User: db4

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db410
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Posts by db4

<prev • 14 results • page 1 of 2 • next >
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Answer: A: pdbbind and mol2 to pdbqt
... http://vina.scripps.edu/tutorial.html ...
written 10 weeks ago by db410
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Where to find compounds IC50 on an enzyme?
... I am looking for compounds IC50 values on a enzyme. I already searched through ChemBL, PubChem and BindingDB. The three seems to give consistent result. However looking in the literature, there more compounds which are not in these databases. These later may provide higher level of curation. I am st ...
enzyme ic50 written 4 months ago by db410
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Comment: C: Computational Time for obspectrophore in Open Babel?
... "On a personal computer equipped with an i7-5500U processor with 12 GB of main memory, the Open Babel version runs fastest, with an average calculation speed of 36 ± 2 ms/molecule." https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5842169/ This is most likely the speed with small molecule not large ones ...
written 5 months ago by db410
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Answer: A: Converting PDBQT output to PDB in VINA
... They are commands here (http://autodock.scripps.edu/faqs-help/faq/is-there-a-way-to-save-a-protein-ligand-complex-as-a-pdb-file-in-autodock) to convert to pdb. ...
written 5 months ago by db410
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(Closed) Why fully functional protein monomer still dimerise ?
... Hello there Some proteins are fully functional as a dimer but most of their crystal structures show a dimer or even a tetramer. Why they still dimerise if they can function as monomer? Thank ...
protein dimer written 5 months ago by db410
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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 6 months ago by db410
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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 6 months ago by db410
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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 7 months ago by db410
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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 9 months ago by db410
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Comment: C: Converting Smiles To Iupac Chemical Name?
... I have installed cactvstools but can't find the executable. :) ...
written 9 months ago by db410

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