Identification of PPARγ ligands with One-dimensional Drug Profile Matching.
Drug Des Devel Ther. 2013 Sep 2;7:917-28.
Experimental confirmation of new drug-target interactions predicted by drug profile matching.
J Med Chem. 2013 Nov 14;56(21):8377-88.
Protein-peptide complex crystallization: a case study on the ERK2 mitogen-activated protein kinase.
Acta Crystallogr D Biol Crystallogr. 2013 Mar;69(Pt 3):486-9. doi: 10.1107/S0907444912051062.
The NM23-H1/H2 homolog NDK-1 is required for full activation of Ras signaling in C. elegans.
Development 2013 Aug;140(16):3486-95. doi: 10.1242/dev.094011.
Quantitative characterization of the activation steps of mannan-binding lectin (MBL)-associated serine proteases (MASPs) points to the central role of MASP-1 in the initiation of the complement lectin pathway.
J Biol Chem. 2013 Mar 29;288(13):8922-34
Biochemical characterization of Acacia schweinfurthii serine proteinase inhibitor
J Enzyme Inhib Med Chem. 2013 Oct 3.
Comparison of complexes formed by a crustacean and a vertebrate trypsin with bovine pancreatic trypsin inhibitor - the key to achieving extreme stability?
FEBS J. 2013 Nov;280(22):5750-63.
Természet Világa 144(6): 271-3.
Mihály Kovács profile interview
Newsletter of the Biophysical Society (USA), January
Visualization of human Blooms syndrome helicase molecules bound to homologous recombination
FASEB J. 27: 4954-64.
From keys to bulldozers: expanding roles for winged helix domains in nucleic acid-binding proteins.
Trends Biochem. Sci. 38: 364-71.
A subdomain interaction at the base of the lever allosterically tunes the mechanochemical mechanism of myosin 5a.
PLoS One 8: e62640
Overdamped mechanical model of myosin II.
Periodica Polytechnica Civil Engineering 57: 11-19.
Inhibition of the serine proteases of the complement system.
Adv Exp Med Biol. 2013;735:23-40.
Internal friction in enzyme reactions.
IUBMB Life. 2013 Jan;65(1):35-42. doi: 10.1002/iub.1101.
The empirical concept of internal friction was introduced 20 years ago. This review summarizes the results of experimental and theoretical studies that help to uncover the nature of internal friction. After the history of the concept, we describe the experimental challenges in measuring and interpreting internal friction based on the viscosity dependence of enzyme reactions. We also present speculations about the structural background of this viscosity dependence. Finally, some models about the relationship between the energy landscape and internal friction are outlined. Alternative concepts regarding the viscosity dependence of enzyme reactions are also discussed.
Virtual Affinity Fingerprints for Target Fishing: A New Application of Drug Profile Matching.
J. Chem. Inf. Model., 2013, 53 (1), pp 103-113
We recently introduced Drug Profile Matching (DPM), a novel virtual affinity fingerprinting bioactivity prediction method. DPM is based on the docking profiles of ca. 1200 FDA-approved small-molecule drugs against a set of nontarget proteins and creates bioactivity predictions based on this pattern. The effectiveness of this approach was previously demonstrated for therapeutic effect prediction of drug molecules. In the current work, we investigated the applicability of DPM for target fishing, i.e. for the prediction of biological targets for compounds. Predictions were made for 77 targets, and their accuracy was measured by Receiver Operating Characteristic (ROC) analysis. Robustness was tested by a rigorous 10-fold cross-validation procedure. This procedure identified targets (N = 45) with high reliability based on DPM performance. These 45 categories were used in a subsequent study which aimed at predicting the off-target profiles of currently approved FDA drugs. In this data set, 79% of the known drug-target interactions were correctly predicted by DPM, and additionally 1074 new drug-target interactions were suggested. We focused our further investigation on the suggested interactions of antipsychotic molecules and confirmed several interactions by a review of the literature.
Structural and biochemical characterization of a NAD+-dependent alcohol dehydrogenase from O. oeni as a new model molecule for bioindustrial applications.
Appl. Micorbiol. Biotechnol.
Structural insights into the trp-cage folding intermediate formation
Chemistry. 2013 Feb 18;19(8):2628-40
In Neil D. Rawlings and Guy S. Salvesen, editors: Handbook of Proteolytic Enzymes, Oxford: Academic Press, pp. 877 - 882.