G-RMSD: Root Mean Square Deviation Based Method for Three-Dimensional Molecular Similarity Determination

Fukutani, Tomonori; Miyazawa, Kazuhiro; Iwata, Satoru; Satoh, Hiroko

doi:10.1246/bcsj.20200258

Cited by 19 publications

(14 citation statements)

References 74 publications

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“…S6, ESI†), which is widely applied in MD simulation. 65,88,89 A large range of RMSD values was found for the BRD4-BD1 systems, between 0.5 and 5.5 Å, due to the long C-terminal chain compared with that in BRD4-BD2. However, the RMSD of residues 61–166 (excluded the C-terminal) was 0.91 ± 1.12 Å (1.43 ± 1.86 Å for all length) in the 1000 ns MD simulation (Fig.…”

Section: Resultsmentioning

confidence: 99%

The binding mechanism of NHWD-870 to bromodomain-containing protein 4 based on molecular dynamics simulations and free energy calculation

Shi

Weng

et al. 2022

Phys. Chem. Chem. Phys.

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Section: Resultsmentioning

confidence: 99%

The binding mechanism of NHWD-870 to bromodomain-containing protein 4 based on molecular dynamics simulations and free energy calculation

Shi

Weng

et al. 2022

Phys. Chem. Chem. Phys.

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“…Determination of near-congruence, i.e., finding if two point sets are approximately superposable, is still a problem in chemistry and other fields with no completely satisfactory solution. − The difficulty to solve the near-congruence problem can vary from easy to extremely hard because it depends on the degree of distortion between the structures, which can become nonsuperposable if the distortion is too large. Nonetheless, the mean square deviation (MSD) of the positions, minimized with respect to orientation and permutation, can be used as a similarity measure for superposable and nonsuperposable sets.…”

Section: Discussion Of the Algorithmmentioning

confidence: 99%

A Practical Algorithm to Solve the Near-Congruence Problem for Rigid Molecules and Clusters

Vásquez-Pérez

Zárate-Hernández

Gómez-Castro

et al. 2023

J. Chem. Inf. Model.

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We present an improved algorithm to solve the near-congruence problem for rigid molecules and clusters based on the iterative application of assignment and alignment steps with biased Euclidean costs. The algorithm is formulated as a quasi-local optimization procedure with each optimization step involving a linear assignment (LAP) and a singular value decomposition (SVD). The efficiency of the algorithm is increased by up to 5 orders of magnitude with respect to the original unbiased noniterative method and can be applied to systems with hundreds or thousands of atoms, outperforming all state-of-the-art methods published so far in the literature. The Fortran implementation of the algorithm is available as an open source library () and is suitable to be used in global optimization methods for the identification of local minima or basins.

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“…The RMSD values observed are quite in agreement with earlier studies in the literature. 48 The angle of Tecovirimat in the binding pocket of Mpox protein was also recorded and found stable with an average value of 93.41°, indicating the stability of Tecovirimat in the binding pocket of Mpox protein (Figure 8).…”

Section: Simulationmentioning

confidence: 94%

Tecovirimat as a Potential Bioavailable inhibitor against MPXVgp158 Established through Molecular Dynamic Simulations and Docking Studies

Sharma¹,

Panwar²,

Garg³

et al. 2022

J. Pure Appl. Microbiol.

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Monkeypox is a zoonotic viral infection caused by monkeypox virus which belongs to the Poxviridae family of genus Orthopoxvirus. Usually, the virus transmission happens when the individual comes in contact with the infected person through body fluids, animal lesions, respiratory droplets or through virus contaminated materials. Clinical presentation of the monkeypox has shown significant resemblance to that of smallpox and chickenpox, belonging to the same orthopoxvirus genus but were eradicated during 1980s globally. Monkeypox may lead to a range of medical complications including clinical symptoms like fever, rashes, headaches, back pain, myodynia and swollen lymph nodes. As far as the treatment modalities are concerned, the antiviral therapeutic agents developed for the smallpox treatment, were also permitted to be used for the monkeypox treatment. However, there is no proven treatment for human monkeypox. In the current study, we have focused on designing of a best probable ligand against the target MPXVgp158 (Monkeypox virus protein). Since Tecovirimat is an FDA approved compound known as an antipoxviral drug, the study aimed to develop a Monkeypox virus protein MPXVgp158 inhibitor which is bioavailable and biocompatible as well through drug designing using computational tools. Molecular docking (MD) analysis displayed Tecovirimat with lesser binding energy, higher non-bonded interaction capability, and more stability against MPXVgp158, with efficient binding mode of interactions. Hence, Tecovirimat was adjudged to be the potential candidate against MPXVgp158 inhibition.

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G-RMSD: Root Mean Square Deviation Based Method for Three-Dimensional Molecular Similarity Determination

Cited by 19 publications

References 74 publications

The binding mechanism of NHWD-870 to bromodomain-containing protein 4 based on molecular dynamics simulations and free energy calculation

The binding mechanism of NHWD-870 to bromodomain-containing protein 4 based on molecular dynamics simulations and free energy calculation

A Practical Algorithm to Solve the Near-Congruence Problem for Rigid Molecules and Clusters

Tecovirimat as a Potential Bioavailable inhibitor against MPXVgp158 Established through Molecular Dynamic Simulations and Docking Studies

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