ArticleComputational and structural biotechnology journal2020
Combining Ramachandran plot and molecular dynamics simulation for structural-based variant classification: Using
Article in Computational and structural biotechnology journal, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Comprehensive In Silico Analysis of the CXCL12, C55Y Mutation Reveals Structural and Functional Disruption in CXCR4/CXCR7 Signaling.Evolutionary bioinformatics online · 2026Article
- Integrated molecular dynamics elucidation of TP53 H179 zinc-binding variants: genomic and structural characterization across NSCLC subtypes.Frontiers in bioinformatics · 2026Article
- Enhanced computational strategies for categorizing HER2 kinase domain variants of uncertain significance through structural and functional analysis.Mammalian genome : official journal of the International Mammalian Genome Society · 2025Article
- A beginner's approach to deep learning applied to VS and MD techniques.Journal of cheminformatics · 2025Review
- Article
- Impact of nonsynonymous single nucleotide polymorphisms inFrontiers in genetics · 2025Article
- Special Issue: "Molecular Dynamics Simulations and Structural Analysis of Protein Domains".International journal of molecular sciences · 2024Article
- Interaction Between SARS-CoV-2 Spike Protein S1 Subunit and Oyster Heat Shock Protein 70.Food and environmental virology · 2024Article
- Review
- Comprehensive classification of TP53 somatic missense variants based on their impact on p53 structural stability.Briefings in bioinformatics · 2024Article
- Clinical-Genomic Analysis of 1261 Patients with Ehlers-Danlos Syndrome Outlines an Articulo-Autonomic Gene Network (Entome).Current issues in molecular biology · 2024Article
- Classification of MLH1 Missense VUS Using Protein Structure-Based Deep Learning-Ramachandran Plot-Molecular Dynamics Simulations Method.International journal of molecular sciences · 2024Article
- Transient Structural Dynamics of Glycogen Phosphorylase from Nonequilibrium Hydrogen/Deuterium-Exchange Mass Spectrometry.Journal of the American Chemical Society · 2024Article
- Complete genome sequence ofFood science and biotechnology · 2024Article
- Pathogenic variants in human DNA damage repair genes mostly arose after the latest human out-of-Africa migration.Frontiers in genetics · 2024Article
- A Molecular Integrative Study on the Inhibitory Effects of WRR and ERW on Amyloid β Peptide (1-42) Polymerization and Cell Toxicity.Polymers · 2023Article
- Article
- A Clinical Qualification Protocol Highlights Overlapping Genomic Influences and Neuro-Autonomic Mechanisms in Ehlers-Danlos and Long COVID-19 Syndromes.Current issues in molecular biology · 2023Article
- Integration of deep learning with Ramachandran plot molecular dynamics simulation for genetic variant classification.iScience · 2023Article
- Ethnic-specificity, evolution origin and deleteriousness of Asian BRCA variation revealed by over 7500 BRCA variants derived from Asian population.International journal of cancer · 2023Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The wide application of new DNA sequencing technologies is generating vast quantities of genetic variation data at unprecedented speed. Developing methodologies to decode the pathogenicity of the variants is imperatively demanding. We hypothesized that as deleterious variants may function through disturbing structural stability of their affected proteins, information from structural change caused by genetic variants can be used to identify the variants with deleterious effects. In order to measure the structural change for proteins with large size, we designed a method named RP-MDS composed of Ramachandran plot (RP) and Molecular Dynamics Simulation (MDS). Ramachandran plot captures the variant-caused secondary structural change, whereas MDS provides a quantitative measure for the variant-caused globular structural change. We tested the method using variants in
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