Case study of molecular docking

With an accout for my. Molecular docking is a technique widely used in drug design. Many studies exist regarding the general accuracy of various docking programs, but case studies for a given group of related compounds are rare. In order to facilitate identification of novel triazole HIV-1 non-nucleoside reverse transcriptase inhibitors NNRTIs , several docking and scoring programs were evaluated for their ability to predict relative biological activity of known 1,2,4-triazole and 76 other azole type NNRTIs. Different protocols, settings, scoring functions, and interaction terms were analyzed. We have found that the programs performance was dependent on the data set, indicating the importance of choosing good quality target data for any comparative study.
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AutoDock Vina Manual

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AutoDock Vina - molecular docking and virtual screening program

Email address protected by JavaScript. Activate javascript to see the email. Have an account? In recent years, OpenCL has been increasingly adopted as it enables software programmers to harness the performance and power efficiency of FPGAs. Despite simplifying the FPGA programming challenge, achieving high performance and energy efficiency with OpenCL is still a difficult task.
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BATMAN-TCM: a Bioinformatics Analysis Tool for Molecular mechANism of Traditional Chinese Medicine

Molecular docking, as one of the widely used virtual screening methods, aims to predict the binding-conformations of small molecule ligands to the appropriate target binding site. Because of the computational complexity and the arrival of the big data era, molecular docking requests High- Performance Computing HPC to improve its performance and accuracy. We discuss, in detail, the advances in accelerating molecular docking software in parallel, based on the different common HPC platforms, respectively.
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Drug repositioning has been attracting increasingly attention for its advantages of reducing costs and risks. Statistics showed that around one quarter of the marketed drugs are organohalogens. However, no study has been reported, to the best of our knowledge, to aim at efficiently repositioning organohalogen drugs, which may be attributed to the lack of accurate halogen bonding scoring function. Here, we present a study to show that two organohalogen drugs were successfully repositioned as potent B-Raf VE inhibitors via molecular docking with halogen bonding scoring function, namely D 3 DOCKxb developed in our lab, and bioassay.
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