User: zappy

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zappy0
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Posts by zappy

<prev • 13 results • page 1 of 2 • next >
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Comment: C: Upload compound to compound Database
... Thank you very much for these links. The PubChem one looks great. There are a lot of compound databases. What other such databases you are interested in ? I just want to upload some compound on the main database to make them available for screening purposes. ...
written 6 weeks ago by zappy0
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Upload compound to compound Database
... Hello there Hope you are doing very well. Can we upload compounds to compound databases such as ZINC, Pubchem..., providing the required information, so that they become accessible to the public? Thanks Best regards ...
compound database written 6 weeks ago by zappy0
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Answer: A: What are the best ways to validate a docking result?
... https://www.biostars.org/p/13806/ ...
written 5 months ago by zappy0
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Answer: A: Binding energy and binding affinity issue in docking.how to solve?
... I think your data is coherent. The lower the binding energy the better the ligand (I think). So clearly your -8.18 has the lowest Ki 1.01 uM. Concordant ! ...
written 5 months ago by zappy0
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Answer: A: AutoDock Vina is reducing my ligand PDB
... I have sketched with Discovery Studio and docked with Autodock Vina. Everything worked fine. Maybe you can try Discovery Studio. ...
written 5 months ago by zappy0
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Answer: A: Molecular docking, Autodock vina
... You can that using Discovery Studio, opening both receptor and ligand (pdbqt) files and saving them as a single pdb file. ...
written 5 months ago by zappy0
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Answer: A: How do I get the GDT_TS for a model
... Have you tried Zhanglab http://zhanglab.ccmb.med.umich.edu/TM-score/ ...
written 6 months ago by zappy0
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Answer: A: DOPE score analysis with Modeller9.17
... You can assess your models using MODELLER assessment script https://salilab.org/modeller/9v6/manual/node242.html ...
written 6 months ago by zappy0
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Answer: A: Is there any borderline of binding energy in docking stated that we should consi
... I'm having the same question and for now, how I solve it is to find a ligand of reference. For example, let's say you are doing docking on a protein and the protein has a well-known inhibitor. A solution can be to add that inhibitor to your set of ligands. You then compare the binding energies of yo ...
written 6 months ago by zappy0
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Residues interacting with a specific ligand in a set of pdb structures
... Dear all, I have a set of PDB structure. They all have a specific ligand. I want to know which residue in each structure interact with that ligand. For a single structure, I can use pdbsum ( for example here: http://www.ebi.ac.uk/thornton-srv/databases/cgi-bin/pdbsum/GetLigInt.pl?pdb=3au9&ligtyp ...
pdb discovery studio pymol ligand residues written 7 months ago by zappy0

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