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" <[EMAIL PROTECTED]> wrote:
Forwarded Conversation Subject: [ccp4bb] Program to evaluate RNA torsion angles? ------------------------ From: Yuan Lin <[EMAIL PROTECTED]> Reply-To: Yuan Lin <[EMAIL PROTECTED]> To: CCP4BB@jiscmail.ac.uk 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 <[EMAIL PROTECTED]> Reply-To: "Das, Debanu" <[EMAIL PROTECTED]> To: CCP4BB@jiscmail.ac.uk 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 <[EMAIL PROTECTED]> Reply-To: William Scott <[EMAIL PROTECTED]> To: CCP4BB@jiscmail.ac.uk 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 <[EMAIL PROTECTED]> 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