Protein-based virtual screening plays an important role in modern drug discovery process. Most protein-based virtual screening experiments are carried out with docking programs. The accuracy of a docking program highly relies on the incorporated scoring function based on various energy terms. The existing scoring functions deal all the energy terms with the equal weight function or other weight...

In recent years, an epidemic of the highly pathogenic avian influenza H7N9 virus has persisted in China, with a high mortality rate. To develop novel anti-influenza therapies, we have constructed a machine-learning-based scoring function (RF-NA-Score) for the effective virtual screening of lead compounds targeting the viral neuraminidase (NA) protein. RF-NA-Score is more accurate than RF-Score,...

A recent research demonstrates that the inhibition of mammalian target of rapamycin (mTOR) improves survival and health for patients with Leigh syndrome. mTOR proteins can be treated as drug target proteins against Leigh syndrome and other mitochondrial disorders. In this study, we aim to identify potent TCM compounds from the TCM Database@Taiwan as lead compounds of mTOR inhibitors. PONDR-Fit ...

BACKGROUND Docking and scoring large libraries of ligands against target proteins forms the basis of structure-based virtual screening. The problem is trivially parallelizable, and calculations are generally carried out on computer clusters or on large workstations in a brute force manner, by docking and scoring all available ligands. CONTRIBUTION In this study we propose a strategy that is b...

Protein structure-based molecular design using the computational techniques of protein structure prediction, ligand docking, and virtual screening is an integral part of drug discovery for limiting the application of the structure-based approach to target proteins such as G-protein-coupled receptors (GPCRs). GPCRs play an important role in living organisms and are of major interest to the pharm...

It has been indicated that tumor necrosis factor receptor-associated factor-6 (TRAF6) will upregulate the expression of hypoxia-inducible factor-1α (HIF-1α) and promote tumor angiogenesis. TRAF6 proteins can be treated as drug target proteins for a differentiation therapy against cancers. As structural disordered disposition in the protein may induce the side-effect and reduce the occupancy for...

The recent emergence and re-emergence of alphaviruses, in particular the chikungunya virus (CHIKV), in numerous countries has invoked a worldwide threat to human health, while simultaneously generating an economic burden on affected countries. There are currently no vaccines or effective drugs available for the treatment of the CHIKV, and with few lead compounds reported, the vital medicinal ch...

Due to low cost, speed, and unmatched ability to explore large numbers of compounds, high throughput virtual screening and molecular docking engines have become widely utilized by computational scientists. It is generally accepted that docking engines, such as AutoDock, produce reliable qualitative results for ligand-macromolecular receptor binding, and molecular docking results are commonly re...