Chem-Bio Informatics Journal
Online ISSN : 1347-0442
Print ISSN : 1347-6297
ISSN-L : 1347-0442
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original
  • Yusuke Kawashima, Natsumi Mori, Norihito Kawashita, Yu-Shi Tian, Tatsu ...
    Type: research-article
    Subject area: Molecular recognition and molecular modeling
    2021 Volume 21 Pages 1-10
    Published: January 29, 2021
    Released: January 29, 2021
    JOURNALS FREE ACCESS
    Supplementary material

    Fragment molecular orbital (FMO) calculation is a useful ab initio method for analyzing protein–ligand interactions in the current structure-based drug design. When multiple ligands exist for one receptor, a post-FMO calculation tool is required because of large numbers of interaction energy decomposition terms calculated using this method. In this study, a method that combines self-organizing maps (SOM) and hierarchical clustering analysis (HCA) was proposed to analyze the results of the FMO energy components. This method could effectively compress the high-dimensional energy terms and is expected to be useful to analyze the interaction between protein and ligands. A case study of antitype 2 diabetes mellitus target DPP-IV and its inhibitors was analyzed to verify the feasibility of the proposed method. After performing dimensional compression using SOM and further grouping using HCA, we obtained superclasses of the inhibitors based on the dispersion energy (DI), which showed consistency with structural information, indicating that further analyses of detailed energies per superclass can be an effective approach for obtaining important ligand–protein interactions.

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  • Yudai Yamashita, Kotaro Watanabe, Satoshi Murata, Ibuki Kawamata
    Type: research-article
    Subject area: Emerging new technology
    2021 Volume 21 Pages 28-38
    Published: April 30, 2021
    Released: April 30, 2021
    JOURNALS FREE ACCESS

    We introduce an automated procedure of coarse-grained molecular dynamic simulation for DNA nanostructure that has great potential for realizing molecular robotics. As DNA origami is now a standardized technology to fabricate DNA nanostructures with high precision, various computer-aided design software has been developed. For example, a design tool called caDNAno with a simple and intuitive interface is widely used for designing DNA origami structures. Further, a simulation tool called oxDNA is used to predict the behavior of such nanostructures based on coarse-grained molecular dynamics. These tools, however, are not linked directly; thus, repeating the cycle of design and simulation is cumbersome to the user. Moreover, the computer skills required to setup, launch, and run an oxDNA simulation are a potential barrier for non-experts. In our proposal, oxDNA simulation can be launched on a web server simply by providing a caDNAno file; the web server then analyzes the simulation results and provides a visual response. The validity of the proposal is demonstrated using an example. The advantages of our proposed method compared with other conventional methods are also described. This simple-to-use interface for user-friendly simulation of DNA origami eliminates stress to users and accelerates the design process of complicated DNA nanostructures such as wireframe architecture.

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calculation report
  • Junie B. Billones, Nina Abigail B. Clavio
    Type: calculation report
    Subject area: In silico drug discovery
    2021 Volume 21 Pages 11-27
    Published: March 15, 2021
    Released: March 15, 2021
    JOURNALS FREE ACCESS

    The viral infection caused by the dengue virus (DENV) is one of the most challenging diseases in the tropical regions of the world. The absence of drugs for dengue to this date calls for intense efforts to discover and develop the much coveted therapeutics for this mosquito-borne disease. One of the most attractive antiviral targets is the DENV RNAdependent RNA polymerase (RdRp), which catalyzes the de novo initiation as well as elongation of the flavivirus RNA genome. In this work, almost 5000 natural products were docked to DENV RdRp. The top 197 molecules with greater binding energies than the known ligand of the target were further clustered down to furnish 35 classes of molecular structures. These compounds with satisfactory predicted drug properties and with known natural origin can be further explored to pave the way for the first anti-dengue drug.

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