Protein-small molecule docking algorithms provide a means to model the structure of protein-small molecule complexes in structural detail and play an important role in drug development. In recent years the necessity of simulating protein side-chain flexibility for an accurate prediction of the protein-small molecule interfaces has become apparent, and an increasing number of docking algorithms ...

IEEE 802.16e based WiMAX networks promise a desirable available quality of service for mobile users and scheduling algorithms provide the best effective use of network resources in it. In this paper, we propose a novel cross-layer scheduling algorithm for OFDMA-based WiMAX networks. Our scheme employs a priority function at the MAC layer and a slot allocation policy at physical layer and by int...

We present the novel docking algorithm based on the Tensor Train decomposition and the TT-Cross global optimization. The algorithm is applied to the docking problem with flexible ligand and moveable protein atoms. The energy of the protein-ligand complex is calculated in the frame of the MMFF94 force field in vacuum. The grid of precalculated energy potentials of probe ligand atoms in the field...

Androgen receptor antagonists have been proved to be effective anti-prostate cancer agents. 3D-QSAR and Molecular docking methods were performed on curcumin derivatives as androgen receptor antagonists. The bioactive conformation was explored by docking the potent compound 29 into the binding site of AR. The constructed Comparative Molecular Field Analysis (CoMFA) and Comparative Similarity Ind...

Kinase insert domain receptor (KDR) inhibitors have been proved to be very effective anticancer agents. Molecular docking, 3D-QSAR methods, CoMFA and CoMSIA were performed on pyrrolo[3,2-d]pyrimidine derivatives as non-ATP competitive KDR inhibitors (type II). The bioactive conformation was explored by docking one potent compound 20 into the active site of KDR in its DFG-out inactive conformati...

The modeling of large biomolecular assemblies frequently requires a combination of multi-resolution data from a variety of biophysical sources. Several algorithmic solutions to this docking problem have been proposed which are usually based on the spatial cross correlation. In [1] it was shown that Laplace-filtering techniques can improve the docking performance of these algorithms. This note p...

Cross-docking is a an important logistics strategy in which freight is unloaded from inbound vehicles and directly loaded into outbound vehicles, with little or no storage in between. This study considers a crossdocking system which combines the vehicle routing problem with crossdocking (VRPCD) for both inbound and outbound operations and truck sequencing problem at docks. The objective is to m...

The quay crane scheduling problem (QCSP) is a global and all ports around the world seek to solve it, get an acceptable time of unloading containers from vessels or loading therefore reducing docking in terminal. This paper proposes three solutions for QCSP port Tripoli-Lebanon, two exact methods which are mixed integer linear programming dynamic algorithm, obtain optimal solution one heuristic...

Computational docking of small-molecule ligands into protein receptors is an important tool for modern drug discovery. Although conformational adjustments are frequently observed between the free and ligand-bound states, the conformational flexibility of the protein is typically ignored in protein-small molecule docking programs. We previously described the program RosettaLigand, which leverage...