Fragment-based approaches have become popular tool in drug design due to their ability to screen large portions of chemical space with comparatively small libraries. However fragments can exhibit unspecific binding and even if they bind to a specific binding site in some cases more than one binding mode is observed [1]. For computational approaches like molecular docking fragments pose also new...

Department of Horticulture, Division of Applied Life Science (BK21 Program), Graduate School, Gyeongsang National University, Jinju 660-701, Korea. E-mail: [email protected] Division of Applied Life Science (BK21 Program), Systems and Synthetic Agrobiotech (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Researh Institute of Natural Science (RINS), Gyeongsang National...

objective(s): tyrosinase is a key enzyme in pigment synthesis. overproduction of melanin in parts of the skin results in hyperpigmentation diseases. this enzyme is also responsible for the enzymatic browning in fruits and vegetables. thus, its inhibitors are of great importance in the medical, cosmetic and agricultural fields. materials and methods: a series of twelve kojic acid derivatives wer...

An unusually large data set of 397 piperazinyl-glutamate-pyridines/pyrimidines as potent orally bioavailable P2Y(12) antagonists for inhibition of platelet aggregation was studied for the first time based on the combination of three-dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking, and molecular dynamics (MD) methods. The comparative molecular field analysis...

Today’s scoring functions are one of the main reasons that state-of-the-art protein-ligand dockings fail in about 20 % to 40 % of the targets due to the sometimes severe approximations they make. However these approximations are necessary for performance reasons. One possibility to overcome these problems is the inclusion of additional, preferably experimental information in the docking process...

In spite of availability of moderately protective vaccine and antibiotics, new antibacterial agents are urgently needed to decrease the global incidence of Klebsiella pneumonia infections. MurF ligase, a key enzyme, which participates in the bacterial cell wall assembly, is indispensable to existence of K. pneumonia. MurF ligase lack mammalian vis-à-vis and have high specificity, uniqueness, an...

In this talk I will discuss the possibility of predicting protein-protein interactions (docking) using a contact map representation. Rather than providing a full three dimensional model of the predicted complex, the method predicts contacting residues across the interface. A scoring function is used that combines structural, physicochemical and evolutionary information, where each potential res...

Molecular docking systems model and simulate in silico the interactions of intermolecular binding. Haptics-assisted docking enables the user to interact with the simulation via their sense of touch but a stringent time constraint on the computation of forces is imposed due to the sensitivity of the human haptic system. To simulate high fidelity smooth and stable feedback the haptic feedback loo...