ArticleProteins2008
Rapid comparison of properties on protein surface.
Article in Proteins, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- SHREC 2025: Protein surface shape retrieval including electrostatic potential.Computers & graphics · 2025Article
- Article
- PLO3S: Protein LOcal Surficial Similarity Screening.Computational and structural biotechnology journal · 2024Article
- Article
- Real-time structure search and structure classification for AlphaFold protein models.Communications biology · 2022Article
- Surface-based protein domains retrieval methods from a SHREC2021 challenge.Journal of molecular graphics & modelling · 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
- A global map of the protein shape universe.PLoS computational biology · 2019Article
- Improved performance in CAPRI round 37 using LZerD docking and template-based modeling with combined scoring functions.Proteins · 2018Article
- Exploring the potential of 3D Zernike descriptors and SVM for protein-protein interface prediction.BMC bioinformatics · 2018Article
- Advances in the Development of Shape Similarity Methods and Their Application in Drug Discovery.Frontiers in chemistry · 2018Review
- Modeling the assembly order of multimeric heteroprotein complexes.PLoS computational biology · 2018Article
- Modeling disordered protein interactions from biophysical principles.PLoS computational biology · 2017Article
- Human and server docking prediction for CAPRI round 30-35 using LZerD with combined scoring functions.Proteins · 2017Article
- Three-dimensional protein model similarity analysis based on salient shape index.BMC bioinformatics · 2016Article
- PatchSurfers: Two methods for local molecular property-based binding ligand prediction.Methods (San Diego, Calif.) · 2016Article
- VASP-E: specificity annotation with a volumetric analysis of electrostatic isopotentials.PLoS computational biology · 2014Article
- Formyl-coenzyme A (CoA):oxalate CoA-transferase from the acidophile Acetobacter aceti has a distinctive electrostatic surface and inherent acid stability.Protein science : a publication of the Protein Society · 2012Article
- Detecting local ligand-binding site similarity in nonhomologous proteins by surface patch comparison.Proteins · 2012Article
- Speeding up the drug discovery process: structural similarity searches using molecular surfaces.EMBnet.journal · 2012Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
The mapping of physicochemical characteristics onto the surface of a protein provides crucial insights into its function and evolution. This information can be further used in the characterization and identification of similarities within protein surface regions. We propose a novel method which quantitatively compares global and local properties on the protein surface. We have tested the method on comparison of electrostatic potentials and hydrophobicity. The method is based on 3D Zernike descriptors, which provides a compact representation of a given property defined on a protein surface. Compactness and rotational invariance of this descriptor enable fast comparison suitable for database searches. The usefulness of this method is exemplified by studying several protein families including globins, thermophilic and mesophilic proteins, and active sites of TIM beta/alpha barrel proteins. In all the cases studied, the descriptor is able to cluster proteins into functionally relevant groups. The proposed approach can also be easily extended to other surface properties. This protein surface-based approach will add a new way of viewing and comparing proteins to conventional methods, which compare proteins in terms of their primary sequence or tertiary structure.
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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.