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This step follows on from Issue #2 where you will have prepared your ligands from SMILES strings using Gypsum-DL. For this virtual screen I have used the [SARS-CoV2 helicase - holo complex, nsp13](htt…
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[Rosetta](https://www.rosettacommons.org/software) is a unique and powerful piece of software, but it appears like there isn't a current open source equivalent ([discussion](https://twitter.com/rbhar9…
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How feasible would the following algorithm be?
Suppose the docking space (the box containing the binding pocket) were divided into 0.67Å voxels. Each atom of the ligand can then be given a probabil…
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Let me first thank you by your program: CONGRATULATIONS!!!.
IT BEATIFULLY WORKED !!
I was looking for years for something similar !!!
I am a user of PyRx for many years. Mostly we used to confi…
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@doi:10.1021/bi501056h
> We have employed molecular dynamics (MD)
simulation to investigate, with atomic details, the structural dynamics
and energetics of three major ATPase states (ADP, APO, and …
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Hi, a few of us at UCL CS (and further afield) have a WIP submission; I realize we're getting down to the wire and we're having a bit of a challenge finishing this this off so I wanted to share our pr…
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I would like to seek your assistance in using MedusaDock to optimize protein-ligand structures. Specifically, I am uncertain about the process of converting docking results obtained from Vina into inp…
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Definition | Parents
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The initial attachment of a membrane or protein to a target membrane. Docking requires only that the proteins come close enough to interact and adhere.
Should this …
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Please see attached ligands that are predicted to bind to the same allosteric pocket as the 373 fragment.
Our method can be largely broken down into two steps. A more complete description can be fo…
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Hallo all,
Let's say that I have a protein to which I would like to dock multiple different proteins but always in a 1:1 ratio.
there is a way to provide a list in the fasta file so that the first…