User: skim

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skim40
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1 year, 2 months ago
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Posts by skim

<prev • 18 results • page 1 of 2 • next >
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Find protein residues in PDB file that is the most exposed (and does not influence residues around it as much)
... I need a technically and logically sound way to find protein residues in PDB file that is the most exposed (and does not influence residues around it as much) by processing the PDB file on a script such as Python. I know about the solvent accessibility method, but I need to focus on the part that ...
pdb sequence protein written 18 months ago by skim40
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Comment: C: Easier Method to Make a Bioinformatics Pipeline Available on the Web
... Thanks for your clarification. I was just worried if my server might get spammed or DDOSed.... I think Galaxy is the best option. ...
written 21 months ago by skim40
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Comment: C: Easier Method to Make a Bioinformatics Pipeline Available on the Web
... Is it possible to make logins optional and instead incorporate a captcha system like reCAPTCHA or any other methods like this? Also, how do you consider other programs in this link: https://omictools.com/workflow-management-systems-category (Select "Web user interface" in "Filters"), such as http: ...
written 21 months ago by skim40
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Easier Method to Make a Bioinformatics Pipeline Available on the Web
... I want to make a website that makes a bioinformatics command line application or a pipeline available on the web, but I really do not want to manually make a graphically inconvenient (like quite a lot of servers published) web frontend for each program. A platform like Mobyle ( http://mobyle.rpbs. ...
ui bioinformatics web pipeline written 21 months ago by skim40
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Comment: C: Newbie Question: How to find overlap of multiple cellline datas
... Thank you for your answer, but I finished this task 9 months ago :) ...
written 23 months ago by skim40
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How can Markov State Models be used for ligand-protein complex Molecular Dynamics simulations?
... I am a novice structural bioinformaticist using Schrodinger Desmond, and I have used MD for ligand-protein complex Molecular Dynamics simulations. While my methods are pretty traditional, I have found that in http://folding.stanford.edu/dig-deeper/ Folding@home uses Markov State Models for folding. ...
molecular dynamics structure written 2.2 years ago by skim40 • updated 14 months ago by db410
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Confusion between PyRosetta and Rosetta and how to operate PyRosetta
... I am trying to use modelling and docking with rosetta. However, I am comparably fluent in Python, so I would like to use PyRosetta if there are no differences in experience except for the language. However, I am confused with some setup processes. First, how do I link the rosetta binaries with the w ...
homology rosetta pyrosetta protein assembly written 2.6 years ago by skim40
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Comment: C: How do I do protein structure homology-modelling similar to SWISS-MODEL without
... By the way, will it be efficient to use MODELLER or I-TASSER for building models with about 15~30 amino acid mutations for 200~450 residue proteins? I need to automate multiple tasks so time can be important if I-TASSER takes like hours to complete one. If one modelling task can be done within 35 mi ...
written 2.7 years ago by skim40
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Comment: C: Efficient way to check pdb enzyme protein models with certain mutations if the a
... Thank you for the recommendation. Is it possible to automate the process using for example python subprocess module with vina? ...
written 2.7 years ago by skim40
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Efficient way to check pdb enzyme protein models with certain mutations if the active site still works?
... Hello. I have an original pdb file of each of some enzyme proteins. I also have pdb files that I have built using homology modelling after making some mutations with the fasta sequrnces. I would like to check if the mutated enzymes still do their functions on their active sites using a computer prog ...
pdb model homology enzyme written 2.7 years ago by skim40 • updated 2.7 years ago by Joe16k

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