In this work, we validate and analyze the results of previously published cross docking experiments and classify failed dockings based on the conformational changes observed in the receptors. We show that a majority of failed experiments (i.e. 25 out of 33, involving four different receptors: cAPK, CDK2, Ricin and HIVp) are due to conformational changes in side chains near the active site. For ...

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 ...

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...

At cross docking terminals, products from incoming trucks are sorted according to their destinations and transferred to outgoing trucks using a small temporary storage. Such terminals allow companies to reduce storage and transportation costs in a supply chain. This paper focuses on the operational activities at cross docking terminals. We consider the trucks scheduling problem with the objecti...

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...

Cross-docking is a logistics technique that minimizes the storage and order picking functions of a warehouse while still allowing it to serve its receiving and shipping functions. In this paper, we propose a novel hybrid meta-heuristic algorithm for solving scheduling trucks in cross-docking problems. This algorithm comprises three components: an initial population generation method based on an...

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...