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APVV project 0117-06 (February 2007 - December 2009) |
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2009 Filtering the CSD database, re-building the DIOL-MAN database, re-docking the DIOL-MAN database into Golgi mannosidase enzyme model (Januar-March 2009) Molecular cloning, expresion and purification of Golgi mannosidases II (drosophila dGMII), inhibition assays (IC50 and Ki) of commercial mannosidase inhibitors (swainsonine and mannostatin A) (Januar-March 2009) The preparation of the compound SAV31 for inhibition tests and co-crystallization with dGMII (January-March 2009) 2008 Running a 64-bit operating system on the Linux Beowulf type cluster, the re-compilation of chemical software (speedup of processing and analysing calculations) (February-April 2008) Docking different substrate fragments into Golgi and lysosomal alpha-mannosidases II with Glide (understanding enzymes specificities) (March 2008) pKa calculations of ionizable residues of the mannosidases and functional groups of their inhibitors with PropKa (building a more accurate model) (May-June 2008) Building 3D structures of drosophila, bovine, mouse, cat, pig and human lysosomal and Golgi alpha-mannosidase II by homology modeling using Modeller (understanding enzymes specificities) (June-August 2008) Benchmark calculations of DFT methods to select the methodology for subsequent QM and QM/MM calculations of the mannosidase systems (building methodology) (September 2007-August 2008) Building a new Linux Beowulf type cluster and small workstations (enlarging computational facilities) (September-November 2008) Molecular cloning, expresion and purification of lysosomal mannosidases (drosophila dLM252 and dLM407) (January-August 2008) Inhibition assays (IC50 and Ki, dLM408) of commercial mannosidase inhibitors (swainsonine and mannostatin A) and novel compounds (2 derivatives of UDII and 14 derivatives of indolizidine, a structure SAV-31 (micromolar level activity)) (March-May 2008) 11th Bratislava's saccharide symposium, Smolenice (presentation of results, 5 participents, 1 oral presentation and 2 posters) (September 21-26, 2008) Filtering the ZINC database, building a DIOL-MAN database, docking the DIOL-MAN database into Golgi mannosidase enzyme model (October-December 2008) Molecular cloning, expresion and purification of Golgi mannosidases IIb (drosophila dGMIIb), inhibition assays (IC50 and Ki) of commercial mannosidase inhibitors (swainsonine and mannostatin A) (September-December 2008) 2007 Design of a boot server and compilation of the cluster operating system Linux Gentoo (April-June 2007) Building Linux Beowulf type cluster and 1Gb network (May-June 2007) Testing parallel computing with the Jaguar, ADF, Gaussian, Gromacs and Amber codes (June-August 2007) Determination of pKa values of amino groups in mannosidase inhibitors at the QM level (July 2007) Building 3D structures (models 01) of human Golgi and lysosomal mannosidases by homology modeling (July 2007) Development of a scoring function (model 01) for the prediction of the enzyme-inhibitors binding affinities (August 2007) Training course on docking modeling (2 students, June-August 2007) Molecular cloning, expresion and purification of lysosomal mannosidase (dLM408) (June-September 2007) In vitro measurements of biological activities of 2 selected inhibitors against recombinant lysosomal mannosidase under different pH conditions (October-December 2007) Poster presentation - EUROCARB14 symposium in Luebeck, Germany (3 participants, September 2007) Poster presentation - eCheminfo workshop in Oxford, United Kingdom (1 participant, September 2007) Smolenice symposium - Advances in Organic synthesis, (1 participant, September 2007) |
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