Forwarded from Jane Richardson:

Yuan Lin,

The sources you've been given (esp. the reduced-variable ones)
are excellent for identifying RNA structural motifs but not very good
for crystallographic validation, and the PDB tools are still primitive
for nucleic acids.  Fortunately, a suitable system is pretty far along
in development and partly available now.
     The backbone committee of the RNA Ontology Consortium (our Duke
group, Helen Berman, Bohdan Schneider, Loren Williams, and Anna Marie
Pyle) has agreed on a nomenclature and a consensus set of valid
all-angle conformers for RNA backbone (soon to be published in RNA).
 As part of that, we developed a program Suitename that will assign
those conformer names or declare an outlier for each suite
(sugar-to-sugar unit) in an RNA structure.  It will soon be part of
our MolProbity validation site (http://molprobity.biochem.duke.edu),
but we'd be glad to send it to you now in advance.  Already on
MolProbity you can get a quick and easy analysis of all-atom steric
clashes and probable bad sugar puckers (Davis 2007 NAR web issue, now
on-line), which can locate most of the backbone fitting errors.

Jane Richardson



- Show quoted text -



On Tue, 8 May 2007 19:41:13 -0400
 "Robert Immormino" <[log in to unmask]> wrote:
>Forwarded Conversation
> Subject: [ccp4bb] Program to evaluate RNA torsion angles?
> ------------------------
>
> From: Yuan Lin <[log in to unmask]>
> Reply-To: Yuan Lin <[log in to unmask]>
> To: [log in to unmask]
> Date: Tue, May 8, 2007 at 5:08 PM
>
> Dear All,
>   I was wonder if anyone knows of a program for evaluating the
>quality of
> nucleic acid torsion angles in a manner comparable to a Ramachandran
>plot
> for proteins? I am working on an A-form dsRNA structure and there
>are some
> deviations from the average torsion angles for A-RNA, due to the
> incorporation of an A-bulge. This might be silly, but how could I
>know
> whether those deviations are outrageous or not?
>
>  Thanks very much!
>
>
> Yuan
>
>
> ------------------------
> Yuan Lin
> Biochemistry and Molecular Biology
> Johns Hopkins University
> Rm. W8702 BSPH
> 615 N. Wolfe St.
> Baltimore, MD 21205
> Ph. 443-287-4988
>
> --------
> From: Das, Debanu <[log in to unmask]>
> Reply-To: "Das, Debanu" <[log in to unmask]>
> To: [log in to unmask]
> Date: Tue, May 8, 2007 at 5:51 PM
>
> This might be silly, but how could I know
> whether those deviations are outrageous or not?
>
>
> The following references may answer your questions:
>
> 1)
>
> Sims GE, Kim SH.
> <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Retrieve&dopt=AbstractPlus&list_uids=14500824&query_hl=9&itool=pubmed_docsum>
> Global mapping of nucleic acid conformational space: dinucleoside
> monophosphate conformations and transition pathways among
> conformational classes.
> Proc Natl Acad Sci U S A. 2005 Jan 18;102(3):618-21. Epub 2005 Jan
>7.
>
>
> 2) Nucleic Acids Res. <javascript:AL_get(this, 'jour', 'Nucleic
>Acids
> Res.');>  2004 Mar 11;32(5):1666-77. RNA conformational classes,
> Schneider B
><http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Search&itool=pubmed_AbstractPlus&term=%22Schneider+B%22%5BAuthor%5D>
> , Moravek Z
><http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Search&itool=pubmed_AbstractPlus&term=%22Moravek+Z%22%5BAuthor%5D>
> , Berman HM
><http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Search&itool=pubmed_AbstractPlus&term=%22Berman+HM%22%5BAuthor%5D>
> .
>
>
> -Debanu.
>
> --------
> From: William Scott <[log in to unmask]>
> Reply-To: William Scott <[log in to unmask]>
> To: [log in to unmask]
> Date: Tue, May 8, 2007 at 5:54 PM
>
> One option is to just use the tools available from the pdb (the
>nucleic
> acid database).
>
> http://ndbserver.rutgers.edu
>
> Another is Anna Marie Pyle's program Amigos.
>
> http://www.csb.yale.edu/people/pyle/software
>
> There are a lot of combinations consistent with A and B form
>helices, so
> this might be worth doing even if you use the first option.
> [Quoted text hidden]
> --------

Richardson Lab
211 Nanaline Duke Bldg.
Duke U Med Ctr
Durham NC 27710-3711 USA
1-919-684-6010; fax 684-8885

On 5/8/07, Yuan Lin <[log in to unmask]> wrote:
> Dear All,
>    I was wonder if anyone knows of a program for evaluating the quality of
> nucleic acid torsion angles in a manner comparable to a Ramachandran plot
> for proteins? I am working on an A-form dsRNA structure and there are some
> deviations from the average torsion angles for A-RNA, due to the
> incorporation of an A-bulge. This might be silly, but how could I know
> whether those deviations are outrageous or not?
>
>   Thanks very much!
>
>
> Yuan
>
>
> ------------------------
> Yuan Lin
> Biochemistry and Molecular Biology
> Johns Hopkins University
> Rm. W8702 BSPH
> 615 N. Wolfe St.
> Baltimore, MD 21205
> Ph. 443-287-4988
>