ArticleMolecular genetics & genomic medicine2020
Analysis of protein missense alterations by combining sequence- and structure-based methods.
Article in Molecular genetics & genomic medicine, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Landscape and Spectrum of VWF Variants in Type 2 Von Willebrand Disease: Insights from a German Patient Cohort.Thrombosis and haemostasis · 2026Article
- AI-derived comparative assessment of the performance of pathogenicity prediction tools on missense variants of breast cancer genes.Human genomics · 2024Article
- Structural and biophysical analysis of cytochrome P450 2C9*14 and *27 variants in complex with losartan.Journal of inorganic biochemistry · 2024Article
- Review
- A Novel Missense SNP in the Fatty Acid-Binding Protein 4 (FABP4) Gene is Associated with Growth Traits in Karakul and Awassi Sheep.Biochemical genetics · 2024Article
- Functional and Molecular Characterization of NewGenes · 2024Article
- A novel deleterious oxytocin variant is associated with the lower twinning ratio in Awassi ewes.Animal biotechnology · 2023Article
- Human Cytochrome P450 1, 2, 3 Families as Pharmacogenes with Emphases on Their Antimalarial and Antituberculosis Drugs and Prevalent African Alleles.International journal of molecular sciences · 2023Review
- Identification and characterization of two SERPINC1 mutations causing congenital antithrombin deficiency.Thrombosis journal · 2023Article
- Possible effect of mutations on serological detection of Borrelia burgdorferi sensu stricto ospC major groups: An in-silico study.PloS one · 2023Article
- Effect of Non-Lethal Selection on Spontaneous Revertants of Frameshift Mutations: The Escherichia coli hisF CaseMicroorganisms · 2022Article
- Missense variants in the TNFA epitopes and their effects on interaction with therapeutic antibodies-in silico analysis.Journal, genetic engineering & biotechnology · 2022Article
- Pierce into Structural Changes of Interactions Between Mutated Spike Glycoproteins and ACE2 to Evaluate Its Potential Biological and Therapeutic Consequences.International journal of peptide research and therapeutics · 2022Article
- Insights into the Genetic Variations of Human Cytochrome P450 2C9: Structural Analysis, Characterization and Comparison.International journal of molecular sciences · 2021Article
- Dissection of pleiotropic effects of variants in and adjacent to F8 exon 19 and rescue of mRNA splicing and protein function.American journal of human genetics · 2021Article
- Functional and structural analyses of novel Smith-Kingsmore Syndrome-Associated MTOR variants reveal potential new mechanisms and predictors of pathogenicity.PLoS genetics · 2021Article
- Protein residue network analysis reveals fundamental properties of the human coagulation factor VIII.Scientific reports · 2021Article
- Prediction of hemophilia A severity using a small-input machine-learning framework.NPJ systems biology and applications · 2021Article
- In Silico Investigation of the New UK (B.1.1.7) and South African (501Y.V2) SARS-CoV-2 Variants with a Focus at the ACE2-Spike RBD Interface.International journal of molecular sciences · 2021Article
- Resources and computational strategies to advance small molecule SARS-CoV-2 discovery: Lessons from the pandemic and preparing for future health crises.Computational and structural biotechnology journal · 2021Review
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7 authors.
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Abstract
backgroundDifferent types of in silico approaches can be used to predict the phenotypic consequence of missense variants. Such algorithms are often categorized as sequence based or structure based, when they necessitate 3D structural information. In addition, many other in silico tools, not dedicated to the analysis of variants, can be used to gain additional insights about the possible mechanisms at play.
methodsHere we applied different computational approaches to a set of 20 known missense variants present on different proteins (CYP, complement factor B, antithrombin and blood coagulation factor VIII). The tools that were used include fast computational approaches and web servers such as PolyPhen-2, PopMusic, DUET, MaestroWeb, SAAFEC, Missense3D, VarSite, FlexPred, PredyFlexy, Clustal Omega, meta-PPISP, FTMap, ClusPro, pyDock, PPM, RING, Cytoscape, and ChannelsDB.
resultsWe observe some conflicting results among the methods but, most of the time, the combination of several engines helped to clarify the potential impacts of the amino acid substitutions.
conclusionCombining different computational approaches including some that were not developed to investigate missense variants help to predict the possible impact of the amino acid substitutions. Yet, when the modified residues are involved in a salt-bridge, the tools tend to fail, even when the analysis is performed in 3D. Thus, interactive structural analysis with molecular graphics packages such as Chimera or PyMol or others are still needed to clarify automatic prediction.
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