A memetic algorithm enables efficient local and global all-atom protein-protein docking with backbone and side-chain flexibility

Varela, Daniel; Karlin, Vera; André, Ingemar

doi:10.1016/j.str.2022.09.005

Cited by 6 publications

(11 citation statements)

References 30 publications

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“…The symmetric docking step in this study is built on an extension of the EvoDOCK method 15 to symmetry. EvoDOCK is based on a memetic algorithm that combines a differential evolution method coupled to a Monte Carlo local docking search and is presented schematically in Fig.…”

Section: Resultsmentioning

confidence: 99%

“…The goal was to produce backbone ensembles with some diversity while keeping them close to the predictions by AF/AFM. We initially experimented using Rosetta 18 to resample backbones from AF/AFM predictions as previously done in EvoDOCK 15 and elsewhere 19 , 20 but found that backbones sampled in this manner have significantly higher RMSD to the native backbones compared to the raw output from AF/AFM. The AF/AFM predictions were therefore used directly, employing random seeds to produce different conformations.…”

Section: Resultsmentioning

confidence: 99%

“…EvoDOCK for heterodimeric docking has been described previously 15 . The program was extensively modified to accommodate symmetry.…”

Section: Methodsmentioning

confidence: 99%

“…The expected time it takes to reach a given probability of success in the stochastic sampling with EvoDOCK was estimated and the results are presented in Table S2 . The strategy is based on the procedure presented in Varela et al 15 The complete data with RMSD and energy values for each run were resampled. A loop over the number of runs (num_runs: 1–100) was constructed.…”

Section: Methodsmentioning

confidence: 99%

“…1a ). We recently presented an efficient atomistic docking algorithm for heterodimeric docking called EvoDOCK 15 . EvoDOCK uses a differential evolution algorithm for efficient sampling of rigid-body space coupled to a Monte Carlo approach for local search optimization of all-atom interactions.…”

Section: Introductionmentioning

confidence: 99%

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Accurate prediction of protein assembly structure by combining AlphaFold and symmetrical docking

Jeppesen,

André

2023

Nat Commun

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AlphaFold can predict the structures of monomeric and multimeric proteins with high accuracy but has a limit on the number of chains and residues it can fold. Here we show that a combination of AlphaFold and all-atom symmetric docking simulations enables highly accurate prediction of the structure of complex symmetrical assemblies. We present a method to predict the structure of complexes with cubic – tetrahedral, octahedral and icosahedral – symmetry from sequence. Focusing on proteins where AlphaFold can make confident predictions on the subunit structure, 27 cubic systems were assembled with a median TM-score of 0.99 and a DockQ score of 0.72. 21 had TM-scores of above 0.9 and were categorized as acceptable- to high-quality according to DockQ. The resulting models are energetically optimized and can be used for detailed studies of intermolecular interactions in higher-order symmetrical assemblies. The results demonstrate how explicit treatment of structural symmetry can significantly expand the size and complexity of AlphaFold predictions.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

“…EvoDOCK for heterodimeric docking has been described previously 15 . The program was extensively modified to accommodate symmetry.…”

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Accurate prediction of protein assembly structure by combining AlphaFold and symmetrical docking

Jeppesen,

André

2023

Nat Commun

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The intracellular helical bundle of human glucose transporter GLUT4 is important for complex formation with ASPL

Huang,

Åbacka,

Varela

et al. 2023

FEBS Open Bio

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Glucose transporters (GLUTs) are responsible for transporting hexose molecules across cellular membranes. In adipocytes, insulin stimulates glucose uptake by redistributing GLUT4 to the plasma membrane. In unstimulated adipose‐like mouse cell lines, GLUT4 is known to be retained intracellularly by binding to TUG protein, while upon insulin stimulation, GLUT4 dissociates from TUG. Here, we report that the TUG homolog in human, ASPL, exerts similar properties, i.e., forms a complex with GLUT4. We describe the structural details of complex formation by combining biochemical assays with cross‐linking mass spectrometry and computational modelling. Combined, the data suggest that the intracellular domain of GLUT4 binds to the helical lariat of ASPL and contributes to the regulation of GLUT4 trafficking by cooperative binding.

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LDS-CNN: a deep learning framework for drug-target interactions prediction based on large-scale drug screening

Wang,

Zhang,

Piao

et al. 2023

Health Inf Sci Syst

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A memetic algorithm enables efficient local and global all-atom protein-protein docking with backbone and side-chain flexibility

Cited by 6 publications

References 30 publications

Accurate prediction of protein assembly structure by combining AlphaFold and symmetrical docking

Accurate prediction of protein assembly structure by combining AlphaFold and symmetrical docking

The intracellular helical bundle of human glucose transporter GLUT4 is important for complex formation with ASPL

LDS-CNN: a deep learning framework for drug-target interactions prediction based on large-scale drug screening

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