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1

Grand challenges less challenging: new possibilities provided by Graphics Processing Units

Kuna D., Makowski M., Mazura G., Russek P., Janiszewski M., Wiatr K.

Bio-Algorithms and Med-Systems

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2011

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Vol. 7, no. 4

23--27

EN

The specific features of general-purpose computing on graphics processing units (GPGPU) in the area of scientific computing are highlighted. The hardware and software resources provided by CYFRONET are presented and selected benchmark calculations are briefly introduced.

2

Theoretical study of new pyranoquinoxaline, pyrimido (pyrido) pyranoquinoxaline and quinoxalinone derivatives

Castro E. A., Moustafa O. S.

Bulletin of the Polish Academy of Sciences. Chemistry

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2003

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Vol. 51, No. 1

59-69

EN

We present the results of structural theoretical calculations made with the Molecular Mechanics method for a series of new pyranoquinoxaline, pyrimido (pyrido) pyranoquinoxaline and quinoxalinone derivatives which have been recently synthetized. The different contributions to the steric energy are analysed for the new 19 molecules, some particular structural features are discussed and some possible extensions are pointed out.

3

Topological "in-out" isomerism in perhydrogenated fullerenes revisited : C60H58R1R2 with two R groups "in" (R1, R2=H, Me)

Dodziuk H., Lukin O., Nowiński K.

Polish Journal of Chemistry

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1999

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vol. 73 nr 2

299-306

EN

Molecular mechanics calculation (using MM+, MMX and AMBER force fields) of all constitutional and topological isomers of C60H58R1R2 with R1,R2=H, Me revealed that "in,in" isomers are always the most stable, while the corresponding "out,out" isomers have the biggest energy. Moreover, a substitution of an "in" hydrogen atom by a methyl group in the confined volume of the C60 cage doesn't change, or even lowers, the steric energy. The dependence of steric energy on the distance between the "in" hydrogen atoms (or between the carbon atoms of "in" methyl groups) reveals highly irregular behaviour, for close neighbours, reflecting differences in the energies associated withconsiderable distortions of the fullerane skeleton.

4

Molecular modelling in the rational design of some anti-tumor and antifungal agents

Mazerski J., Borowski E.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

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1998

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Vol. 2, No 4

511-550

EN

In this paper we present our approaches and results concerning application of molecular modelling techniques in the design of new chemotherapeutic agents for the control of eukariotic systems, comprising compounds for the treatment of systemic fungal infections and tumor deseases. In the case of anti-tumor agents we focused our attention on molecular properties of natural and synthetic anthraquinones. In the area of antifungal compounds we adopted two approaches. In one of them we examine molecular nature of undesirable properties of polyene macrolide antifungal antibiotic - amphotericin B using molecular modelling techniques. Another approach was aimed at the development of selective inactivator of glucosamine synthase, a novel target for antifungal compounds. In this problem we have used computational chemistry methods to identify structural features responsible for the selective inactivation of the target enzyme.

5

Modelling drug-receptor interactions in an average binding site for NK2

Alagona G., Ghio C., Monti S.

TASK Quarterly : scientific bulletin of Academic Computer Centre in Gdansk

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1998

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Vol. 2, No 4

563-581

EN

A tentative procedure applied to the search for a new antagonist of neurokinin A (NKA) is presented. In parallel a tentative 3-D model of the NK2 receptor was created, using bacteriorhodopsin (BRD) as a template. The residue substitutions were performed in BRD to obtain the sequence for NK2R_H and the seven a-helical segments were optimized forcing the a-helical backbone to match the corresponding aligned parts of BRD, while the arrangements of the side chains were model built based on available site-directed mutagenesis studies. Constrained MM and molecular dynamics simulations were carried out H-bonding a low energy conformer of the known drugs to residues in the receptor site, allowing both the receptor site and drugs to relax. The Connolly surface for each ligand allowed to determine an "average" binding site in which all the low energy conformers of known and prospective drugs were docked and classified according to a statistical index. The whole procedure was repeated exploiting the lately published structure of an actual G protein coupled receptor as a better template, thus producing a cavity in the binding site to directly dock the drugs. Corollary validations of the force fields used are also mentioned. In addition intra- and intermolecular interactions suitable to produce more active drugs were evaluated.