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bowen-gao / DrugCLIP

[NeurIPS 2023] DrugCLIP: Contrastive Protein-Molecule Representation Learning for Virtual Screening
MIT License
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Instructions #6

Closed CLG68 closed 6 months ago

CLG68 commented 6 months ago

Hi,

Do you have ex of a command line to launch a screen of a library X on a target Y? What is the format of the library, smiles, 2D sd files, 3D sd files, mol2 files? The receptor is in pdb?

In your figure 3, you have "pre-encoded library", how do you create a pre-encoded library?

I would like to compare the speed of DrugCLIP to BANANA and Panther/ShaEP.

Thanks for your help, Christian

bowen-gao commented 6 months ago

you can see the "retrieval" section in readme to launch a screen.

pre-encoded means encoding all the mols in the library using the pocket encoder to embedding representations.

On Sun, Apr 21, 2024 at 10:48 PM CLG68 @.***> wrote:

Hi,

Do you have ex of a command line to launch a screen of a library X on a target Y? What is the format of the library, smiles, 2D sd files, 3D sd files, mol2 files? The receptor is in pdb?

In your figure 3, you have "pre-encoded library", how do you create a pre-encoded library?

I would like to compare the speed of DrugCLIP to BANANA and Panther/ShaEP.

Thanks for your help, Christian

— Reply to this email directly, view it on GitHub https://github.com/bowen-gao/DrugCLIP/issues/6, or unsubscribe https://github.com/notifications/unsubscribe-auth/AF2UUFO57DYDH4ONAKKN4IDY6PGVJAVCNFSM6AAAAABGROAXZSVHI2DSMVQWIX3LMV43ASLTON2WKOZSGI2TKMJRGU2TENI . You are receiving this because you are subscribed to this thread.Message ID: @.***>

bowen-gao commented 6 months ago

sorry, should be using the "molecular encoder"

On Mon, Apr 22, 2024 at 12:11 AM Bowen Gao @.***> wrote:

you can see the "retrieval" section in readme to launch a screen.

pre-encoded means encoding all the mols in the library using the pocket encoder to embedding representations.

On Sun, Apr 21, 2024 at 10:48 PM CLG68 @.***> wrote:

Hi,

Do you have ex of a command line to launch a screen of a library X on a target Y? What is the format of the library, smiles, 2D sd files, 3D sd files, mol2 files? The receptor is in pdb?

In your figure 3, you have "pre-encoded library", how do you create a pre-encoded library?

I would like to compare the speed of DrugCLIP to BANANA and Panther/ShaEP.

Thanks for your help, Christian

— Reply to this email directly, view it on GitHub https://github.com/bowen-gao/DrugCLIP/issues/6, or unsubscribe https://github.com/notifications/unsubscribe-auth/AF2UUFO57DYDH4ONAKKN4IDY6PGVJAVCNFSM6AAAAABGROAXZSVHI2DSMVQWIX3LMV43ASLTON2WKOZSGI2TKMJRGU2TENI . You are receiving this because you are subscribed to this thread.Message ID: @.***>

CLG68 commented 6 months ago

Thank you very much for your reply, I will try that.

Best