ArticleBiophysics and physicobiology2019
Detection of cave pockets in large molecules: Spaces into which internal probes can enter, but external probes from outside cannot.
Article in Biophysics and physicobiology, 2019. 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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17 citing papers in PubMed.
- Advances in Methods for Accurate Prediction of RNA-Small Molecule Binding Sites: From Isolated to AI-Integrated Strategies.Pharmaceuticals (Basel, Switzerland) · 2025Review
- Decoding allosteric landscapes: computational methodologies for enzyme modulation and drug discovery.RSC chemical biology · 2025Review
- Mycobacterium susceptibility to ivermectin by inhibition of eccD3, an ESX-3 secretion system component.PLoS computational biology · 2025Article
- Exploring Binding Sites on Proteins for Function Prediction Using the PoSSuM Databases.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Databases of ligand-binding pockets and protein-ligand interactions.Computational and structural biotechnology journal · 2024Review
- Enhanced prediction of protein functional identity through the integration of sequence and structural features.Computational and structural biotechnology journal · 2024Article
- Insights into the structure of NLR family member X1: Paving the way for innovative drug discovery.Computational and structural biotechnology journal · 2024Article
- GPCR-BSD: a database of binding sites of human G-protein coupled receptors under diverse states.BMC bioinformatics · 2024Article
- PoSSuM v.3: A Major Expansion of the PoSSuM Database for Finding Similar Binding Sites of Proteins.Journal of chemical information and modeling · 2023Article
- Structure-based prediction of nucleic acid binding residues by merging deep learning- and template-based approaches.PLoS computational biology · 2023Article
- Molecular docking in organic, inorganic, and hybrid systems: a tutorial review.Monatshefte fur chemie · 2023Review
- MAHOMES II: A webserver for predicting if a metal binding site is enzymatic.Protein science : a publication of the Protein Society · 2023Article
- MAHOMES II: A webserver for predicting if a metal binding site is enzymatic.bioRxiv : the preprint server for biology · 2023Article
- Computational Biology of BRCA2 in Male Breast Cancer, through Prediction of Probable nsSNPs, and Hit Identification.ACS omega · 2022Article
- Colicin E1 opens its hinge to plug TolC.eLife · 2022Article
- Utilization of the zebrafish model to unravel the harmful effects of biomass burning during Amazonian wildfires.Scientific reports · 2021Article
- Combinatorial Biosynthesis of Sulfated Benzenediol Lactones with a Phenolic Sulfotransferase from Fusarium graminearum PH-1.mSphere · 2020Article
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Abstract
Geometric features of macromolecular shapes are important for binding with other molecules. Kawabata, T. and Go, N. (2007) defined a pocket as a space into which a small probe can enter, but a large probe cannot. In 2010, mathematical morphology (MM) was introduced to provide a more rigorous definition, and the program GHECOM was developed using the grid-based representation of molecules. This method was simple, but effective in finding the binding sites of small compounds on protein surfaces. Recently, many 3D structures of large macromolecules have been determined to contain large internal hollow spaces. Identification and size estimation of these spaces is important for characterizing their function and stability. Therefore, we employ the MM definition of pocket proposed by Manak, M. (2019)-a space into which an internal probe can enter, but an external probe cannot enter from outside of the macromolecules. This type of space is called a "cave pocket", and is identified through molecular grid-representation. We define a "cavity" as a space into which a probe can enter, but cannot escape to the outside. Three types of spaces: cavity, pocket, and cave pocket were compared both theoretically and numerically. We proved that a cave pocket includes a pocket, and it is equal to a pocket if no cavity is found. We compared the three types of spaces for a variety of molecules with different-sized spherical probes; cave pockets were more sensitive than pockets for finding almost closed internal holes, allowing for more detailed representations of internal surfaces than cavities provide.
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