ArticleBiophysical journal2015
Minimalistic predictor of protein binding energy: contribution of solvation factor to protein binding.
Article in Biophysical journal, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Superchaotropic Stabilization of Monomeric Protein States.Biomacromolecules · 2026Article
- Exploring market-approved azoles as potential breast cancer therapeutics targeting the VEGFR-2 biotarget.Scientific reports · 2025Article
- Systematic investigation of machine learning on limited data: A study on predicting protein-protein binding strength.Computational and structural biotechnology journal · 2024Article
- Unveiling the Multifaceted Capabilities of EndophyticPharmaceuticals (Basel, Switzerland) · 2024Article
- Mutational biases favor complexity increases in protein interaction networks after gene duplication.Molecular systems biology · 2024Article
- Article
- Spatial organization of hydrophobic and charged residues affects protein thermal stability and binding affinity.Scientific reports · 2022Article
- Evaluation of kinetics and thermodynamics of interaction between immobilized SARS-CoV-2 nucleoprotein and specific antibodies by total internal reflection ellipsometry.Journal of colloid and interface science · 2021Article
- A Comprehensive Review on Current Advances in Peptide Drug Development and Design.International journal of molecular sciences · 2019Review
- Differential protein structural disturbances and suppression of assembly partners produced by nonsense GABRG2 epilepsy mutations: implications for disease phenotypic heterogeneity.Scientific reports · 2016Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
It has long been known that solvation plays an important role in protein-protein interactions. Here, we use a minimalistic solvation-based model for predicting protein binding energy to estimate quantitatively the contribution of the solvation factor in protein binding. The factor is described by a simple linear combination of buried surface areas according to amino-acid types. Even without structural optimization, our minimalistic model demonstrates a predictive power comparable to more complex methods, making the proposed approach the basis for high throughput applications. Application of the model to a proteomic database shows that receptor-substrate complexes involved in signaling have lower affinities than enzyme-inhibitor and antibody-antigen complexes, and they differ by chemical compositions on interfaces. Also, we found that protein complexes with components that come from the same genes generally have lower affinities than complexes formed by proteins from different genes, but in this case the difference originates from different interface areas. The model was implemented in the software PYTHON, and the source code can be found on the Shakhnovich group webpage: http://faculty.chemistry.harvard.edu/shakhnovich/software.
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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.