ArticleNucleic acids research2017
Decomposing protein-DNA binding and recognition using simplified protein models.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
6 citing papers in PubMed.
- Structural predictions of protein-DNA binding: MELD-DNA.Nucleic acids research · 2023Article
- How acidic amino acid residues facilitate DNA target site selection.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- High-throughput CRISPR technology: a novel horizon for solid organ transplantation.Frontiers in immunology · 2023Review
- Duplex DNA Retains the Conformational Features of Single Strands: Perspectives from MD Simulations and Quantum Chemical Computations.International journal of molecular sciences · 2022Article
- DNA-protein interaction: identification, prediction and data analysis.Molecular biology reports · 2019Review
- Computational approaches to macromolecular interactions in the cell.Current opinion in structural biology · 2019Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We analyze the role of different physicochemical factors in protein/DNA binding and recognition by comparing the results from all-atom molecular dynamics simulations with simulations using simplified protein models. These models enable us to separate the role of specific amino acid side chains, formal amino acid charges and hydrogen bonding from the effects of the low-dielectric volume occupied by the protein. Comparisons are made on the basis of the conformation of DNA after protein binding, the ionic distribution around the complex and the sequence specificity. The results for four transcription factors, binding in either the minor or major grooves of DNA, show that the protein volume and formal charges, with one exception, play a predominant role in binding. Adding hydrogen bonding and a very small number of key amino acid side chains at the all-atom level yields results in DNA conformations and sequence recognition close to those seen in the reference all-atom simulations.
Indexed as
Identifiers
What OpenQuestion holds
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.