ArticleProteins2012
Detecting local ligand-binding site similarity in nonhomologous proteins by surface patch comparison.
Article in Proteins, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- PL-PatchSurfer3: improved structure-based virtual screening for structure variation using 3D Zernike descriptors.Journal of cheminformatics · 2026Article
- SHREC 2025: Protein surface shape retrieval including electrostatic potential.Computers & graphics · 2025Article
- Article
- Quantitative comparison of protein-protein interaction interface using physicochemical feature-based descriptors of surface patches.Frontiers in molecular biosciences · 2023Article
- Classification of Protein-Binding Sites Using a Spherical Convolutional Neural Network.Journal of chemical information and modeling · 2022Article
- Estimating the Similarity between Protein Pockets.International journal of molecular sciences · 2022Review
- Exploring Ligand Binding Domain Dynamics in the NRs Superfamily.International journal of molecular sciences · 2022Article
- What Makes GPCRs from Different Families Bind to the Same Ligand?Biomolecules · 2022Article
- ContactPFP: Protein function prediction using predicted contact information.Frontiers in bioinformatics · 2022Article
- Real-time structure search and structure classification for AlphaFold protein models.Communications biology · 2022Article
- Three-Dimensional Krawtchouk Descriptors for Protein Local Surface Shape Comparison.Pattern recognition · 2019Article
- PatchSearch: a web server for off-target protein identification.Nucleic acids research · 2019Article
- A Novel Geometry-Based Approach to Infer Protein Interface Similarity.Scientific reports · 2018Article
- Comparative assessment of strategies to identify similar ligand-binding pockets in proteins.BMC bioinformatics · 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
- Protein 3D Structure and Electron Microscopy Map Retrieval Using 3D-SURFER2.0 and EM-SURFER.Current protocols in bioinformatics · 2017Article
- MTLD, a Database of Multiple Target Ligands, the Updated Version.Molecules (Basel, Switzerland) · 2017Article
- Discovery of Nicotinamide Adenine Dinucleotide Binding Proteins in the Escherichia coli Proteome Using a Combined Energetic- and Structural-Bioinformatics-Based Approach.Journal of proteome research · 2017Article
- PL-PatchSurfer2: Improved Local Surface Matching-Based Virtual Screening Method That Is Tolerant to Target and Ligand Structure Variation.Journal of chemical information and modeling · 2016Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Functional elucidation of proteins is one of the essential tasks in biology. Function of a protein, specifically, small ligand molecules that bind to a protein, can be predicted by finding similar local surface regions in binding sites of known proteins. Here, we developed an alignment free local surface comparison method for predicting a ligand molecule which binds to a query protein. The algorithm, named Patch-Surfer, represents a binding pocket as a combination of segmented surface patches, each of which is characterized by its geometrical shape, the electrostatic potential, the hydrophobicity, and the concaveness. Representing a pocket by a set of patches is effective to absorb difference of global pocket shape while capturing local similarity of pockets. The shape and the physicochemical properties of surface patches are represented using the 3D Zernike descriptor, which is a series expansion of mathematical 3D function. Two pockets are compared using a modified weighted bipartite matching algorithm, which matches similar patches from the two pockets. Patch-Surfer was benchmarked on three datasets, which consist in total of 390 proteins that bind to one of 21 ligands. Patch-Surfer showed superior performance to existing methods including a global pocket comparison method, Pocket-Surfer, which we have previously introduced. Particularly, as intended, the accuracy showed large improvement for flexible ligand molecules, which bind to pockets in different conformations.
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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.