ArticleBiophysical journal2009
Modeling effects of human single nucleotide polymorphisms on protein-protein interactions.
Article in Biophysical journal, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 62 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
62 citing papers in PubMed, 134 citations in OpenAlex.
- Atomic-level protein-ligand recognition with PBCNet2.0 for probe discovery.Nature chemical biology · 2026Article
- Identification of high-risk non-synonymous SNPs (nsSNPs) in DNAH1 and DNAH17 genes associated with male infertility: a bioinformatics analysis.Journal of applied genetics · 2025Article
- Computational analysis of congenital heart disease associated SNPs: unveiling their impact on the gene regulatory system.BMC genomics · 2025Article
- Association of rs4588 polymorphism in vitamin D binding protein gene with polycystic ovarian syndrome in Iranian women: a case-control study.BMC research notes · 2024Article
- In Silico Prediction and Molecular Docking of SNPs in NRP1 Gene Associated with SARS-COV-2.Biochemical genetics · 2024Article
- A mutation-induced drug resistance database (MdrDB).Communications chemistry · 2023Article
- Assessing variants of uncertain significance implicated in hearing loss using a comprehensive deafness proteome.Human genetics · 2023Article
- Assessing Variants of Uncertain Significance Implicated in Hearing Loss Using a Comprehensive Deafness Proteome.Research square · 2023Article
- Mannose-binding lectin gene polymorphism in psoriasis and vitiligo: an observational study and computational analysis.Frontiers in medicine · 2023Article
- Predicting the effects of rare genetic variants on oncogenic signaling pathways: A computational analysis of HRAS protein function.Frontiers in chemistry · 2023Article
- Review
- Genome interpretation using in silico predictors of variant impact.Human genetics · 2022Review
- Electrostatics in Computational Biophysics and Its Implications for Disease Effects.International journal of molecular sciences · 2022Review
- The properties of human disease mutations at protein interfaces.PLoS computational biology · 2022Article
- rs7041 and rs4588 Polymorphisms in Vitamin D Binding Protein Gene (VDBP) and the Risk of Diseases.International journal of molecular sciences · 2022Review
- HBD-2 variants and SARS-CoV-2: New insights into inter-individual susceptibility.Frontiers in immunology · 2022Article
- Analysis and Interpretation of the Impact of Missense Variants in Cancer.International journal of molecular sciences · 2021Review
- PremPRI: Predicting the Effects of Missense Mutations on Protein-RNA Interactions.International journal of molecular sciences · 2020Article
- MutaBind2: Predicting the Impacts of Single and Multiple Mutations on Protein-Protein Interactions.iScience · 2020Article
- Insights into the Effects of Cancer Associated Mutations at the UPF2 and ATP-Binding Sites of NMD Master Regulator: UPF1.International journal of molecular sciences · 2019Article
2 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
A large set of three-dimensional structures of 264 protein-protein complexes with known nonsynonymous single nucleotide polymorphisms (nsSNPs) at the interface was built using homology-based methods. The nsSNPs were mapped on the proteins' structures and their effect on the binding energy was investigated with CHARMM force field and continuum electrostatic calculations. Two sets of nsSNPs were studied: disease annotated Online Mendelian Inheritance in Man (OMIM) and nonannotated (non-OMIM). It was demonstrated that OMIM nsSNPs tend to destabilize the electrostatic component of the binding energy, in contrast with the effect of non-OMIM nsSNPs. In addition, it was shown that the change of the binding energy upon amino acid substitutions is not related to the conservation of the net charge, hydrophobicity, or hydrogen bond network at the interface. The results indicate that, generally, the effect of nsSNPs on protein-protein interactions cannot be predicted from amino acids' physico-chemical properties alone, since in many cases a substitution of a particular residue with another amino acid having completely different polarity or hydrophobicity had little effect on the binding energy. Analysis of sequence conservation showed that nsSNP at highly conserved positions resulted in a large variance of the binding energy changes. In contrast, amino acid substitutions corresponding to nsSNPs at nonconserved positions, on average, were not found to have a large effect on binding affinity. pKa calculations were performed and showed that amino acid substitutions could change the wild-type proton uptake/release and thus resulting in different pH-dependence of the binding energy.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.