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The (soon-to-be-implemented) treatment for this is:
* We do not add the restraint to the fully interacting state if in explicit solvent.
* We add the restraint if in implicit solvent/vacuum.
Is t…
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Hi pdb2pqr user!
I have complex structure of receptor and ligand in the pdb format. I am trying to convert this pdb file into pqr file format for binding energy calculation. During running command li…
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I apologize if I have missed something obvious in the documentation! I remember in the AF3 paper, a feature for specifying binding pockets is described, i.e. to predict a ligand binding poses in a spe…
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Dear all,
I am trying to create a pipeline to automate the binding energy calculation of several variants of a homotetrameric protein in complex with a medium/big-sized ligand (CoA). I haven't deci…
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# RESP charges calculation using Psikit (Psi4 + RdKit)
The Personal Homepage for Melchor Sanchez-Martinez. A research scientist with experience in project management and science management, passionat…
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My docking experiments of OSM-S-106 vs all crystal structures of Plasmodium kinases supports PKA (protein kinase A) as the top target (PDB 5kbf).
OSM-S-106 was docked into the ligand binding site w…
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https://doi.org/10.1101/099358 (http://biorxiv.org/content/early/2017/01/10/099358)
> Many biological processes are governed by protein-ligand interactions. Of such is the recognition of self and n…
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Hello, glad to see your excellent work!
I encountered a TypeError: string indices must be integers when I tried to reproduce the result of protein-ligand binding affinity prediction using command `py…
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Hello authors,
I am in the process of modifying dMaSIF for the downstream task of protein-ligand binding affinity prediction. While reading & modifying your code, I noticed that in `data_iteration.…
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### Colocar um resumo ou as partes mais importante do abstract (4 linhas máx.) dos seguintes artigos:
- [ ] _P. Zhou et al., A pneumonia outbreak associated with a new coronavirus of probable bat o…