ArticleComputational and structural biotechnology journal2021
2D Zernike polynomial expansion: Finding the protein-protein binding regions.
Article in Computational and structural biotechnology journal, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Preventing Pathogenic Dimerization in a Misfolded Antibody Light Chain through the Design of an Inhibitory Peptide.The journal of physical chemistry. B · 2026Article
- Exploring neural networks to uncover information-richer features for protein interaction prediction.European biophysics journal : EBJ · 2026Article
- Beyond contacts: The important role of the support region in protein complex assembly.Protein science : a publication of the Protein Society · 2026Article
- Uncovering the molecular details of the 14-3-3 recruitment by mutant Sod1 species.Scientific reports · 2025Article
- A Complementarity-Based Approach to De Novo Binder Design.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Compact Assessment of Molecular Surface Complementarities Enhances Neural Network-Aided Prediction of Key Binding Residues.Journal of chemical information and modeling · 2025Article
- Zepyros: a webserver to evaluate the shape complementarity of protein-protein interfaces.Bioinformatics advances · 2025Article
- PLO3S: Protein LOcal Surficial Similarity Screening.Computational and structural biotechnology journal · 2024Article
- Synchronized motion of interface residues for evaluating protein-RNA complex binding affinity: Application to aptamer-mediated inhibition of TDP-43 aggregates.Protein science : a publication of the Protein Society · 2024Article
- FP-Zernike: An Open-source Structural Database Construction Toolkit for Fast Structure Retrieval.Genomics, proteomics & bioinformatics · 2024Article
- Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments.Chemical reviews · 2024Review
- High-Throughput Interactome Determination via Sulfur Anomalous Scattering.The journal of physical chemistry letters · 2024Article
- Lactoferrins in Their Interactions with Molecular Targets: A Structure-Based Overview.Pharmaceuticals (Basel, Switzerland) · 2024Review
- Two Receptor Binding Strategy of SARS-CoV-2 Is Mediated by Both the N-Terminal and Receptor-Binding Spike Domain.The journal of physical chemistry. B · 2024Article
- SiteFerret: Beyond Simple Pocket Identification in Proteins.Journal of chemical theory and computation · 2023Article
- Electrostatic complementarity at the interface drives transient protein-protein interactions.Scientific reports · 2023Article
- Revitalizing an important field in biophysics: The new frontiers of molecular crowding.Frontiers in molecular biosciences · 2023Article
- Computational structural-based GPCR optimization for user-defined ligand: Implications for the development of biosensors.Computational and structural biotechnology journal · 2023Article
- Differences in the organization of interface residues tunes the stability of the SARS-CoV-2 spike-ACE2 complex.Frontiers in molecular biosciences · 2023Article
- Design of protein-binding peptides with controlled binding affinity: the case of SARS-CoV-2 receptor binding domain and angiotensin-converting enzyme 2 derived peptides.Frontiers in molecular biosciences · 2023Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present a method for efficiently and effectively assessing whether and where two proteins can interact with each other to form a complex. This is still largely an open problem, even for those relatively few cases where the 3D structure of both proteins is known. In fact, even if much of the information about the interaction is encoded in the chemical and geometric features of the structures, the set of possible contact patches and of their relative orientations are too large to be computationally affordable in a reasonable time, thus preventing the compilation of reliable interactome. Our method is able to rapidly and quantitatively measure the geometrical shape complementarity between interacting proteins, comparing their molecular iso-electron density surfaces expanding the surface patches in term of 2D Zernike polynomials. We first test the method against the real binding region of a large dataset of known protein complexes, reaching a success rate of 0.72. We then apply the method for the blind recognition of binding sites, identifying the real region of interaction in about
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