Bujnicki lab - GALLERY
  • 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

Restriction endonuclease SfiI
Our model was cited in the article describing the crystal structure (Vanamee et al., 2005), which appeared in press ten months after the paper describing our model. We appreciate it.  
Restriction endonuclease R.MvaI
Our theoretical model and the crystallographic model were described in independent articles submitted at the same time. Read More
Restriction endonuclease R.Hpy188I
Our manuscript describing the model was cited in the article describing the crystal structure (Sokolowska et al., 2010), which appeared in press two years after our paper. We appreciate it.  
HsdR subunit of the restriction-modification enzyme EcoR124I
Our manuscript describing the model was submitted before the publication of the crystal structure, but appeared in press already after submission of the crystallographic article (and was not cited by the crystallographers).  
Restriction endonuclease R.Eco29kI
Our manuscript describing the model was cited in the article describing the crystal structure (Mak et al., 2010), which appeared in press three years after our paper. We appreciate it.  
Restriction endonuclease R.PspGI
Our model was cited in the article describing the crystal structure (Szczepanowski et al., 2008), which appeared in press two years after the paper describing our model. We appreciate it.  
Homing Endonuclease I-Ssp6803I
Our model was cited in the article describing the crystal structure (Zhao et al. 2007), which appeared in press two months after the paper describing our model. We appreciate it. Read More
small RNA methyltransferase HEN1
Our model was cited in the articles describing the crystal structures of A.thaliana HEN1 (Huang et al., 2009) and two bacterial orthologs of HEN1 (Mui Chan et al., 2009). We appreciate it.  
mRNA cap (Guanine-N7) methyltransferase - Cap0
The experimental model is available in the PDB only for near homologue. We are looking forward to see fair assessment of our model by the crystallographers.  
Methyltransferase Tgs1 
Our manuscript describing the model was cited in the article describing the crystal structure (Monecke et al., 2009), which appeared in press five years after our paper. We appreciate it.  
Methyltransferase Sgm
Our model was confirmed by us and collaboration in the article, which appeared in press two years later.  
Methyltransferase TrmK
The crystal structure is available in the PDB, but to our knowledge describing paper has not been published yet.  
Methyltransferase KamB
Our manuscript describing the model was cited in the article describing the crystal structure (Macmaster et al., 2010), which appeared in press three years after our paper. We appreciate it.  
Methyltransferase TrmB
Our model was cited in the article describing the crystal structure (Zhou et al., 2009), which appeared in press four years after the paper describing our model. We appreciate it.  
S-adenosylhomocysteine hydrolase from P.falciparum
Our model was cited in the article describing the crystal structure (Tanaka et al., 2004), which appeared in press one year after the paper describing our model. We appreciate it.  
Arr4p ATPase
Our manuscript describing the model was cited in the article describing the crystal structure (Suloway et al., 2009), which appeared in press four years after our paper. We appreciate it.  
tRNA modification enzyme MiaA
Our manuscript describing the model was submitted before the publication of the crystal structure, but appeared in press already after submission of the crystallographic article (and was not cited by the crystallographers). Read More
tRNA modification enzyme MiaE
The experimental model is available in the PDB, but to our knowledge has not been described in a publication yet. We are looking forward to see fair assessment of our model by the crystallographers. Read More
DNA repair enzyme Endonuclease V
Our manuscript describing the model was submitted before the publication of the crystal structure, but appeared in press already after submission of the crystallographic article (and was not cited by the crystallographers). Read More
3-methyladenine DNA glycosylase I (TAG)
Our manuscript describing the model was cited in the article describing the crystal structure (Kwon et al., 2003), which appeared in press one year after our paper. We appreciate it.