Although some docking methods accounting for protein flexibility exist, most large scale virtual screening approaches work with rigid protein models. A first step towards flexibility integration is the consideration of degrees of freedom resulting from hydrogens, especially, if involved in hydrogen bonding. To account for this type of flexibility, we present a flexible-hydrogen interaction mode...

Protein docking is a new and challenging application for query processing in database systems. Our architecture for an efficient support of docking queries is based on the multistep query processing paradigm, a technique well-known from spatial database system. Along with physicochemical parameters, the geometry of the molecules plays a fundamental role for docking retrieval. Thus, 3D structure...

Multi-echelon distribution networks are quite common in supply chain and logistics. Deliveries of multiple items from factories to customers aremanagedby routing and consolidating shipments inwarehouses carrying on long-term inventories. On the other hand, cross-docking is a logistics technique that differs from warehousing because products are no longer stored at intermediate depots. Instead, ...

Predicting the three-dimensional native structures of protein dimers, a problem known as protein-protein docking, is key to understanding molecular interactions. Docking is a computationally challenging problem due to the diversity of interactions and the high dimensionality of the configuration space. Existing methods draw configurations systematically or at random from the configuration space...

Monoamine oxidase B (MAO-B) inhibitory potential of adenosine A(2A) receptor (AA(2A)R) antagonists has raised the possibility of designing dual-target-directed drugs that may provide enhanced symptomatic relief and that may also slow the progression of Parkinson's disease (PD) by protecting against further neurodegeneration. To explain the dual inhibition of MAO-B and AA(2A)R at the molecular l...

The computer program DAIM (Decomposition and Identification of Molecules) has been developed to automatically break up compounds in small-molecule libraries for fragment-based docking as well as database analysis. Here, DAIM is evaluated on 130 ligands derived from known crystal structures of ligand-protein complexes. The decomposition and a new fingerprint-based identification technique are us...

Prediction of the binding mode of a ligand (a drug molecule) to its macromolecular receptor, or molecular docking, is an important problem in rational drug design. We have developed a new docking method in which a non-conventional Monte Carlo (MC) simulation technique is employed. A computer program, MCDOCK, was developed to carry out the molecular docking operation automatically. The current v...