Questions tagged [computational-biochemistry]
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Do you know any virtual screening libraries with small, soluble compounds?
I had a quick question on virtual libraries. I'm hoping to perform a virtual screen using a library that contains very small, soluble compounds - think glycerol and smaller (<100MW). As far as I ...
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Building small molecules de novo
Can anyone recommend a protocol for building the 3D structure of a small molecule de novo, given only a 2D rendering? So far my idea has been to build the molecule using the fragment builder in PyMol, ...
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Are codons in RNA layered? Are we misinterpreting RNA codons?
I am analyzing nucleotide base-pair patterns in RNA and DNA, and had a thought about RNA and DNA (Let me first state though, I am not a biologist; I am an algorithmatician, employing a sort of ...
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2answers
59 views
How are different forcefields developed/evaluated?
The Rosetta software can use a variety of different energy functions:
Ref2015
GenPot
Beta-Nov16
How are these energy functions developed and validated? Is it common to do a single protein design ...
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31 views
B-factor analysis in nanobodies
I am doing my research on nanobodies. Currently, I am trying to do a comparison study of the flexibility of CDR loops using B-factor values. I would like to know if there is any statistical analysis ...
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Issues with AutoDock Vina
I am trying to use AutoDock Vina to do docking however I am getting this error. I would really appreciate any help as I have not been able to resolve this error despite trying numerous times.
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Question about Using MDAPackmol (packmol in python)
I would like to use the python wrapper for packmol (MDAPackmol) for my research. In order to do so, I have tried to work with the example code and pdb files provided on GitHub so I can gain an ...
0
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1answer
108 views
How do I convert an Excel file (.xlsx) to an .smi file format?
How do I convert an Excel file(.xlsx) to .smi file format?
The original file I have is an excel file containing over 27,000 ligands. I am going to using the Padel Descriptor software to calculate the ...
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Error in ROSETTA flex ddG tutorial
I'm trying out the ROSETTA flex ddg tutorial (https://github.com/Kortemme-Lab/flex_ddG_tutorial). When running "Example 1" I get an output but with apparently empty folder.
When running the "Analysis"...
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How many models should be generated by rosetta for denovo protein structure prediction?
How many models should be generated by rosetta for de novo protein structure prediction of a 382 long sequence? In the tutorial, it says 50,000 models but practically it takes a lot of time (weeks) to ...
