ArticleJournal of chemical information and modeling2020
Quantitative Characterization of Binding Pockets and Binding Complementarity by Means of Zernike Descriptors.
Article in Journal of chemical information and modeling, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Molecular docking to homology models of human and Trypanosoma brucei ERK8 that identified ortholog-specific inhibitors.PLoS neglected tropical diseases · 2025Article
- Cordycepin Triphosphate as a Potential Modulator of Cellular Plasticity in Cancer via cAMP-Dependent Pathways: An In Silico Approach.International journal of molecular sciences · 2024Article
- FP-Zernike: An Open-source Structural Database Construction Toolkit for Fast Structure Retrieval.Genomics, proteomics & bioinformatics · 2024Article
- ZMPY3D: accelerating protein structure volume analysis through vectorized 3D Zernike moments and Python-based GPU integration.Bioinformatics advances · 2024Article
- Shape Theory Applied to Molecular Docking and Automatic Localization of Ligand Binding Pockets in Large Proteins.ACS omega · 2022Article
- Inferring the stabilization effects of SARS-CoV-2 variants on the binding with ACE2 receptor.Communications biology · 2022Article
- Binding site identification of G protein-coupled receptors through a 3D Zernike polynomials-based method: application to C. elegans olfactory receptors.Journal of computer-aided molecular design · 2022Article
- Shape Complementarity Optimization of Antibody-Antigen Interfaces: The Application to SARS-CoV-2 Spike Protein.Frontiers in molecular biosciences · 2022Article
- A novel computational strategy for defining the minimal protein molecular surface representation.PloS one · 2022Article
- 2D Zernike polynomial expansion: Finding the protein-protein binding regions.Computational and structural biotechnology journal · 2021Article
- In-Silico Evidence for a Two Receptor Based Strategy of SARS-CoV-2.Frontiers in molecular biosciences · 2021Article
- Computational optimization of angiotensin-converting enzyme 2 for SARS-CoV-2 Spike molecular recognition.Computational and structural biotechnology journal · 2021Article
- Molecular Mechanisms Behind Anti SARS-CoV-2 Action of Lactoferrin.Frontiers in molecular biosciences · 2021Article
- Quantitative Description of Surface Complementarity of Antibody-Antigen Interfaces.Frontiers in molecular biosciences · 2021Article
- Insights into the Interaction Mechanism of DTP3 with MKK7 by Using STD-NMR and Computational Approaches.Biomedicines · 2020Article
- Molecular Dynamics Simulations Reveal Canonical Conformations in Different pMHC/TCR Interactions.Cells · 2020Article
- A novel strategy for molecular interfaces optimization: The case of Ferritin-Transferrin receptor interaction.Computational and structural biotechnology journal · 2020Article
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4 authors.
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Abstract
In this work, we describe the application of the Zernike formalism to quantitatively characterize the binding pockets of two sets of biologically relevant systems. Such an approach, when applied to molecular dynamics trajectories, is able to pinpoint the subtle differences between very similar molecular regions and their impact on the local propensity to ligand binding, allowing us to quantify such differences. The statistical robustness of our procedure suggests that it is very suitable to describe protein binding sites and protein-ligand interactions within a rigorous and well-defined framework.
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