@article {Knizewski2008,
	title = {Uncharacterized DUF1574 leptospira proteins are SGNH hydrolases},
	journal = {Cell Cycle (Georgetown, Tex.)},
	volume = {7},
	number = {4},
	year = {2008},
	month = {feb},
	pages = {542{\textendash}4},
	keywords = {Amino Acid Sequence, Bacterial Proteins, Bacterial Proteins: genetics, Base Sequence, Computational Biology, DNA, Hydrolases, Hydrolases: genetics, Leptospira, Leptospira: enzymology, Models, Molecular, Molecular Sequence Data, Sequence Alignment, Sequence Analysis},
	issn = {1551-4005},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/18235229},
	author = {Lukasz Knizewski and Kamil Steczkiewicz and Krzysztof Kuchta and Lucjan Wyrwicz and Dariusz Plewczynski and Andrzej Koli{\'n}ski and Leszek Rychlewski and Krzysztof Ginalski}
}
@article {Hoffmann2006,
	title = {Three dimensional model of severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain and molecular design of severe acute respiratory syndrome coronavirus helicase inhibitors},
	journal = {Journal of Computer-Aided Molecular Design},
	volume = {20},
	number = {5},
	year = {2006},
	month = {may},
	pages = {305{\textendash}319},
	abstract = {The modeling of the severe acute respiratory syndrome coronavirus helicase ATPase catalytic domain was performed using the protein structure prediction Meta Server and the 3D Jury method for model selection, which resulted in the identification of 1JPR, 1UAA and 1W36 PDB structures as suitable templates for creating a full atom 3D model. This model was further utilized to design small molecules that are expected to block an ATPase catalytic pocket thus inhibit the enzymatic activity. Binding sites for various functional groups were identified in a series of molecular dynamics calculation. Their positions in the catalytic pocket were used as constraints in the Cambridge structural database search for molecules having the pharmacophores that interacted most strongly with the enzyme in a desired position. The subsequent MD simulations followed by calculations of binding energies of the designed molecules were compared to ATP identifying the most successful candidates, for likely inhibitors - molecules possessing two phosphonic acid moieties at distal ends of the molecule.},
	keywords = {Amino Acid Sequence, Catalytic Domain, Conserved Sequence, DNA Helicases, DNA Helicases: antagonists \& inhibitors, DNA Helicases: chemistry, Drug Design, Enzyme Inhibitors, Enzyme Inhibitors: pharmacology, Models, Molecular, Molecular Sequence Data, Protein, SARS Virus, SARS Virus: enzymology, Sequence Alignment, Structural Homology, Thermodynamics},
	issn = {0920-654X},
	doi = {10.1007/s10822-006-9057-z},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/16972168},
	author = {Marcin Hoffmann and Krystian Eitner and Marcin von Grotthuss and Leszek Rychlewski and Ewa Banachowicz and Tomasz Grabarkiewicz and Tomasz Szkoda and Andrzej Koli{\'n}ski}
}
@article {Bujnicki2001,
	title = {Three-dimensional modeling of the I-TevI homing endonuclease catalytic domain, a GIY-YIG superfamily member, using NMR restraints and Monte Carlo dynamics},
	journal = {Protein Engineering},
	volume = {14},
	number = {10},
	year = {2001},
	month = {oct},
	pages = {717{\textendash}721},
	abstract = {Using a recent version of the SICHO algorithm for in silico protein folding, we made a blind prediction of the tertiary structure of the N-terminal, independently folded, catalytic domain (CD) of the I-TevI homing endonuclease, a representative of the GIY-YIG superfamily of homing endonucleases. The secondary structure of the I-TevI CD has been determined using NMR spectroscopy, but computational sequence analysis failed to detect any protein of known tertiary structure related to the GIY-YIG nucleases (Kowalski et al., Nucleic Acids Res., 1999, 27, 2115-2125). To provide further insight into the structure-function relationships of all GIY-YIG superfamily members, including the recently described subfamily of type II restriction enzymes (Bujnicki et al., Trends Biochem. Sci., 2000, 26, 9-11), we incorporated the experimentally determined and predicted secondary and tertiary restraints in a reduced (side chain only) protein model, which was minimized by Monte Carlo dynamics and simulated annealing. The subsequently elaborated full atomic model of the I-TevI CD allows the available experimental data to be put into a structural context and suggests that the GIY-YIG domain may dimerize in order to bring together the conserved residues of the active site.},
	keywords = {Algorithms, Binding Sites, Biomolecular, Endodeoxyribonucleases, Endodeoxyribonucleases: chemistry, Models, Molecular, Monte Carlo Method, Nuclear Magnetic Resonance, Protein Structure, Sequence Alignment, Tertiary},
	issn = {0269-2139},
	url = {http://www.ncbi.nlm.nih.gov/pubmed/11739889},
	author = {Janusz M. Bujnicki and Piotr Rotkiewicz and Andrzej Koli{\'n}ski and Leszek Rychlewski}
}
