ArticleBiophysical journal2011
Predicting the effects of basepair mutations in DNA-protein complexes by thermodynamic integration.
Article in Biophysical journal, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Article
- In silico λ-dynamics predicts protein binding specificities to modified RNAs.Nucleic acids research · 2025Article
- Biomolecular dynamics with machine-learned quantum-mechanical force fields trained on diverse chemical fragments.Science advances · 2024Article
- In silico λ-dynamics predicts protein binding specificities to modified RNAs.bioRxiv : the preprint server for biology · 2024Article
- Dawn of a New Era for Membrane Protein Design.Biodesign research · 2022Review
- Interaction of Thymine DNA Glycosylase with Oxidised 5-Methyl-cytosines in Their Amino- and Imino-Forms.Molecules (Basel, Switzerland) · 2021Article
- Tautomeric Equilibria of Nucleobases in the Hachimoji Expanded Genetic Alphabet.Journal of chemical theory and computation · 2020Article
- Rapid and accurate structure-based therapeutic peptide design using GPU accelerated thermodynamic integration.Proteins · 2019Article
- The Role of Proton Transfer on Mutations.Frontiers in chemistry · 2019Review
- Saturation Mutagenesis by Efficient Free-Energy Calculation.Journal of chemical theory and computation · 2018Article
- Evaluation of Sox2 binding affinities for distinct DNA patterns using steered molecular dynamics simulation.FEBS open bio · 2017Article
- Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein-DNA Binding Free Energy Landscapes.The journal of physical chemistry. B · 2017Article
- A computational approach for designing D-proteins with non-canonical amino acid optimised binding affinity.PloS one · 2017Article
- Article
- Structure-based modeling of protein: DNA specificity.Briefings in functional genomics · 2015Review
- Study of base pair mutations in proline-rich homeodomain (PRH)-DNA complexes using molecular dynamics.European biophysics journal : EBJ · 2013Article
- Computation of relative binding free energy for an inhibitor and its analogs binding with Erk kinase using thermodynamic integration MD simulation.Journal of computer-aided molecular design · 2012Article
- Atomistic modeling of protein-DNA interaction specificity: progress and applications.Current opinion in structural biology · 2012Review
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Thermodynamically rigorous free energy methods in principle allow the exact computation of binding free energies in biological systems. Here, we use thermodynamic integration together with molecular dynamics simulations of a DNA-protein complex to compute relative binding free energies of a series of mutants of a protein-binding DNA operator sequence. A guanine-cytosine basepair that interacts strongly with the DNA-binding protein is mutated into adenine-thymine, cytosine-guanine, and thymine-adenine. It is shown that basepair mutations can be performed using a conservative protocol that gives error estimates of ∼10% of the change in free energy of binding. Despite the high CPU-time requirements, this work opens the exciting opportunity of being able to perform basepair scans to investigate protein-DNA binding specificity in great detail computationally.
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