ModeRNA: a tool for comparative modeling of RNA 3D structure

RNA is a large group of functionally important biomacromolecules. In striking analogy to proteins, the function of RNA depends on its structure and dynamics, which in turn is encoded in the linear sequence. However, while there are numerous methods for computational prediction of protein three-dimensional (3D) structure from sequence, with comparative modeling being the most reliable approach, there are very few such methods for RNA. Here, we present ModeRNA, a software tool for comparative modeling of RNA 3D structures. As an input, ModeRNA requires a 3D structure of a template RNA molecule, and a sequence alignment between the target to be modeled and the template. It must be emphasized that a good alignment is required for successful modeling, and for large and complex RNA molecules the development of a good alignment usually requires manual adjustments of the input data based on previous expertise of the respective RNA family. ModeRNA can model post-transcriptional modifications, a functionally important feature analogous to post-translational modifications in proteins. ModeRNA can also model DNA structures or use them as templates. It is equipped with many functions for merging fragments of different nucleic acid structures into a single model and analyzing their geometry. Windows and UNIX implementations of ModeRNA with comprehensive documentation and a tutorial are freely available

RNA and protein 3D structure modeling: similarities and differences

In analogy to proteins, the function of RNA depends on its structure and dynamics, which are encoded in the linear sequence. While there are numerous methods for computational prediction of protein 3D structure from sequence, there have been very few such methods for RNA. This review discusses template-based and template-free approaches for macromolecular structure prediction, with special emphasis on comparison between the already tried-and-tested methods for protein structure modeling and the very recently developed “protein-like” modeling methods for RNA. We highlight analogies between many successful methods for modeling of these two types of biological macromolecules and argue that RNA 3D structure can be modeled using “protein-like” methodology. We also highlight the areas where the differences between RNA and proteins require the development of RNA-specific solutions

Prediction of RNA structure and protein-RNA interactions

Wydział Biologii: Instytut Biologii Molekularnej i BiotechnologiiCelem pracy doktorskiej pt. „Przewidywanie struktury RNA i oddziaływań białko-RNA” było opracowanie i przetestowanie w praktyce programów komputerowych do przewidywania struktury drugorzędowej RNA oraz oddziaływań białek z RNA. W przypadku pierwszego zadania przeprowadzono zarówno testy dostępnych narzędzi, jak i opracowano meta-metodę do przewidywania oddziaływań białek z RNA, która została udostępniona za pomocą meta-serwera GeneSilico http://www.genesilico.pl/meta2. Z kolei w wyniku realizacji drugiego z celów stworzono automatyczny system testów narzędzi do przewidywania struktury drugorzędowej RNA, który udostępniony został poprzez internetowy serwer CompaRNA (http://comparna.amu.edu.pl/ oraz http://iimcb.genesilico.pl/comparna/). Projekt CompaRNA to inicjatywa analogiczna do projektów CASP (ang. Critical Assessment of Techniques for Protein Structure Prediction) oraz Livebench, które doprowadziły do przełomu w rozwoju metod do modelowania struktur białek. Mam nadzieję, że wyniki testów narzędzi do przewidywania oddziaływań białek z RNA oraz struktury drugorzędowej RNA będą impulsem dla naukowców zajmujących się rozwijaniem metodologii do wypróbowania nowych rozwiązań, które przyczynią się do zwiększenia dokładności generowanych przewidywań.The aim of the PhD project entitled „Prediction of RNA structure and protein-RNA interactions” was the benchmarking and development of new bioinformatics methods for 1) the prediction of protein-RNA interactions and 2) the prediction of RNA secondary structure. The first aim was achieved by an in-depth testing of web servers for the prediction of protein-RNA interactions and the development of a new meta-method, which is available via GeneSilico web server http://www.genesilico.pl/meta2. The second task was realized by implementing the CompaRNA server (http://comparna.amu.edu.pl/ & http://iimcb.genesilico.pl/comparna/) for the continuous benchmarking of programs for RNA secondary structure prediction. The CompaRNA project is analogous to the CASP (Critical Assessment of Techniques for Protein Structure Prediction) and LiveBench initiatives, which allowed for a breakthrough in the field of protein structure prediction. I hope that the results of the benchmarks for the prediction of protein-RNA interactions and the prediction of RNA secondary structure will stimulate developers of such methods for trying new methodologies which will make predictions more accurate

Academis Leadership for Scientists

<p>Introductory material for post-graduate scientists who would like to start developing mentoring and leadership skills.</p

RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction

The authors report the results of a first, collective, blind experiment in RNA three-dimensional structure prediction, encompassing three prediction puzzles. The goals were to assess the leading edge of RNA structure prediction techniques; compare existing methods and tools; and evaluate their relative strengths, weaknesses, and limitations in terms of sequence length and structural complexity. The results should give potential users insight into the suitability of available methods for different applications and facilitate efforts in the RNA structure prediction community in ongoing efforts to improve prediction tools