ArticleProceedings of the National Academy of Sciences of the United States of America2016
Protein-protein docking by fast generalized Fourier transforms on 5D rotational manifolds.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Article
- MEGA PROTAC, MEGA DOCK-based PROTAC mediated ternary complex formation pipeline with sequential filtering and rank aggregation.Scientific reports · 2025Article
- Navigating structure-based drug discovery with emerging innovations in physics- and knowledge-based approaches.npj drug discovery · 2025Review
- AI-integrated network for RNA complex structure and dynamic prediction.Biophysics reviews · 2024Review
- Inhibitory effect of truncated isoforms on GPCR dimerization predicted by combinatorial computational strategy.Computational and structural biotechnology journal · 2024Article
- Docking Foundations: From Rigid to Flexible Docking.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Assessment of Protein-Protein Docking Models Using Deep Learning.Methods in molecular biology (Clifton, N.J.) · 2024Review
- Sampling and Scoring in Protein-Protein Docking.Methods in molecular biology (Clifton, N.J.) · 2024Article
- The ClusPro AbEMap web server for the prediction of antibody epitopes.Nature protocols · 2023Review
- Predicting structures of large protein assemblies using combinatorial assembly algorithm and AlphaFold2.bioRxiv : the preprint server for biology · 2023Article
- Critical Assessment of Methods for Predicting the 3D Structure of Proteins and Protein Complexes.Annual review of biophysics · 2023Review
- Fast and versatile sequence-independent protein docking for nanomaterials design using RPXDock.PLoS computational biology · 2023Article
- Protein-protein interfaces in molecular glue-induced ternary complexes: classification, characterization, and prediction.RSC chemical biology · 2023Review
- Protein-Protein Docking: Past, Present, and Future.The protein journal · 2022Review
- Klotho upregulates the interaction between RANK and TRAF6 to facilitate RANKL-induced osteoclastogenesis via the NF-κB signaling pathway.Annals of translational medicine · 2021Article
- Advances to tackle backbone flexibility in protein docking.Current opinion in structural biology · 2021Review
- InterPepRank: Assessment of Docked Peptide Conformations by a Deep Graph Network.Frontiers in bioinformatics · 2021Review
- Protein Docking Model Evaluation by Graph Neural Networks.Frontiers in molecular biosciences · 2021Article
- Article
- Macromolecular modeling and design in Rosetta: recent methods and frameworks.Nature methods · 2020Review
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10 authors.
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Abstract
Energy evaluation using fast Fourier transforms (FFTs) enables sampling billions of putative complex structures and hence revolutionized rigid protein-protein docking. However, in current methods, efficient acceleration is achieved only in either the translational or the rotational subspace. Developing an efficient and accurate docking method that expands FFT-based sampling to five rotational coordinates is an extensively studied but still unsolved problem. The algorithm presented here retains the accuracy of earlier methods but yields at least 10-fold speedup. The improvement is due to two innovations. First, the search space is treated as the product manifold [Formula: see text], where [Formula: see text] is the rotation group representing the space of the rotating ligand, and [Formula: see text] is the space spanned by the two Euler angles that define the orientation of the vector from the center of the fixed receptor toward the center of the ligand. This representation enables the use of efficient FFT methods developed for [Formula: see text] Second, we select the centers of highly populated clusters of docked structures, rather than the lowest energy conformations, as predictions of the complex, and hence there is no need for very high accuracy in energy evaluation. Therefore, it is sufficient to use a limited number of spherical basis functions in the Fourier space, which increases the efficiency of sampling while retaining the accuracy of docking results. A major advantage of the method is that, in contrast to classical approaches, increasing the number of correlation function terms is computationally inexpensive, which enables using complex energy functions for scoring.
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