ArticleProteins2011
Surface-based protein binding pocket similarity.
Article in Proteins, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers, 1 of them a synthesis that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
17 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Protein Spatial Structure Meets Artificial Intelligence: Revolutionizing Drug Synergy-Antagonism in Precision Medicine.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Pooled it
- Sunsetting Binding MOAD with its last data update and the addition of 3D-ligand polypharmacology tools.Scientific reports · 2023Article
- PDBspheres: a method for finding 3D similarities in local regions in proteins.NAR genomics and bioinformatics · 2022Article
- Epitranscriptomics and epiproteomics in cancer drug resistance: therapeutic implications.Signal transduction and targeted therapy · 2020Review
- On the evolution of protein-adenine binding.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Electrostatic-field and surface-shape similarity for virtual screening and pose prediction.Journal of computer-aided molecular design · 2019Article
- LibME-automatic extraction of 3D ligand-binding motifs for mechanistic analysis of protein-ligand recognition.FEBS open bio · 2016Article
- Proteins and Their Interacting Partners: An Introduction to Protein-Ligand Binding Site Prediction Methods.International journal of molecular sciences · 2015Review
- Knowledge-guided docking: accurate prospective prediction of bound configurations of novel ligands using Surflex-Dock.Journal of computer-aided molecular design · 2015Article
- Chemical and protein structural basis for biological crosstalk between PPARα and COX enzymes.Journal of computer-aided molecular design · 2015Article
- Article
- A structure-guided approach for protein pocket modeling and affinity prediction.Journal of computer-aided molecular design · 2013Article
- Identification of distant drug off-targets by direct superposition of binding pocket surfaces.PloS one · 2013Article
- Iterative refinement of a binding pocket model: active computational steering of lead optimization.Journal of medicinal chemistry · 2012Article
- Surflex-Dock: Docking benchmarks and real-world application.Journal of computer-aided molecular design · 2012Article
- FunFOLDQA: a quality assessment tool for protein-ligand binding site residue predictions.PloS one · 2012Article
- A fast topological analysis algorithm for large-scale similarity evaluations of ligands and binding pockets.Journal of cheminformaticsArticle
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Protein similarity comparisons may be made on a local or global basis and may consider sequence information or differing levels of structural information. We present a local three-dimensional method that compares protein binding site surfaces in full atomic detail. The approach is based on the morphological similarity method which has been widely applied for global comparison of small molecules. We apply the method to all-by-all comparisons two sets of human protein kinases, a very diverse set of ATP-bound proteins from multiple species, and three heterogeneous benchmark protein binding site data sets. Cases of disagreement between sequence-based similarity and binding site similarity yield informative examples. Where sequence similarity is very low, high pocket similarity can reliably identify important binding motifs. Where sequence similarity is very high, significant differences in pocket similarity are related to ligand binding specificity and similarity. Local protein binding pocket similarity provides qualitatively complementary information to other approaches, and it can yield quantitative information in support of functional annotation.
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Registered trials
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