User: db4

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db410
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Posts by db4

<prev • 16 results • page 1 of 2 • next >
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Comment: C: map protein structure to cellular location through their pdb id
... Thank you. I have come across this python package also https://bioservices.readthedocs.io/ ...
written 9 weeks ago by db410
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map protein structure to cellular location through their pdb id
... I want to map PDB id to their cellular locations using python. Which programmatic tools, API can I use for that? ...
pdb go written 9 weeks ago by db410
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Answer: A: pdbbind and mol2 to pdbqt
... http://vina.scripps.edu/tutorial.html ...
written 14 months 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 17 months ago by db410 • updated 8 months ago by Biostar ♦♦ 20
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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 17 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 18 months ago by db410 • updated 10 months ago by RamRS30k
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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 18 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 18 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 19 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 19 months ago by db410

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