ArticleProteins2022
Insights into protein-DNA interactions from hydrogen bond energy-based comparative protein-ligand analyses.
Article in Proteins, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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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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Who cites it
19 citing papers in PubMed, 43 citations in OpenAlex.
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- High Prevalence of GALC Gene Variants in Adults With Neurodegenerative Conditions.European journal of neurology · 2025Article
- Data Mining and in Silico Analysis of Ethiopian Traditional Medicine: Unveiling the Therapeutic Potential of Rumex abyssinicus Jacq.Cell biochemistry and biophysics · 2025Article
- Network Pharmacology and Molecular Docking Approach to Identify and Investigate the Mechanisms of Active Components of Areca Catechu in Relation to Gut Disorders.Acta informatica medica : AIM : journal of the Society for Medical Informatics of Bosnia & Herzegovina : casopis Drustva za medicinsku informatiku BiH · 2025Article
- WGS-based screening of the co-chaperone protein DjlA-induced curved DNA binding protein A (CbpA) from a new multidrug-resistant zoonotic mastitis-causing Klebsiella pneumoniae strain: a novel molecular target of selective flavonoids.Molecular diversity · 2024Article
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- Oncoinformatic screening of the gene clusters involved in the HER2-positive breast cancer formation along with the in silico pharmacodynamic profiling of selective long-chain omega-3 fatty acids as the metastatic antagonists.Molecular diversity · 2023Article
- Single-Stranded DNA Binding Proteins and Their Identification Using Machine Learning-Based Approaches.Biomolecules · 2022Review
- Insights into protein-DNA interactions from hydrogen bond energy-based comparative protein-ligand analyses.Proteins · 2022Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
Abstract
Hydrogen bonds play important roles in protein folding and protein-ligand interactions, particularly in specific protein-DNA recognition. However, the distributions of hydrogen bonds, especially hydrogen bond energy (HBE) in different types of protein-ligand complexes, is unknown. Here we performed a comparative analysis of hydrogen bonds among three non-redundant datasets of protein-protein, protein-peptide, and protein-DNA complexes. Besides comparing the number of hydrogen bonds in terms of types and locations, we investigated the distributions of HBE. Our results indicate that while there is no significant difference of hydrogen bonds within protein chains among the three types of complexes, interfacial hydrogen bonds are significantly more prevalent in protein-DNA complexes. More importantly, the interfacial hydrogen bonds in protein-DNA complexes displayed a unique energy distribution of strong and weak hydrogen bonds whereas majority of the interfacial hydrogen bonds in protein-protein and protein-peptide complexes are of predominantly high strength with low energy. Moreover, there is a significant difference in the energy distributions of minor groove hydrogen bonds between protein-DNA complexes with different binding specificity. Highly specific protein-DNA complexes contain more strong hydrogen bonds in the minor groove than multi-specific complexes, suggesting important role of minor groove in specific protein-DNA recognition. These results can help better understand protein-DNA interactions and have important implications in improving quality assessments of protein-DNA complex models.
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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 Socratic graph.