Molecular docking is one of the primary computational methods used by pharmaceutical companies to try to reduce the cost of drug discovery. A common docking technique, used for low-resolution screening or as an intermediate step, performs a threedimensional correlation between two molecules to test for favorable interactions between them. We extend our previous work on FPGA-based docking accele...

the interaction between [pt(phen)(pyrr-dtc)]no3 (where phen = 1,10-phenanthroline and pyrr-dtc =pyrrolidinedithiocarbamat) with human serum albumin (hsa) was studied by fluorescence, uv–vis absorption, circular dichroism (cd) spectroscopy and molecular docking technique under like physiological condition in tris–hcl buffer solution at ph 7.4. uv-vis absorption spectroscopy indicates that the pro...

Human immunodeficiency virus infection / acquired immunodeficiency syndrome (HIV/AIDS) is a disease pertained to the human immune system. Given its crucial role in viral replication, HIV-1 protease (HIV-1 PR) is a prime therapeutic target in AIDS therapy. In this regard, the dynamic aspects of ligand-enzyme interactions may indicate an important role of conformational variability in HIV-1 PR in...

Control of flavonoid derivatives inhibitors release through the inhibition of neuraminidase has been identified as a potential target for the treatment of H1N1 influenza disease. We have employed molecular dynamics simulation techniques to optimize the 2009 H1N1 influenza neuraminidase X-ray crystal structure. Molecular docking of the compounds revealed the possible binding mode. Our molecular ...

Virtual screening, especially the structure-based virtual screening, has emerged as a reliable, cost-effective and time-saving technique for the discovery of lead compounds. Here, the basic ideas and computational tools for virtual screening have been briefly introduced, and emphasis is placed on aspects of recent development of docking-based virtual screening, scoring functions in molecular do...

We present a comprehensive molecular simulation program package, the Peking University Drug Design System (PKUDDS), which runs on personal computers. PKUDDS has been developed mainly for computer-aided drug design using the methods of two-dimensional quantitative structure-activity relationships, three-dimensional quantitative structure-activity relationships, molecular docking, and database sc...

Crystallization of protein-protein complexes can often be problematic and therefore computational structural models are often relied on. Such models are often generated using protein-protein docking algorithms, where one of the main challenges is selecting which of several thousand potential predictions represents the most near-native complex. We have developed a novel technique that involves t...

The protein-protein docking server ClusPro is used by thousands of laboratories, and models built by the server have been reported in over 300 publications. Although the structures generated by the docking include near-native ones for many proteins, selecting the best model is difficult due to the uncertainty in scoring. Small angle X-ray scattering (SAXS) is an experimental technique for obtai...

Molecular docking study was performed on a series of 28 Diarylsulfonylureas LD1-LD28 as potential cyclin-dependent kinase 2 (CDK2) inhibitors. The docking technique was applied to dock a set of representative compounds within the active site region of 3PY1 using Molegro Virtual Docker v 5.0. For these compounds, the binding free energy (kcal/mol) was determined. The docking simulation clearly p...

Prediction of small molecule binding modes to macromolecules of known three-dimensional structure is a problem of paramount importance in rational drug design (the "docking" problem). We report the development and validation of the program GOLD (Genetic Optimisation for Ligand Docking). GOLD is an automated ligand docking program that uses a genetic algorithm to explore the full range of ligand...