We developed an algorithm for predicting three-dimensional structure of proteins. This algorithm is based on the electrostatic screening model of conformational preferences. We have tested this algorithm in the four CASP experiments (http://predictioncenter.gc.ucdavis.edu). In these experiments researchers predict structures of proteins. We have competed in the category of ab-initio predictions. Our algorithm has been shown to be competitive in the two CASP experiments, which has been awarded by the invited lectures. Our algorithm for predicting structures is using a simple physical model.
B.04 Guest lecture
COBISS.SI-ID: 2818586Our contribution was among 10% of studies, which were selected by the scientific committee for the lecture from the thousand of conference contributions. Achievements of investigation of denatured states of proteins, which confirmed our electrostatic model for prediction of structural preferences in denatured proteins, were presented. We reported that fluctuating ß-strands exist in urea denatured ubiquitin (8M urea, pH 2). At these conditions ubiquitin contains no detectable ß-sheet secondary structures; nevertheless, the fluctuating ß-strands coincide to the ß-strands in the native state.
B.03 Paper at an international scientific conference
COBISS.SI-ID: 3344410In the period 2004-2007 dr. S. Golič Grdadolnik performed four industrial projects for the Lek Pharmaceuticals. Projects involved research of conformational and dynamic properties of new biologically active molecules, which were developed in Lek Pharmaceuticals. Modern approaches of NMR spectroscopy were applied. Dr. Jože Grdadolnik performed two industrial projects for Lek Pharmaceuticals and one industrial project for the Krka Pharmaceuticals. Projects involved implementation of the vibrational spectroscopy for structural studies of new pharmaceutically active molecules.
F.17 Transfer of existing technologies, know-how, methods and procedures into practice
COBISS.SI-ID: 1111111Dr. Jože Grdadolnik was research mentor for diploma work of Barbara Grobelnik with the title: Calculation of optical constants in infrared region by applying the attenuated total reflection. They have calculated the expected error of the reflection spectra. The results were used to improve the procedure for calculation of absorbance spectrum. The work has been awarded in 2006 with Prešern Award by the Faculty of mathematics and physics, University of Ljubljana.
E.01 National awards
COBISS.SI-ID: 1917796The paper entitled: Protein Chemical Shifts Arising form ? -Helices and ß -Sheets Depend on Solvent Exposure (F. Avbelj, D. Kocjan, R.L. Baldwin, Proc. Natl. Acad. Sci. USA, 101, 17394-17397, 2004) has been ranked 6th of the most read papers of PNAS (November 2006). In this paper we describe the effect of electrostatic screening on NMR chemical shifts.
B.06 Other
COBISS.SI-ID: 1111111In the period 2004-2007 dr. S. Golič Grdadolnik performed four industrial projects for the Lek Pharmaceuticals. Projects involved research of conformational and dynamic properties of new biologically active molecules, which were developed in Lek Pharmaceuticals. Modern approaches of NMR spectroscopy were applied. Dr. Jože Grdadolnik performed two industrial projects for Lek Pharmaceuticals and one industrial project for the Krka Pharmaceuticals. Projects involved implementation of the vibrational spectroscopy for structural studies of new pharmaceutically active molecules.
F.17 Transfer of existing technologies, know-how, methods and procedures into practice
The paper entitled: Protein Chemical Shifts Arising form ? -Helices and ß -Sheets Depend on Solvent Exposure (F. Avbelj, D. Kocjan, R.L. Baldwin, Proc. Natl. Acad. Sci. USA, 101, 17394-17397, 2004) has been ranked 6th of the most read papers of PNAS (November 2006). In this paper we describe the effect of electrostatic screening on NMR chemical shifts.
B.06 Other