ArticleJournal of computer-aided molecular design2018
A cross docking pipeline for improving pose prediction and virtual screening performance.
Article in Journal of computer-aided molecular design, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Teaching old docks new tricks with machine learning enhanced ensemble docking.Scientific reports · 2024Article
- Open-ComBind: harnessing unlabeled data for improved binding pose prediction.Journal of computer-aided molecular design · 2023Article
- Computational approaches for the design of modulators targeting protein-protein interactions.Expert opinion on drug discovery · 2023Review
- Development of an Automatic Pipeline for Participation in the CELPP Challenge.International journal of molecular sciences · 2022Article
- A Structure Based Study of Selective Inhibition of Factor IXa over Factor Xa.Molecules (Basel, Switzerland) · 2021Article
- Computational Selectivity Assessment of Protease Inhibitors against SARS-CoV-2.International journal of molecular sciences · 2021Article
- Merging Ligand-Based and Structure-Based Methods in Drug Discovery: An Overview of Combined Virtual Screening Approaches.Molecules (Basel, Switzerland) · 2020Review
- D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.Journal of computer-aided molecular design · 2020Article
- Molecular Docking: Shifting Paradigms in Drug Discovery.International journal of molecular sciences · 2019Review
- Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking.Structure (London, England : 1993) · 2019Article
- Shape similarity guided pose prediction: lessons from D3R Grand Challenge 3.Journal of computer-aided molecular design · 2019Article
- A facile consensus ranking approach enhances virtual screening robustness and identifies a cell-active DYRK1α inhibitor.Future medicinal chemistry · 2018Article
- Advances in the Development of Shape Similarity Methods and Their Application in Drug Discovery.Frontiers in chemistry · 2018Review
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2 authors.
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Abstract
Pose prediction and virtual screening performance of a molecular docking method depend on the choice of protein structures used for docking. Multiple structures for a target protein are often used to take into account the receptor flexibility and problems associated with a single receptor structure. However, the use of multiple receptor structures is computationally expensive when docking a large library of small molecules. Here, we propose a new cross-docking pipeline suitable to dock a large library of molecules while taking advantage of multiple target protein structures. Our method involves the selection of a suitable receptor for each ligand in a screening library utilizing ligand 3D shape similarity with crystallographic ligands. We have prospectively evaluated our method in D3R Grand Challenge 2 and demonstrated that our cross-docking pipeline can achieve similar or better performance than using either single or multiple-receptor structures. Moreover, our method displayed not only decent pose prediction performance but also better virtual screening performance over several other methods.
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