ArticleJournal of molecular graphics & modelling2020
Identification of correlated inter-residue interactions in protein complex based on the fragment molecular orbital method.
Article in Journal of molecular graphics & modelling, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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8 citing papers in PubMed, 22 citations in OpenAlex.
- Protein-Protein Interactions Analyzed by the Fragment Molecular Orbital Method.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Leveraging the Fragment Molecular Orbital Method to Explore the PLK1 Kinase Binding Site and Polo-Box Domain for Potent Small-Molecule Drug Design.International journal of molecular sciences · 2023Article
- Protein-Protein Interaction Modelling with the Fragment Molecular Orbital Method.Methods in molecular biology (Clifton, N.J.) · 2023Article
- The Importance of Charge Transfer and Solvent Screening in the Interactions of Backbones and Functional Groups in Amino Acid Residues and Nucleotides.International journal of molecular sciences · 2022Article
- Article
- Molecular recognition of SARS-CoV-2 spike glycoprotein: quantum chemical hot spot and epitope analyses.Chemical science · 2021Article
- Interaction analyses of SARS-CoV-2 spike protein based on fragment molecular orbital calculations.RSC advances · 2021Article
- pyProGA-A PyMOL plugin for protein residue network analysis.PloS one · 2021Article
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Authors and funding
6 authors at 6 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A theoretical scheme to systematically describe correlated (network-like) interactions between molecular fragments is proposed within the framework of the fragment molecular orbital (FMO) method. The method is mathematically based on the singular value decomposition (SVD) of the inter-fragment interaction energy (IFIE) matrix obtained by the FMO calculation, and can be applied to a comprehensive description of protein-protein interactions in the context of molecular recognition. In the present study we apply the proposed method to a complex of measles virus hemagglutinin and human SLAM receptor, thus finding a usefulness for efficiently eliciting the correlated interactions among the amino-acid residues involved in the two proteins. Additionally, collective interaction networks by amino-acid residues important for mutation experiments can be clearly visualized.
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