Sirtuin 1 (SIRT1) is a nicotinamide adenine dinucleotide-dependent deacetylase, and its dysregulation can lead to ageing, diabetes, and cancer. From 346 experimentally confirmed SIRT1 inhibitors, an inhibitor structure pattern was generated by inductive logic programming (ILP) with DMax Chemistry Assistant software. The pattern contained amide, amine, and hetero-aromatic five-membered rings, ea...

The popular docking programs AutoDock, FlexX, and GOLD were used to predict binding modes of ligands in crystallographic complexes including X-ray water molecules or computationally predicted water molecules. Isoenzymes of two different enzyme systems were used, namely cytochromes P450 (n = 19) and thymidine kinases (n = 19) and three different "water" scenarios: i.e., docking (i) into water-fr...

The novel 3-methyladenine DNA glycosylase enzyme from oral pathogen Streptococcus sanguinisin involves in DNA repair mechanisms and participates in base excision repair. Its 3D structure is still unknown which may be a potential drug target, therefore here we proposed its putative 3D structure by homology modeling approach. EsyPred3d software produced more precise modeled structure as compare t...

Molecular docking can be reasonably successful at reproducing X-ray poses of a ligand in the binding site of a protein. However, scoring functions are typically unsuccessful at correctly ranking ligands according to their binding affinity. Using cyclooxygenase-1 (COX-1), a particularly challenging workhorse in virtual screening (VS) we show how the use of support vector machines (SVMs), trained...

MOTIVATION The efficiency indices (EI's) have been derived from the experimental binding affinities of drug candidates to macromolecules. These 'two-in-one' measures include information on both pharmacodynamics and pharmacokinetics of the candidate molecules. The time-consuming experimental measurement of binding affinities of extensive molecule libraries may become a bottle-neck of large scale...

Cationic porphyrin-anthraquinone hybrids bearing peripheral substituents, either pyridine, imidazole, or pyrazole rings have been investigated for their binding mode to DNA duplexes. The four kinds of DNA duplexes were used, which represent intercalation and groove binding modes. AutoDock 4.2 was used to dock nine hybrid compounds to four DNA duplexes, while monitoring of conformational changes...

VEGFR-2 tyrosine kinase receptor draws attention of the scientific fraternity in drug discovery for its important role in cancer, cardiopulmonary, cardiovascular diseases etc. Hence there is a need for novel VEGFR-2 inhibitors screening and testing for their biological activities. The 3D-structure was collected from PDB and stability was checked by using WHATIF and PROCHECK programs and subject...

Protein kinases are important drug targets in human cancers, inflammation and metabolic diseases. Docking studies was performed for all the benzimidazopyrimidine and coumarin substituted benzimidazopyridimine derivatives with human Aurora A kinase target (3FDN) employing flexible ligand docking approach by using AutoDock 4.2. All the compounds were found to have minimum binding energy ranging f...

UNLABELLED Sliding Box Docking is a program that manages simulations of ligand docking at different defined positions of a three-dimensional DNA structure. The procedure is similar to inverse docking, which is a method that performs docking simulations of a single ligand in the active sites of different targets. Sliding Box Docking manages docking simulations of one ligand into a box that slide...

Tanshinone IIA is a pharmacologically active ingredient extracted from Danshen, a Chinese traditional medicine. Its molecular mechanisms are still unclear. The present study utilized computational approaches to uncover the potential targets of this compound. In this research, PharmMapper server was used as the inverse docking tool and the results were verified by Autodock vina in PyRx 0.8, and ...