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Automated benchmarking of combined protein structure and ligand conformation prediction
  • +3
  • Xavier Robin,
  • Michèle Leemann,
  • Ander Sagasta,
  • Jerome Eberhardt,
  • Torsten Schwede,
  • Janani Durairaj
Xavier Robin
Universitat Basel Department Biozentrum
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Michèle Leemann
Universitat Basel Department Biozentrum
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Ander Sagasta
Universitat Basel Department Biozentrum
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Jerome Eberhardt
Universitat Basel Department Biozentrum
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Torsten Schwede
Universitat Basel Department Biozentrum

Corresponding Author:torsten.schwede@unibas.ch

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Janani Durairaj
Universitat Basel Department Biozentrum
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Abstract

The prediction of protein-ligand complexes (PLC), using both experimental and predicted structures, is an active and important area of research, underscored by the inclusion of the Protein-Ligand Interaction category in the latest round of the Critical Assessment of Protein Structure Prediction experiment CASP15. The prediction task in CASP15 consisted of predicting both the 3-dimensional structure of the receptor protein as well as the position and conformation of the ligand. This paper addresses the challenges and proposed solutions for devising automated benchmarking techniques for PLC prediction. The reliability of experimentally solved PLC as ground truth reference structures is assessed using various validation criteria. Similarity of PLC to previously released complexes are employed to judge the novelty and difficulty of a PLC as a prediction target. We show that the commonly used PDBBind time-split test-set is inappropriate for comprehensive PLC evaluation. Finally, we introduce a fully automated pipeline that predicts PLC and evaluates the accuracy of the protein structure, ligand pose, and protein-ligand interactions.
11 May 2023Submitted to PROTEINS: Structure, Function, and Bioinformatics
11 May 2023Submission Checks Completed
11 May 2023Assigned to Editor
11 May 2023Review(s) Completed, Editorial Evaluation Pending
24 May 2023Reviewer(s) Assigned
21 Aug 2023Editorial Decision: Revise Major
16 Sep 20231st Revision Received
16 Sep 2023Submission Checks Completed
16 Sep 2023Assigned to Editor
16 Sep 2023Review(s) Completed, Editorial Evaluation Pending
16 Sep 2023Reviewer(s) Assigned
21 Sep 2023Editorial Decision: Accept