Seminars of the Focus Area Complex Systems

Prof. Dr. C. Beta, Prof. Dr. K. Dethloff, Prof. Dr. R. Engbert, Prof. Dr. M. Holschneider, Prof. Dr. W. Huisinga, Prof. Dr. Ralf Metzler, Prof. Dr. A. Pikovsky, Prof. Dr. S. Reich, Prof. Dr. M. Rosenblum, Prof. Dr. G. Rüdiger, Prof. Dr. T. Scheffer, Prof. Dr. F. Scherbaum, Prof. Dr. J. Selbig, Prof. Dr. F. Spahn

Seminar

Speaker: Magdalena Rother, Laboratory of Structural Bioinformatics, Adam Mickiewicz University, Poznan

Title: ModeRNA - a tool for RNA 3D structure modeling

Time: Wed, Oct 6, 2010, 10:00am

Place: MPI für Molekulare Pflanzenphysiologie, Room 0.21 in The Box

Abstract:
RNA is a large group of functionally important biomacromolecules whose function depends on its structure. To facilitate research on RNA structure and function without expensive and time consuming experiments we developed ModeRNA a computer program for RNA 3D structure prediction with the comparative modeling approach. The software provides:

- RNA structure modeling based on the 3D structure of a template RNA molecule, and a sequence alignment between the target to be modeled and the template

- modeling of posttranscriptionally modified nucleotides

- merging fragments of different nucleic acid structures into a single model

- altering a structure (e.g. removing some parts or changing the sequence)

- analyzing a structure‘s geometry

- DNA structure modeling

The program was tested on a set of 99 tRNAs for which 9801 models were built (for each tRNA from this set 98 models based on all other tRNAs as a template plus the control model structure built on itself).

The software is written in the Python programming language and has been released under an Open Source license, which means that it can be customized. Windows and UNIX implementations of ModeRNA with comprehensive documentation and a tutorial are freely available at http://iimcb.genesilico.pl/moderna.

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Past NLD Seminars (1994-2007) & (2008 ...)

Students' seminar: Theoretical Physics, PIK, Modeling & TSA Berlin-Potsdam-Colloquia: PhysGesellschaft Berlin, TU Berlin, Pro Physik, AIP, AEI, MPI-KGF, GFZ, HMI, PIK, AWI, Max Planck Institute for the History of Science, Mathematik, DPG Disputationen, & Vorschau UP

Udo Schwarz, Zentrum für Dynamik komplexer Systeme,
Universität Potsdam, Campus Golm Karl-Liebknecht-Str. 24, 14476 Potsdam, building 28, room 2.107
Phone: (+49-331) 977-1658, Fax : (+49-331) 977-1045

Email: Udo.Schwarz AT uni-potsdam.de

DFG SFB 1294

DFG Sonderforschungsbereich 1294 Data assimilation

DFG SPP 1488

DFG Schwerpunktprogramm 1488 Planetmag


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