ArticleFrontiers in molecular biosciences2017
A Simple PB/LIE Free Energy Function Accurately Predicts the Peptide Binding Specificity of the Tiam1 PDZ Domain.
Article in Frontiers in molecular biosciences, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 13 citations in OpenAlex.
- Retinal ribbon synapses and the potential functional role of TIAM1: A structural and molecular perspective.Molecular vision · 2026Review
- Cyclodextrin: Dual Functions as a Therapeutic Agent and Nanocarrier for Regulating Cholesterol Homeostasis in Atherosclerosis.Pharmaceutics · 2025Review
- Relative Binding Free Energy Estimation of Congeneric Ligands and Macromolecular Mutants with the Alchemical Transfer Method with Coordinate Swapping.Journal of chemical information and modeling · 2025Article
- Review
- Article
- Computational Design of PDZ-Peptide Binding.Methods in molecular biology (Clifton, N.J.) · 2021Article
- A Fluorescence-Based Assay to Determine PDZ-Ligand Binding Thermodynamics.Methods in molecular biology (Clifton, N.J.) · 2021Article
- A physics-based energy function allows the computational redesign of a PDZ domain.Scientific reports · 2020Article
- Combined Linear Interaction Energy and Alchemical Solvation Free-Energy Approach for Protein-Binding Affinity Computation.Journal of chemical theory and computation · 2020Article
- Electrostatically Driven Guanidinium Interaction Domains that Control Hydrogel-Mediated Protein Delivery In Vivo.ACS central science · 2019Article
- Accurate PDZ/Peptide Binding Specificity with Additive and Polarizable Free Energy Simulations.Biophysical journal · 2018Article
- Accuracy Comparison of Generalized Born Models in the Calculation of Electrostatic Binding Free Energies.Journal of chemical theory and computation · 2018Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
Abstract
PDZ domains generally bind short amino acid sequences at the C-terminus of target proteins, and short peptides can be used as inhibitors or model ligands. Here, we used experimental binding assays and molecular dynamics simulations to characterize 51 complexes involving the Tiam1 PDZ domain and to test the performance of a semi-empirical free energy function. The free energy function combined a Poisson-Boltzmann (PB) continuum electrostatic term, a van der Waals interaction energy, and a surface area term. Each term was empirically weighted, giving a Linear Interaction Energy or "PB/LIE" free energy. The model yielded a mean unsigned deviation of 0.43 kcal/mol and a Pearson correlation of 0.64 between experimental and computed free energies, which was superior to a Null model that assumes all complexes have the same affinity. Analyses of the models support several experimental observations that indicate the orientation of the α
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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.