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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

 Networking:

Reduntant 1Gbps fiber optic - Internet Access
10Gbps Ethernet Core Switching  (Juniper Ex45xx/42xx stacks & EX33xx VCP)
40Gb Infiniband QDR HPC network and/or 10GbE
10Gb LAN uplink to server room


Clusters:

64bit Computing Cluster of approx. 35 48&64 core AMD nodes + HTS & big memory nodes (approx. 1750 cores, 13.5 TFLOPs), 3,7TB RAM, Infiniband QDR Interconnect, 10GbE, Ubuntu 16.04 & 10.04, OGE 6.2u7
64bit Virtualization Cluster Pool with pool, networking & storage redundancy, approx. 2x768G RAM, 10Gb iSCSI, FC8G, XenServer 7.0, approx 12TB incl. SSD pools

 

Storage systems:

500 TB (0,5 PB) storage on Isilon Dell EMC Isilon NL410 nodes (5x) - incl. zoning, snapshots & ACL - accessible with NFS & Windows SMB
Approximately 200 TB of varied (cut to fit) storage incl. NL-SAS, SAS, SSD, SATA & varuious interfaces for interpoerability (FC, IB, 10GbE, SAS)

 

Servers:

(list is currently being updated)

Workstations:

Mostly Core i5, Core i7 or Xeon-bases motherboards with dedicated NVidia GPUs,
(list is currently being updated)

Laptops:

(this list is currently being updated)

Other:

Digital Projector S40, 3M, USA
Kyocera C2126MFP

 

 

COMPUTER SOFTWARE:

 

 OS:

Production servers: Ubuntu LTS, Debian Stable
Testing: Gentoo/Slackware/Ubuntu Linux, MS Windows 2003
Workstations: Ubuntu, Debian, MacOS, MS Windows Terminal Services

 

Molecular Modeling:

AMBER, University of California, San Francisco, USA
CABS, Warsaw University, Warsaw, Poland
CHARMM, Harvard University, Cambridge, USA
CNS, Yale University, New Haven, USA
HYPERCHEM 7.1, Hypercube, Inc., Gainesville, USA
INSIGHT II, Catalyst, Accelrys Software Inc., USA
MODELLER 9v1, University of California, San Francisco, USA
MOLSCRIPT 2.1.2, Avatar Software AB, Sweden
MC-SYM 3.3.2. UniversitĂŠ de MontrĂŠal, Canada
NAMD 2.6, Beckman Institute, USA
REFINER, Warsaw University, Warsaw, Poland
ROSETTA, University of Washington, Seattle, USA
SCULPT 3.0, Elsevier MDL, San Ramon, USA
SCWRL 3.0, Fox Chase Cancer Center, Philadelphia, USA
SYBYL 7.3, Tripos, USA
UNRES, University of Gdansk, Gdansk, Poladnd
ERNA3D, PENTAFOLIUM-SOFT, Rosengarten, Germany

 

Docking:

AUTODOCK, The Scripps Research Institute, La Jolla, USA
BIGGER, Universidade Nova de Lisboa, Caparica, Portugal
DOCK, University of California, San Francisco, USA
GRAMM, University of Kansas, Lawrence, USA
HADDOCK, Utrecht University, the Netherlands
RDOCK, Boston University, Boston, USA
SURFLEX, BioPharmics LLC, USA
ZDOCK, Boston University, Boston, USA

 

Sequence Analysis:

Clone Manager 7, Scientific & Educational Software, USA
CLANS & HHpred, Max Planck Institute of Developmental Biology, Tuebingen, Germany
NCBI Toolkit 6.1, NCBI, Bethesda, USA
Statistica 7 & Data Mining, StatSoft., USA

 

Office:

ENDNOTE, ISI ResearchSoft, Berkeley, USA
MS Office XP, Microsoft Corp., USA
VMware Workstation 5, Mware, Inc., USA
CrossOver Office 4.2, CodeWeavers, USA
MS Office 2010, Microsoft Corp., USA
MS Windows 7 Pro, Microsoft Corp., USA

 

 

WET LAB HARDWARE:

Protein and nucleic acid biochemistry:

CD Spectropolarimeter JASCO J-810, Jasco, Japan
ASM-800 DNA Synthesizer, Biosset Ltd., Russia
OPS-201 Oligonucleotide Purification System, Biosset Ltd., Russia
ABI Prism 310 Genetic Analyzer, Capillary DNA Sequencer, Applied Biosystems, USA
Minicycler, MJ Reasearch, USA
MJ Mini Personal Thermal Cycler, Bio-Rad Laboratories, Inc., USA
C1000 Thermal Cycler Chassis, Bio-Rad Laboratories, Inc., USA
Immersion Circulator 7312, PolyScience, USA
Fraction collector, Brandel, USA
Tensor 27, FTIR Spectrometer, Bruker, German

 

Chromatographic systems:

2x BioLogic LP, Bio-Rad Laboratories, Inc., USA
AKTA Purifier, GE Healthcare, USA
Avant, GE Healthcare, USA
HPLC, Waters, USA

 

Cell cultures:

2x Incubated orbital shaker Unitron - plus, Infors AG, Switzerland

 

Electrophoresis:

DNA - horizontal gel electrophoresis systems:
​2x SUBDNA, Kucharczyk TE, Poland
SUBMINI, Kucharczyk TE, Poland
SHU13, Sigma-Aldrich, USA
SHU6, Sigma-Aldrich, USA

 

Protein - vertical gel electrophoresis systems:

​3x PROTEAN II, Bio-Rad Laboratories, Inc., USA,
MINI PROTEAN tetra electrophoresis system, Bio-Rad Laboratories, Inc., USA,
MINIPOL 2, Kucharczyk TE, Poland
2x Vertical Electrophoresis system large scale, C.B.S Scientific, USA

 

Power supplies:

​2x E844, Consort nv, Belgium
2x EV232, Consort nv, Belgium
E132, Consort nv, Belgium

 

Protein blotting:

Mini Trans-Blot Cell, Bio-Rad Laboratories, Inc., USA,
2x Semi-dry blotters SV20-SDB, Sigma-Aldrich, USA
96 well Dot-Blot Hybridization Manifold, SciePlas Ltd., UK

 

 Microcentrifuges:

Mikro 20, Hettich, Germany
5415 D, Eppendorf, Germany
5804 R, Eppendorf, Germany
5418, Eppendorf, Germany
5117R, Eppendorf, Germany
5810R, Eppendorf, Germany

 

 Other equipment:

pH 211 Microprocessor pHMeter, Hanna Instruments, USA
Water Bath (Model WB), Memmert, Germany
Unimax shaker, Heidolph Instruments GmbH & Co. KG, Germany
3xThermomixer comfort, Eppendorf, Germany
Deepfreezer ULT 2186-3, Revco Thermo Electron Corporation, USA
Micro-Pulser, Bio-Rad Laboratories, Inc., USA

 

A CATALOG of other equipment freely available to the Bujnicki lab in IIMCB.