User: zappy

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zappy0
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diallobakary4
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Posts by zappy

<prev • 11 results • page 1 of 2 • next >
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Answer: A: What are the best ways to validate a docking result?
... https://www.biostars.org/p/13806/ ...
written 3 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 3 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 3 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 3 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 3 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 3 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 4 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 4 months ago by zappy0
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Comment: C: Biology side of bioinformatics
... my email is diallobakary4@gmail.com Thanks ...
written 15 months ago by zappy0
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Comment: C: Biology side of bioinformatics
... Hi @kirannbishwa01 I have also a background in biology, currently learning python. I'm interested to what process you want to do with you vcf file. ...
written 15 months ago by zappy0

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