• 1

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

PROTMAP2D v. 1.2.2

Two-dimensional maps of contacts summarize interactions between amino acids in the structure. They reveal characteristic patterns of interactions between secondary and super-secondary structures and are very attractive for visual analysis. The overlap of the residue contact maps of two structures can be easily calculated, providing a sensitive measure of protein structure similarity.

PROTMAP2D is a tool for calculation, visualization and comparison of contact maps. It can be used for quantitative and qualitative characterization of differences and similarities between alternative models of the same protein, e.g. members of the ensemble calculated from the results of the nuclear magnetic resonance (NMR) analysis, crystal structures solved under different conditions, theoretical models calculated with different programs, or series of conformations obtained in the course of  molecular dynamics (MD) simulations. PROTMAP2D allows analyzing multimeric proteins, and can be used to visualize intermolecular contacts in protein-protein complexes.

The MacOSX and Windows standalone binary versions of PROTMAP2D are available for download. Linux binary bundle has some prerequisites to install (see the README file enclosed for details).

Program's ftp directory:
ftp://ftp.genesilico.pl/pub/software/protmap2d/

PROTMAP2D 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.

We would greatly appreciate feedback from users, including compliments, bug reports, suggestions for new options to be implemented, etc. Send your messages to Michal J. Pietal, the principal developer of PROTMAP2D.

 

Important Notice: After most recent Windows7 update (SP1) we observed that PROTMAP2D ceased to work on Windows7.  In such case, we advise the users to use either other version, on either other systems (other Windows systems seem unaffected).  A temporary workaround is not to install SP1 on Windows7, however we do not recommend this as it might cause exposing the system to certain vulnerabilities.  We expect that this issue will be adressed by Windows7 SP2.

Technical Notice:  Because since the software was originally built and published, a number of Linux/BSD and macOS systems were made available, the respective target builds may no longer be supported.  Thus in order to use the program, we encourage the users to use either the Windows build natively or launch one with the use of Wine / Darwine frameworks (https://www.winehq.org , http://darwine.sourceforge.net ), under most recent Linux/BSD or macOS flavours, respectively.  These auxiliary tools been mentioned are freeware and easily installable, so no additional license or substantial effort is needed.

 

Please cite:
Pietal, M. J., Tuszynska, I., & Bujnicki, J. M. (2007). PROTMAP2D: visualization, comparison and analysis of 2D maps of protein structure. Bioinformatics, 23(11), 1429-1430.
 


PROTMAP2D gallery

A simple contact map of a dimer 1acv.  Secondary structure visible (red bars- helices, green bars- sheets) was read out from the pdb file



 

A distance map of the first model of an NMR ensemble 1aca

 

Distance map of 1aca, cropped by lower and upper contact threshold, 7 and 20 A, respectively

 

 

A comparison two models of I-TevI catalytic domain.  Right-upper: x-ray model (Van Roey, et al., 2002), left-lower: de-novo prediction (Bujnicki, et al., 2001)

 

A two-layer contact map on a 1acv ensemble.  White contacts exist in all models, while grey exist only in some

 

Frequency contact map of a MD unfolding trajectory. Left-lower contacts co-exist in a native (starting) structure, whilst right-upper do not

 

A comparison of two MD unfolding trajectories (same parameters, temperature set to 300 and 500 K).  Direction of the colour shift show stability of the structure during time (x and y axes)

 

A contact map similarity calculated for MD trajcetory



500.mpg

A MD trajectory movie exported to a file (feature available on windows and linux only)

NOTE: To open this file you not only need an appropriate MPEG file player, but also adequate video codecs installed. An example cross-platform tool capable of playing PROTMAP2D movie files is VLC program to be downloaded from http://www.videolan.org/vlc/