User: skim

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skim20
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Posts by skim

<prev • 17 results • page 1 of 2 • next >
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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 7 weeks ago by skim20
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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 8 weeks ago by skim20
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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 8 weeks ago by skim20
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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 3 months ago by skim20
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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 6 months ago by skim20
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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 11 months ago by skim20
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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 12 months ago by skim20
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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 12 months ago by skim20
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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 12 months ago by skim20 • updated 12 months ago by jrj.healey7.4k
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How do I do protein structure homology-modelling similar to SWISS-MODEL without using a web api for computing and only use online databases for searching templates?
... How do I do protein structure homology-modelling similar to SWISS-MODEL without using a web api for computing and only use online databases for searching templates? I would like to use python (I heard salilab modeller can do this in some way) to integrate this into another additional script. It wou ...
homology swiss-model modelling protein written 13 months ago by skim20 • updated 13 months ago by jrj.healey7.4k

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