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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2answers
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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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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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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 ...
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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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1answer
120 views

How to specify input resfile for Rosetta?

I'm trying to run the following Rosetta command. ...
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1answer
72 views

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 ...