecular NMR community. While several programs do exist to detect and/or 
correct chemical shift mis-referencing or chemical shift mis-assignments, most 
can only do one, or the other. The one program (SHIFTCOR) that is capable of 
handling both chemical shift mis-referencing and mis-assignments, requires the 
3D structure coordinates of the target protein. Given that chemical shift 
mis-assignments and chemical shift re-referencing issues should ideally be 
addressed prior to 3D structure determination, there is a clear need to develop 
a structure-independent approach. Here, we present a new structure-independent 
protocol, which is based on using residue-specific and secondary 
structure-specific chemical shift distributions calculated over 
small (3–6 residue) fragments to identify mis-assigned resonances. The method 
is also able to identify and re-reference mis-referenced chemical shift 
assignments. Comparisons against existing re-referencing or mis-assignment 
detection programs show that the method is as good or superior to existing 
approaches.
</longdescription>
</pkgmetadata>

Lint Warnings

• [Error] Missing md5-cache for ebuild panav-0.20130730

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