ArticleJournal of computer-aided molecular design2014
A functional feature analysis on diverse protein-protein interactions: application for the prediction of binding affinity.
Article in Journal of computer-aided molecular design, 2014. 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.
- Exploring β-catenin and TCF4 interaction in complex environments by means of novel biosensing platform focal molography.PloS one · 2025Article
- Spatial organization of hydrophobic and charged residues affects protein thermal stability and binding affinity.Scientific reports · 2022Article
- Protein-Protein Binding Free Energy Predictions with the MM/PBSA Approach Complemented with the Gaussian-Based Method for Entropy Estimation.ACS omega · 2022Article
- Protein-Specific Prediction of RNA-Binding Sites Based on Information Entropy.Computational intelligence and neuroscience · 2022Article
- Computational Assessment of Protein-protein Binding Affinity by Reversely Engineering the Energetics in Protein Complexes.Genomics, proteomics & bioinformatics · 2021Article
- Multiscale simulation unravel the kinetic mechanisms of inflammasome assembly.Biochimica et biophysica acta. Molecular cell research · 2020Article
- Individually double minimum-distance definition of protein-RNA binding residues and application to structure-based prediction.Journal of computer-aided molecular design · 2018Article
- A structural dissection of protein-RNA interactions based on different RNA base areas of interfaces.RSC advances · 2018Article
- A structural dissection of large protein-protein crystal packing contacts.Scientific reports · 2015Article
- Article
- Characterizing informative sequence descriptors and predicting binding affinities of heterodimeric protein complexes.BMC bioinformatics · 2015Article
- A minimal model of protein-protein binding affinities.Protein science : a publication of the Protein Society · 2014Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein-protein interactions (PPIs) play crucial roles in diverse cellular processes. There are different types of PPIs based on the composition, affinity and whether the association is permanent or transient. Analyzing the diversity of PPIs at the atomic level is crucial for uncovering the key features governing the interactions involved in PPI. A systematic physico-chemical and conformational studies were implemented on interfaces involved in different PPIs, including crystal packing, weak transient heterodimers, weak transient homodimers, strong transient heterodimers and homodimers. The comparative analysis shows that the interfaces tend to be larger, less planar, and more tightly packed with the increase of the interaction strength. Meanwhile the strong interactions undergo greater conformational changes than the weak ones involving main chains as well as side chains. Finally, using 18 features derived from our analysis, we developed a support vector regression model to predict the binding affinity with a promising result, which further demonstrate the reliability of our studies. We believe this study will provide great help in more thorough understanding the mechanism of diverse PPIs.
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