It is well known that computer-aided docking of large ligands, with many rotatable bonds, is extremely difficult. AutoDock is a widely used docking program that can dock small ligands, with upto 5 or 6 rotatable bonds, accurately and quickly. Docking of larger ligands, however, is not very accurate and is computationally expensive. In this paper we present an AutoDock-based incremental docking ...

The Hardware-In-the-Loop (HIL) simulation system for on-orbit docking dynamics is a large-scale complex test equipment. It establishes working conditions for the docking mechanism similar with those on orbit. The kernel of above dynamics HIL simulation system is a mechanical force and movement actions simulator. Besides the mechanical force and movement actions simulator, it also includes an en...

Bike sharing systems consist of a fleet of bikes placed in a network of docking stations. These bikes can then be rented and returned to any of the docking stations after usage. Predicting unrealized bike demand at locations currently without bike stations is important for effectively designing and expanding bike sharing systems. We predict pairwise bike demand for New York City’s Citi Bike sys...

78 Ghezel and 76 Mehraban sheep were used to evaluate the effect of fat-tail docking on reproductive performance. Within two days after birth the tails of 32 Ghezel female lambs and 28 Mehraban female lambs were docked using a tight rubber ring. The lambs were allowed to reproduce for three lambing opportunities and their reproductive performances were evaluated. The effect of docking on the fe...

Alzheimer’s disease (AD) as a complicated and progressive neurodegenerative disorder is the most common form of dementia and memory loss. On account of the multifactorial etiology of AD, the multi-target-directed ligand (MTDL) approach is a promising method in searching new drug candidates for this disease. Here, in this paper more than 500 tacrine-coumarin hybrids have been designed and drug-l...

A database of about 700 high-resolution kinase structures was used to test the reliability of 17 docking procedures (using six docking software packages) by means of self- and cross-docking studies. The analysis of about 80 000 docking calculations suggests that the docking of an unknown ligand into a kinase has a probability of only 30-37% to be a correct ligand pose. However, based on the hyp...

Protein-protein and protein-DNA/RNA interactions play a fundamental role in a variety of biological processes. Determining the complex structures of these interactions is valuable, in which molecular docking has played an important role. To automatically make use of the binding information from the PDB in docking, here we have presented HDOCK, a novel web server of our hybrid docking algorithm ...

Target fishing often relies on the use of reverse docking to identify potential target proteins of ligands from protein database. The limitation of reverse docking is the accuracy of current scoring funtions used to distinguish true target from non-target proteins. Many contemporary scoring functions are designed for the virtual screening of small molecules without special optimization for reve...

UNLABELLED A protein-protein docking decoy set is built for the Dockground unbound benchmark set. The GRAMM-X docking scan was used to generate 100 non-native and at least one near-native match per complex for 61 complexes. The set is a publicly available resource for the development of scoring functions and knowledge-based potentials for protein docking methodologies. AVAILABILITY The decoys...

In recent years, the importance of considering induced fit effects in molecular docking calculations has been widely recognised in the molecular modelling community. While small-scale protein side-chain movements are now accounted for in many state-of-the-art docking strategies, the explicit modelling of large-scale protein motions such as loop movements in kinase domains is still a challenging...