User: db4

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db40
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Posts by db4

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Answer: A: Script to list residues within a given distance from ligand
... Pytraj is a possibility. You can load you load your file into pytraj and use the atom selection to select residues around distance from ligand. https://amber-md.github.io/pytraj/latest/atom_mask_selection.html ...
written 2 days ago by db40
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Answer: A: Extract all the residues of chain A between the z coordinate (-14.000 to 14.000)
... An approach could use distances: any atom close enough to any atom in the DUM section should be selected and then you filter them by the only those in CHAIN A or in DUM region. ...
written 20 days ago by db40
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Answer: A: How can Markov State Models be used for ligand-protein complex Molecular Dynamic
... I think you will have to use tools: PyEMMA or MSMBuilder builder. I am using Gromacs to run simulations and there is no MSM capability (to be confirmed though) ...
written 28 days ago by db40
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STITCH Api chemicals ID
... Hello I am trying to access the STITCH website api to retrieve interactions network for some DrugBank compound. When I search the website interface with DrugBank ID (eb: DB08877), I get the result. But when I use the API first to try to map the DrugBank ID to the one of STITCH, using: https://str ...
stitch api id chemicals written 3 months ago by db40
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Comment: C: Converting Smiles To Iupac Chemical Name?
... I have installed cactvstools but can't find the executable. :) ...
written 3 months ago by db40
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Answer: A: What are the terms to look forward to for proper equilibration in GROMACS?
... Any solution ? I am facing the same error. For the protein I am working on, I had to model some residues that missing in the crystal structure using: https://salilab.org/modeller/wiki/Missing%20residues. But I don't think the problem is related to that. The system can pass energy minimization but th ...
written 5 months ago by db40
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Comment: A: BioPandas - Working with molecular structures in pandas DataFrames
... This is completely awesome ! I have been writing scripts to do many of these things ...
written 7 months ago by db40
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Map plasmodb gene ID to pdb crystal structure if exist
... I have a [list of genes with their Plasmodb ids.][1] I want to map the genes to their corresponding protein structures if it exists in the PDB. So far I have tried two different strategies: Using NCBI etulils to find the gene id in NCBI, then the related protein ID and finally the related structure( ...
gene pdb id plasmodb structure written 7 months ago by db40 • updated 5 months ago by Biostar ♦♦ 20
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Find polymorphic/variant sequences of a given protein sequence.
... Good day Hope you are doing great. I'm looking for the variants/polymorphic sequences of a given protein sequence. Which database should I search in? It would really nice if someone can help me out. Thanks a lot! ...
variant sequence polymorphism written 11 months ago by db40

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