Protein tyrosine phosphatase 1B (PTP1B) is an attractive target for treating cancer, obesity, and type 2 diabetes. In our work, the way of combined ligand- and structure-based approach was applied to analyze the characteristics of PTP1B enzyme and its interaction with competitive inhibitors. Firstly, the pharmacophore model of PTP1B inhibitors was built based on the common feature of sixteen co...

We present a molecular docking study aimed to identify the binding site of protonated aminopyridines for the blocking of voltage dependent K(+) channels. Several active aminopyridines are considered: 2-aminopyridine, 3-aminopyridine, 4-aminopyridine, 3,4-diaminopyridine, and 4-aminoquinoleine. We apply the AutoDock force field with a lamarckian genetic algorithm, using atomic charges for the li...

The MIEC-SVM approach, which combines molecular interaction energy components (MIEC) derived from free energy decomposition and support vector machine (SVM), has been found effective in capturing the energetic patterns of protein-peptide recognition. However, the performance of this approach in identifying small molecule inhibitors of drug targets has not been well assessed and validated by exp...

BACKGROUND & OBJECTIVES Cysteine proteases (falcipains), a papain-family of enzymes of Plasmodium falciparum, are responsible for haemoglobin degradation and thus necessary for its survival during asexual life cycle phase inside the human red blood cells while remaining non-functional for the human body. Therefore, these can act as potential targets for designing antimalarial drugs. The P. falc...

The use of synthetic drugs is associated with various side effects and it important to look for other from medicinal plants. Therefore, this study aimed at assessing the inhibitory activities Calotropis procera leaf against ?-glucosidase hydrolase Sus B it?s possible mode inhibiting enzyme through molecular docking studies. From analysis, results shows that out thirty six (36) screened phytoche...

Methods The mutation frequency of subtype d in untreated persons was obtained from Stanford DR database, http://hivdb. stanford.edu/. Based on the database the wild type PTD sequence was generated. Crystal structure 3LZS showed more similarity based on BLASTp program. The protein structure 3LZS was used as a template to build wild type, major (L10V, N37D, K69Y), minor (K20I, L33I, P39T, Q61N), ...

Docking of small molecule compounds into the binding site of a receptor and estimating the binding affinity of the complex is an important part of the structure-based drug design process. For a thorough understanding of the structural principles that determine the strength of a protein/ligand complex both, an accurate and fast docking protocol and the ability to visualize binding geometries and...