ArticleJournal of computer-aided molecular design2018
Protein-ligand docking using FFT based sampling: D3R case study.
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 10 papers.
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Who cites it
10 citing papers in PubMed.
- MEGA PROTAC, MEGA DOCK-based PROTAC mediated ternary complex formation pipeline with sequential filtering and rank aggregation.Scientific reports · 2025Article
- Sampling and Scoring in Protein-Protein Docking.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Unveiling the N-Terminal Homodimerization of BCL11B by Hybrid Solvent Replica-Exchange Simulations.International journal of molecular sciences · 2021Article
- Accelerated CDOCKER with GPUs, Parallel Simulated Annealing, and Fast Fourier Transforms.Journal of chemical theory and computation · 2020Article
- A Review of Deep Learning Methods for Antibodies.Antibodies (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
- Sampling and refinement protocols for template-based macrocycle docking: 2018 D3R Grand Challenge 4.Journal of computer-aided molecular design · 2020Article
- CB-Dock: a web server for cavity detection-guided protein-ligand blind docking.Acta pharmacologica Sinica · 2020Article
- Monte Carlo on the manifold and MD refinement for binding pose prediction of protein-ligand complexes: 2017 D3R Grand Challenge.Journal of computer-aided molecular design · 2019Article
- Inhibition of protein interactions: co-crystalized protein-protein interfaces are nearly as good as holo proteins in rigid-body ligand docking.Journal of computer-aided molecular design · 2018Article
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Authors and funding
8 authors.
Funding
Abstract
Fast Fourier transform (FFT) based approaches have been successful in application to modeling of relatively rigid protein-protein complexes. Recently, we have been able to adapt the FFT methodology to treatment of flexible protein-peptide interactions. Here, we report our latest attempt to expand the capabilities of the FFT approach to treatment of flexible protein-ligand interactions in application to the D3R PL-2016-1 challenge. Based on the D3R assessment, our FFT approach in conjunction with Monte Carlo minimization off-grid refinement was among the top performing methods in the challenge. The potential advantage of our method is its ability to globally sample the protein-ligand interaction landscape, which will be explored in further applications.
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Registered trials
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