Efficient generation of protein pockets with PocketGen

2 days ago · Benchmarking generated protein pockets. We benchmark PocketGen on two datasets. The CrossDocked dataset 42 consists of protein–molecule pairs generated through …

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Efficient Generation Of Protein Pockets With PocketGen

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PocketGen can generate high-fidelity protein pockets with superior binding affinity and structural validity. It operates ten times faster than physics-based methods and achieves a 95% success …

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Efficient Generation Of Protein Pockets With PocketGen

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2 days ago · The ratio of the generated pockets by PocketGen with higher affinity than the corresponding reference pocket are 11%, 40% and 45%, respectively. g,h, Protein–ligand …

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FAQs about Efficient generation of protein pockets with PocketGen Coupon?

Is pocketgen a good protein pocket generator?

Experimental results demonstrate that PocketGen significantly outperforms current state-of-the-art methods in protein pocket generation across two popular benchmarks. PocketGen achieves an average amino acid recovery rate of 63.40% and a Vina score of -9.655 for top-1 generated protein pockets on the CrossDocked dataset. ...

Is pocketgen a physics based method?

PocketGen is ten times faster than physics-based methods and achieves a 95% success rate (percentage of generated pockets with higher binding afinity than reference pockets) with over 64% amino acid recovery rate. A primary method for modulating protein functions involves the interaction between proteins and small molecule ligands1–4. ...

What is pocketgen?

We introduce PocketGen, a deep generative model that simultaneously produces both the residue sequence and atomic structure of the protein regions where ligand interactions occur. ...

How does pocketgen improve sequence refinement?

To enhance sequence refinement, PocketGen integrates a structural adapter into the protein language model, ensuring that structure-based predictions align with sequence-based predictions. PocketGen can generate high-fidelity protein pockets with superior binding affinity and structural validity. ...

How effective is pocketgen?

With a 97% success rate in creating pockets with higher afinity than the reference cases (the success rate of the strongest baseline method is 92%) on CrossDocked, PocketGen’s efectiveness and broad applicability across various ligand molecules are clearly demonstrated. ...

What is pocketgen vs pocketoptimizer18?

PocketGen is compared with five state-of-the-art representative baseline methods. PocketOptimizer18 is a physics-based method that optimizes energies such as packing and binding-related energies for ligand-binding protein design. Following the suggestion of the paper, we set the backbone structures fixed. ...