Bujnicki lab - SimRNA
  • RNA has recently emerged as an attractive target for new drug development. Our team is developing new methods to study the interactions between RNA and ligands. Recently, we have developed a new machine learning method called AnnapuRNA to predict how small chemical molecules interact with structured RNA molecules. Research published in PLoS Comput Biol. 2021 Feb 1;17(2):e1008309. doi: 10.1371/journal.pcbi.1008309. Read More
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About Laboratory Of Bioinformatics And Protein Engineering

Our group is involved in theoretical and experimental research on nucleic acids and proteins. The current focus is on RNA sequence-structure-function relationships (in particular 3D modeling), RNA-protein complexes, and enzymes acting on RNA.
 
We study the rules that govern the sequence-structure-function relationships in proteins and nucleic acids and use the acquired knowledge to predict structures and functions for uncharacterized gene products, to alter the known structures and functions of proteins and RNAs and to engineer molecules with new properties.
 
Our key strength is in the integration of various types of theoretical and experimental analyses. We develop and use computer programs for modeling of protein three-dimensional structures based on heterogenous, low-resolution, noisy and ambivalent experimental data. We are also involved in genome-scale phylogenetic analyses, with the focus on identification of proteins that belong to particular families. Subsequently, we characterize experimentally the function of the most interesting new genes/proteins identified by bioinformatics. We also use theoretical predictions to guide protein engineering, using rational and random approaches. Our ultimate goal is to identify complete sets of enzymes involved in particular metabolic pathways (e.g. RNA modification, DNA repair) and to design proteins with new properties, in particular enzymes with new useful functions, which have not been observed in the nature.
 
We are well-equipped with respect to both theoretical and experimental analyses. Our lab offers excellent environment for training of young researchers in both bioinformatics and molecular biology/biochemistry of protein-nucleic acid interactions.


More Good Science

SimRNA - a tool for simulations of RNA conformational dynamics, including RNA 3D structure prediction

 

Program Summary:

SimRNA is a tool for simulations of RNA conformational dynamics (folding, unfolding, multiple chain complex formation etc.), and its applications include RNA 3D structure prediction. SimRNA can be initiated with input files that include either the RNA sequence (or sequences) in a single line (similar to the Vienna format) or in the form of a structure written in PDB format. The PDB format should be simply the structure of the RNA with no heteroatoms or unusual names. In the current version readable residues are A, C, G and U only (i.e. no modified residues are supported as of yet). 

Current version:
The current version is 3.20. 

 

Availability:

SimRNA is available for academic users under the [license] (details enclosed in the license file to be found in each package). Non-academic users and those, who do not accept the license, may NOT download or use the software. A separate commercial license will be issued in the future. Both MacOSX and Linux standalone binary versions of SimRNA3 are available for download.  

Program's download location: https://genesilico.pl/software/simrna/

SimRNA is also available free of charge as a SimRNAweb server

 

 

User Manual:

http://genesilico.pl/DOWNLOAD/SimRNA_UserManual_v3_20_20141002.pdf

 

Bug reports:

All feedback, including bug reports and suggestions for new options to be implemented, should be sent to simrna@genesilico.pl.

 

Citations:

SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction.
Michał J. Boniecki, Grzegorz Łach, Konrad Tomala, Wayne Dawson, Paweł Łukasz, Tomasz Sołtysiński, Kristian M. Rother, and Janusz M. Bujnicki.
Nucleic Acids Res. 2015 Dec 19. doi: 10.1093/nar/gkv1479

 

SimRNA examples:

The following are examples of SimRNA de novo folding results.