This article describes and reviews our efforts using Hex 3.1 to predict the docking modes of the seven target protein-protein complexes presented in the CAPRI (Critical Assessment of Predicted Interactions) blind docking trial. For each target, the structure of at least one of the docking partners was given in its unbound form, and several of the targets involved large multimeric structures (e....

Despite the importance of protein-RNA interactions in the cellular context, the number of available protein-RNA complex structures is still much lower than those of other biomolecules. As a consequence, few computational studies have been addressed towards protein-RNA complexes, and to our knowledge, no systematic benchmarking of protein-RNA docking has been reported. In this study we have extr...

This article describes and reviews our efforts using Hex 3.1 to predict the docking modes of the seven target protein-protein complexes presented in the CAPRI (Critical Assessment of Predicted Interactions) blind docking trial. For each target, the structure of at least one of the docking partners was given in its unbound form, and several of the targets involved large multimeric structures (e....

The Chemscore function was implemented as a scoring function for the protein-ligand docking program GOLD, and its performance compared to the original Goldscore function and two consensus docking protocols, "Goldscore-CS" and "Chemscore-GS," in terms of docking accuracy, prediction of binding affinities, and speed. In the "Goldscore-CS" protocol, dockings produced with the Goldscore function ar...

Receptor flexibility is a critical issue in structure-based virtual screening methods. Although a multiple-receptor conformation docking is an efficient way to account for receptor flexibility, it is still too slow for large molecular libraries. It was reported that a fast ligand-centric, shape-based virtual screening was more consistent for hit enrichment than a typical single-receptor conform...

We have developed an interactive docking program called VRDD. It offers various modes of displaying molecules in an immersive, three-dimensional virtual reality (VR) environment. It allows a user to interactively perform molecular docking aided by automatic docking and side chain conformational search. Binding free energies are computed in real time, and the program enables the user to explore ...

The hairpin ribozyme is a prototype small, self-cleaving RNA motif. It exists naturally as a four-way RNA junction containing two internal loops on adjoining arms. These two loops interact in a cation-driven docking step prior to chemical catalysis to form a tightly integrated structure, with dramatic changes occurring in the conformation of each loop upon docking. We investigate the thermodyna...

This paper describes visual-based behaviors for docking operations in mobile robotics. Two diierent situations are presented : in the ego-docking, each robot is equipped with a camera, and the motion is controlled when docking to a surface , whereas in the eco-docking, the camera and all the necessary computational resources are placed in a single external docking station, which may serve sever...

We have developed a computational pipeline for the prediction of protein-small molecule interactions and have applied it to the drug repositioning problem through a large-scale analysis of known drug targets and small molecule drugs. Our pipeline combines forward and inverse docking, the latter of which is a twist on the conventional docking procedure used in drug discovery: instead of docking ...

Nowadays, one of the major goals of the distribution environment is to reduce lead times and inventories. Cross-docking is a logistics technique which removes the storage and picking up the functions of a warehouse. The term cross-docking refers to moving products directly from incoming to outgoing trailers with little or no storage in between. According to the recent related papers, the truck ...