CavBench: A benchmark for protein cavity detection methods

Autoři: Sérgio Dias aff001;  Tiago Simões aff001;  Francisco Fernandes aff003;  Ana Mafalda Martins aff005;  Alfredo Ferreira aff003;  Joaquim Jorge aff003;  Abel J. P. Gomes aff001
Působiště autorů: Instituto de Telecomunicações, Delegação da Covilhã, Covilhã, Portugal aff001;  Universidade da Beira Interior, Departamento de Informática, Covilhã, Portugal aff002;  INESC-ID, Lisboa, Portugal aff003;  Universidade de Lisboa, IST, Lisboa, Portugal aff004;  Universidade Europeia, Lisboa, Portugal aff005
Vyšlo v časopise: PLoS ONE 14(10)
Kategorie: Research Article


Extensive research has been applied to discover new techniques and methods to model protein-ligand interactions. In particular, considerable efforts focused on identifying candidate binding sites, which quite often are active sites that correspond to protein pockets or cavities. Thus, these cavities play an important role in molecular docking. However, there is no established benchmark to assess the accuracy of new cavity detection methods. In practice, each new technique is evaluated using a small set of proteins with known binding sites as ground-truth. However, studies supported by large datasets of known cavities and/or binding sites and statistical classification (i.e., false positives, false negatives, true positives, and true negatives) would yield much stronger and reliable assessments. To this end, we propose CavBench, a generic and extensible benchmark to compare different cavity detection methods relative to diverse ground truth datasets (e.g., PDBsum) using statistical classification methods.

Klíčová slova:

Database and informatics methods – Drug discovery – Protein interactions – Protein structure – Software design – Statistical data – Parsers – Drug design


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