[Biojava-l] binning structures by quality....

[Steve Darnell]

Hi Jay,

Perhaps this snippet from Proteopedia will help in your search:

http://www.proteopedia.org/wiki/index.php/Structural_alignment_tools

Evaluating Structural Alignments

The structural differences between two optimally aligned models are usually measured as the Root Mean Square Deviation (RMSD) between the aligned alpha-carbon positions (excluding deviations from the non-aligned positions). To provide a frame of reference for RMSD values, note that up to 0.5 Å RMSD of alpha carbons occurs in independent determinations of the same protein[3]. Crystallographic models of proteins with about 50% sequence identity differ by about 1 Å RMSD[3][4]. Deviations can be much larger for models determined by NMR[4].

[3] Chothia C, Lesk AM. The relation between the divergence of sequence and structure in proteins. EMBO J. 1986 Apr;5(4):823-6. PMID:3709526
[4] Schwede T, Diemand A, Guex N, Peitsch MC. Protein structure computing in the genomic era. Res Microbiol. 2000 Mar;151(2):107-12. PMID:10865955

--

Of course, large RMSD values can occur due to misoriented regions (loops, termini, etc.) even though the core structure aligns well.  See Zhang and Skolnick for one example.

Zhang Y, Skolnick J. TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res. 2005 2005 Apr 22;33(7):2302-9. PMID:15849316

Maybe others have a more direct answer to your question.

Regards,
Steve

--
Steve Darnell
DNASTAR, Inc.
Madison, WI USA


-----Original Message-----
From: biojava-l-bounces at lists.open-bio.org [mailto:biojava-l-bounces at lists.open-bio.org] On Behalf Of Jay Vyas
Sent: Monday, June 20, 2011 11:32 AM
To: biojava-l at lists.open-bio.org
Subject: [Biojava-l] binning structures by quality....

Hi Guys : I'm trying to bin some structures, about 30 of them.  I was
wondering if anyone knows the upper "limit" for a structure to have a
correct backbone, in RMSD units.  For example, a structure bundle with RMSD
of 9 would clearly have an undefined backbone, whereas a structure bundle
with an RMSD of 1 would definetely be precise enough to convey backbone
information.

I wanted a more precise bound.  I'm thinking, by eye, that anything above 4
angstroms is to imprecise to convey a backbone.

But I figured maybe there was a formal treatment of such RMSD "categories"
somewhere.

Any thoughts would be appreciated.

-- 
 Jay Vyas
MMSB/UCHC
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