Molecular docking is a widely-used computational tool for the study of molecular recognition, which aims to predict the binding mode and binding affinity of a complex formed by two or more constituent molecules with known structures. An important type of molecular docking is protein-ligand docking because of its therapeutic applications in modern structure-based drug design. Here, we review the...

The idea in molecular docking is to design pharmaceuticals computationally by identifying potential drug candidates targeted against proteins. The candidates can be found using a docking algorithm that tries to identify the bound conformation of a small molecule ligand to a macromolecular target at its active site, which is the region of an enzyme where natural substrate binds. Mathematically, ...

The p38 MAP kinases play a critical role in regulating stress-activated pathways, and serve as molecular targets for controlling inflammatory diseases. Computer-aided efforts for developing p38 inhibitors have been hampered by the necessity to include the enzyme conformational flexibility in ligand docking simulations. A useful strategy in such complicated cases is to perform ensemble-docking p...

objective(s): a fast and reliable evaluation of the binding energy from a single conformation of a molecular complex is an important practical task. artificial neural networks (anns) are strong tools for predicting nonlinear functions which are used in this paper to predict binding energy. we proposed a structure that obtains binding energy using physicochemical molecular descriptions of the se...

Tiagabine (Gabitril) is a selective inhibitor of the human gamma-aminobutyric acid (GABA) transporter 1 (hGAT-1), a transport protein belonging to the family of neurotransmitter-sodium-symporters (NSS). It is a marketed drug, used for treatment of epilepsy. However, the molecular basis of protein-ligand interaction remains obscure due to the lack of a 3D structure of the target protein. In orde...

Alkaptonuria is an inherited disease that is caused by homogenticate accumulation. Deficiency or mutation in Homogentisate 1,2 dioxygenase gene (chromosome 3q21-q23) leads to production of incorrectly folded or truncated enzyme. Several studies indicated that competitive inhibitors of Homogentisate 1,2 dioxygenase like Nitisinone could be used for Alkaptonuria treatment. Therefore, it is of int...

Survivin (IAP proteins) remains an important target for anticancer drug development as it is reported to be over-expressed in tumor cells to enhance resistance to apoptotic stimuli. The study focuses on virtual screening of marine compounds inhibiting survivin, a multifunctional protein, using a computational approach. Structures of compounds were prepared using ChemDraw Ultra 10. Software and ...

Curcumin analogues were evaluated for COX-2 inhibitory as anti-inflammatory activities. The designed analogues significantly enhance COX-2 selectivity. The three compounds could dock into the active site of COX-2 successfully. The binding energies of -8.2, - 7.6 and -7.5 kcal/mol were obtained for three analogues of curcumin respectively. Molecular docking study revealed the binding orientation...

The efficient and accurate quantification of protein-ligand interactions using computational methods is still a challenging task. Two factors strongly contribute to the failure of docking methods to predict free energies of binding accurately: the insufficient incorporation of protein flexibility coupled to ligand binding and the neglected dynamics of the protein-ligand complex in current scori...