To study the involvement of compounds stigmasterol and oleic acid isolated from marine sponge Aurora globostellata and docking against the Human Epidermal Growth Factor Receptor-2 in breast cancer. The comparative molecular docking was performed with the natural compounds from marine sponge and the synthetic drugs used in breast cancer treatment against the target HER2. The molecular docking an...

Microbial Transglutaminase (MTgase) shows a wide specificity of action in its ability to interact with proteins from different families. Previous experimental data (in collaboration with BIOKER, POLARIS, Pula, Italy) demonstrated that MTGase interacts and transglutaminates the Granulocyte-Colony-StimulatingFactor (GCSF) at residue Q135. In this work this interaction is investigated through the ...

A newly developed statistical pair potential based on Distance-scaled Finite Ideal-gas REference (DFIRE) state is applied to unbound protein-protein docking structure selections. The performance of the DFIRE energy function is compared to those of the well-established ZDOCK energy scores and RosettaDock energy function using the comprehensive decoy sets generated by ZDOCK and RosettaDock. Despi...

Many proteins of widely differing functionality and structure are capable of binding heparin and heparan sulfate. Since crystallizing protein-heparin complexes for structure determination is generally difficult, computational docking can be a useful approach for understanding specific interactions. Previous studies used programs originally developed for docking small molecules to well-defined p...

Maneuvers performed with tractor-trailers vehicles (N-trailers) belong to the most demanding motion control tasks in the transportation practice. Very frequent maneuvers concern the lining-up process of a vehicle chain, usually as a preliminary stage which prepares the system to subsequent parking/docking maneuvers. The most common lining-up control approach results from utilization of the open...

With the advancement of novel techniques in drug discovery, various approaches have been used in the structure based drug designing. One of the most important strategies is molecular docking. The study of molecular docking and simulation deals with the intermolecular interaction of drug targets i.e. proteins, nucleic acids, lipids and ligands. The aim of molecular docking is to achieve an optim...

Loops connect regular secondary structures. In many instances, they are known to play crucial biological roles. To bypass the limitation of secondary structure description, we previously defined a structural alphabet composed of 16 structural prototypes, called Protein Blocks (PBs). It leads to an accurate description of every region of 3D protein backbones and has been used in local structure ...

CYP719A14 structure analysis and its interaction with ligands via bioinformatic methods. Methods. Homologous modeling of three-dimensional enzyme. Molecular docking. Results. enzyme, which shows cheilanthifoline synthase activity, model was build based on results homologous modeling. Interaction built possible substrates – benzylisoquinoline compounds: (S)-Scoulerine, (S)-Cheilanthifoline, (S)-...

The ligand-receptor interaction between some peptidomimetic inhibitors and a class II MHC peptide presenting molecule, the HLA-DR4 receptor, was modeled using some three-dimensional (3D) quantitative structure-activity relationship (QSAR) methods such as the Comparative Molecular Field Analysis (CoMFA), Comparative Molecular Similarity Indices Analysis (CoMSIA), and a pharmacophore building met...