Docking functions are believed to be the essential component of docking algorithms. Both physically and statistically based functions have been proposed, but there is no consensus about their relative performances. Here, we propose an evaluation approach based on exhaustive enumeration of all possible docking solutions obtained with a discretized description of a rigid docking process. We apply...

Ligand docking to flexible protein molecules can be efficiently carried out through ensemble docking to multiple protein conformations, either from experimental X-ray structures or from in silico simulations. The success of ensemble docking often requires the careful selection of complementary protein conformations, through docking and scoring of known co-crystallized ligands. False positives, ...

Protein-ligand docking is an essential technique in computer-aided drug design. While generally available docking programs work well for most drug classes, carbohydrates and carbohydrate-like compounds are often problematic for docking. We discuss the peculiarities of protein-carbohydrate interactions and their impact on protein-carbohydrate docking and review the state of the art in docking of...

Autonomous underwater vehicles (AUVs) have been deployed for underwater exploration. However, its potential is confined by its limited on-board battery energy and data storage capacity. This problem has been addressed using docking systems by underwater recharging and data transfer for AUVs. In this work, we propose a vision based framework for underwater docking following these systems. The pr...

BACKGROUND Computational approaches have emerged as an instrumental methodology in modern research. For example, virtual screening by molecular docking is routinely used in computer-aided drug discovery. One of the critical parameters for ligand docking is the size of a search space used to identify low-energy binding poses of drug candidates. Currently available docking packages often come wit...

The effective integration of detailed structural information with computational chemistry, medicinal chemistry, and informatics transforms the dream of virtual screening into reality. One of the most important technologies essential for virtual screening is an effective docking method to find molecules that efficaciously interact with their target molecules. Since an efficient docking method ca...

The docking algorithms were developed incrementally throughout the five tests sessions, making heavy use of the reconfiguration and modularity features of the SPHERES design. The architecture for the docking algorithms is based on the development of smaller simple modules that implement: two estimation algorithms based on extended Kalman filters; mixer functions to convert forces and torques to...

ABSTRACT: Quantitative structure-activity relationship (QSAR) study on the piperidone-grafted mono- and bis-spirooxindole-hexahydropyrrolizines as potent butyrylcholinestrase (BuChE) inhibitors were carried out using statistical methods, molecular dynamics and molecular docking simulation. QSAR methodologies, including classification and regression tree (CART), multiple linear regression (MLR),...

A set of Xanthohumol derivatives were selected and molecular docking studies of these ‎compounds on thioredoxin reductase were conducted. Based on new structural patterns using in ‎silico-screening study, new potent lead compounds were designed. The results due to validated ‎docking protocols lead to find that Thr58, Gly57, Gly21, Asp334, Glu163, Ala130, IIe332, ‎Val44 and Gly132 are the main a...