ArticleJournal of computer-aided molecular design2013
Protein pocket and ligand shape comparison and its application in virtual screening.
Article in Journal of computer-aided molecular design, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Oxidative Ring-Opening of Dimethylfuran in Zeolitic Imidazolate Frameworks through Computational Design.The journal of physical chemistry. C, Nanomaterials and interfaces · 2026Article
- An Ecosystem for Digital Reticular Chemistry.ACS central science · 2023Article
- RPocket: an intuitive database of RNA pocket topology information with RNA-ligand data resources.BMC bioinformatics · 2021Article
- CAVIAR: a method for automatic cavity detection, description and decomposition into subcavities.Journal of computer-aided molecular design · 2021Article
- On the origins of three-dimensionality in drug-like molecules.Future medicinal chemistry · 2016Article
- Considerations of Protein Subpockets in Fragment-Based Drug Design.Chemical biology & drug design · 2016Article
- PDB-Explorer: a web-based interactive map of the protein data bank in shape space.BMC bioinformatics · 2015Article
- p38α MAPK and Type I Inhibitors: Binding Site Analysis and Use of Target Ensembles in Virtual Screening.Molecules (Basel, Switzerland) · 2015Article
- Stereoselective virtual screening of the ZINC database using atom pair 3D-fingerprints.Journal of cheminformatics · 2015Article
- POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics.Journal of chemical theory and computation · 2014Article
- Drug-Like Protein-Protein Interaction Modulators: Challenges and Opportunities for Drug Discovery and Chemical Biology.Molecular informatics · 2014Review
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Authors and funding
7 authors.
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Abstract
Understanding molecular recognition is one major requirement for drug discovery and design. Physicochemical and shape complementarity between two binding partners is the driving force during complex formation. In this study, the impact of shape within this process is analyzed. Protein binding pockets and co-crystallized ligands are represented by normalized principal moments of inertia ratios (NPRs). The corresponding descriptor space is triangular, with its corners occupied by spherical, discoid, and elongated shapes. An analysis of a selected set of sc-PDB complexes suggests that pockets and bound ligands avoid spherical shapes, which are, however, prevalent in small unoccupied pockets. Furthermore, a direct shape comparison confirms previous studies that on average only one third of a pocket is filled by its bound ligand, supplemented by a 50 % subpocket coverage. In this study, we found that shape complementary is expressed by low pairwise shape distances in NPR space, short distances between the centers-of-mass, and small deviations in the angle between the first principal ellipsoid axes. Furthermore, it is assessed how different binding pocket parameters are related to bioactivity and binding efficiency of the co-crystallized ligand. In addition, the performance of different shape and size parameters of pockets and ligands is evaluated in a virtual screening scenario performed on four representative targets.
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