From cheatham@chpc.utah.edu Date: Mon, 9 Jun 2003 17:36:12 -0600 (Mountain Daylight Time) From: "Thomas E. Cheatham, III" To: Manju Bansal , David Beveridge , tec3@utah.edu, martin.egli , agor , heinemann , ponzy , Xiangjun LU , Karolin.Luger , Stephen Neidle , olson , Remo Rohs , schlick , Zippi Shakked , 'Heinz Sklenar' , Jiri Sponer , Juan.A.Subirana , e.westhof , loren.williams , m.zacharias , Krystyna.Zakrzewska , haim.rozenberg , "Zhurkin, Victor (NIH/NCI)" , Richard Lavery , Peter Varnai , Nada Spackova , sarma Cc: Rama Sarma , tec3@utah.edu Subject: Albany, Pre-conv workshop on NA structural parameters Dear Friends and colleagues, Given the lively e-mail on this list, it can be surmised that there is still a lack of complete consensus on how to fully and consistently describe nucleic acid structural parameters. A common and standard platform for reliable comparison of nucleic acid structural properties between labs (and the various structural methods used to characterize nucleic acid structure) is highly desirable. This avoids having to recalculate the structural parameters with a particular group's favorite program and removes uncertainties in the interpretation of the data. Towards this end, Sarma and the 13th Conversation program committee thought it would be useful to hold an informal workshop highlighting and debating the features, performance and limitations of some of the available programs for calculating nucleic acid structural parameters. Additionally, we ultimately would like to provide a snapshot of where we are now and where we need to go to reach a consensus regarding these methods. I was asked to Chair this discussion. The planned format was for the program developers to spend a little time discussing their methods followed by presentation or discussion with the larger community highlighting various groups personal experiences with the programs and needs. We can discuss differences in the results, global vs. local helicoidal parameters, estimates of bending angles, groove width definitions, and other common and useful descriptors of nucleic acid structure. The current format of the Workshop (to be held on Tuesday June 17th from 2-5 pm on LC-18) is planned as follows (timings are approximate): 2:00-2:10 Short introduction by the Chair (Cheatham) to provide an overview and to discuss the reasons for convening this workshop on structural parameters. 2:10-2:40 Presentation by Heinz Sklenar on the new CURVES with a focus on new features and differences from other programs (global vs. local parameters), strengths and weaknesses, and planned modifications. Some discussion of the performance and reliability of the methods for describing nucleic acid structure may be presented in this short overview. 2:45-3:15 Presentation by Wilma Olson, Victor Zhurkin and/or co-workers on 3DNA (and other programs) for calculating nucleic acid structural parameters with a focus on features, issues, problems, strengths and weaknesses. Hopefully this talk will also highlight the main differences seen among the various programs, briefly summarize the Tsukuba conventions and their experiences in comparing the common programs, and demonstrate the performance and reliability of their methods for describing nucleic acid structure. 3:30- ??? Optional discussion/presentations (if pre-arranged) by participants on their experiences with the programs. This will be an appropriate forum for participants to discuss what problems (or features) have been encountered and also to delineate what do we the users want/need to properly "define" and "compare" nucleic acid structure. If someone wants to give a brief (formal) presentation, please contact the Chair (tec3@utah.edu). ??? -5:00 Open discussion (and informal presentations) on what is needed and how to provide this. This is where I (as Chair) anticipate or hope that the major discussions about "closing the gap" between the various programs will be discussed. Here details regarding the definitions (reference frames, rotations, ...) and mathematical nitty-gritty can get debated or discussed (as opposed to in the talks discussing the individual programs). Our goal is to look for consensus or forward movement on the definition of nucleic acid structural descriptors. Please feel free to e-mail (or call) me if you have concerns related to this Workshop. The hope is to provide a friendly and constructive environment for discussing and debating how to properly and reliably describe nucleic acid structure. Thanks a bunch and see you all rather soon! --tom \ Thomas E. Cheatham, III (Assistant Professor) College of Pharmacy | Departments of Medicinal Chemistry and of University of Utah | Pharmaceutics and Pharmaceutical Chemistry 30 South 2000 East, Room 201 | & Center for High Performance Computing Salt Lake City, Utah 84112 | | e-mail: tec3@utah.edu phone: (801) 587-9652 FAX: (801) 585-9119 \ http://www.chpc.utah.edu/~cheatham Offices: BPRP295A / INSCC 418