CavBench: A benchmark for protein cavity detection methods

PLoS One. 2019 Oct 14;14(10):e0223596. doi: 10.1371/journal.pone.0223596. eCollection 2019.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Models, Molecular*
  • Protein Conformation
  • Proteins / chemistry*
  • Reproducibility of Results
  • Sensitivity and Specificity
  • Software*

Substances

  • Proteins

Grants and funding

This research has been partially supported by the Portuguese ResearchCouncil (Fundação para a Ciência e Tecnologia), under the FCT Projects UID/EEA/50008/2019, UID/CEC/50021/2019, PTDC/EEI-SII/6038/2014, the doctoral grant SFRH/BD/99813/2014, and postdoctoral grants SFRH/BPD/97449/2013 and SFRH/BPD/111836/2015. No additional support was received for this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.