Present docking methodologies simulate only one single ligand at a time during docking process. In reality, the molecular recognition process always involves multiple molecular species. Typical protein-ligand interactions are, for example, substrate and cofactor in catalytic cycle; metal ion coordination together with ligand(s); and ligand binding with water molecules. To simulate the real mole...

he present art of drug discovery and design of new drugs is based on suicidal irreversible inhibitors. Covalent inhibition is the strategy that is used to achieve irreversible inhibition. Irreversible inhibitors interact with their targets in a time-dependent fashion, and the reaction proceeds to completion rather than to equilibrium. Covalent inhibitors possessed some significant advantages ov...

Autodock and its various variants are widely utilized docking approaches, which adopt optimization methods as search algorithms for flexible ligand virtual screening. However, many of them have their limitations, such poor accuracy dockings with highly ligands low efficiency. In this paper, a multi-swarm algorithm integrated environment is proposed to design high-performance high-efficiency pro...

In silico drug design using virtual screening, absorption, distribution, metabolism and excretion (ADME)/Tox data analysis, automated docking and molecular dynamics simulations for the determination of lead compounds for further in vitro analysis is a cost effective strategy. The present study used this strategy to discover novel lead compounds from an in-house database of Traditional Chinese M...

Many protein-protein docking protocols are based on a shotgun approach, in which thousands of independent random-start trajectories minimize the rigid-body degrees of freedom. Another strategy is enumerative sampling as used in ZDOCK. Here, we introduce an alternative strategy, ReplicaDock, using a small number of long trajectories of temperature replica exchange. We compare replica exchange sa...

As reported in earlier work, methods for hybrid optimal control can be used for optimal path planning of multi-agent systems. This paper considers a multi-vehicle transport scenario in which a hybrid model is used to represent the continuous dynamics of the vehicle motion and the dynamics arising from the docking-events between vehicles and a transported object. The decisions on the vehicles’ h...

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...