CavityPlus: a web server for protein cavity detection with pharmacophore modelling, allosteric site identification and covalent ligand binding ability prediction

By Youjun Xu, Shiwei Wang, Qiwan Hu, Shuaishi Gao, Xiaomin Ma, Weilin Zhang, Yihang Shen, Fangjin Chen, Luhua Lai, Jianfeng Pei. Nucleic Acids Res., 2018

342 citations recorded by the source corpus.

Abstract CavityPlus is a web server that offers protein cavity detection and various functional analyses. Using protein three-dimensional structural information as the input, CavityPlus applies CAVITY to detect potential binding sites on the surface of a given protein structure and rank them based on ligandability and druggability scores. These potential binding sites can be further analysed using three submodules, CavPharmer, CorrSite, and CovCys. CavPharmer uses a receptor-based pharmacophore modelling program, Pocket, to automatically extract pharmacophore features within cavities. CorrSite identifies potential allosteric ligand-binding sites based on motion correlation analyses between cavities. CovCys automatically detects druggable cysteine residues, which is especially useful to identify novel binding sites for designing covalent allosteric ligands. Overall, CavityPlus provides an integrated platform for analysing comprehensive properties of protein binding cavities. Such analyses are useful for many aspects of drug design and discovery, including target selection and identification, virtual screening, de novo drug design, and allosteric and covalent-binding drug design. The CavityPlus web server is freely available at http://repharma.pku.edu.cn/cavityplus or http://www.pkumdl.cn/cavityplus.

Subfields: Computational Theory and Mathematics, Molecular Biology, Radiology, Nuclear Medicine and Imaging

View Paper: https://www.semanticscholar.org/paper/ddaf0eaa5ac0f0ff48c8e11ab449b8845686009e

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Computational Theory and Mathematics

1. Shiwei Wang
2. Jianfeng Pei
3. Luhua Lai

In Molecular Biology

1. Shiwei Wang
2. Jianfeng Pei
3. Luhua Lai

Citations in the corpus

• CavitySpace: A Database of Potential Ligand Binding Sites in the Human Proteome (2022, methodology): “We recommend that based on the CavitySpace results, users further analyze the potential binding sites with more accurate structures after carefully considering inter-domain orientations and oligomeric states using our CavityPlus webserver [38] or other cavity detection tools.”