3 votes
Accepted

Are codons in RNA layered? Are we misinterpreting RNA codons?

This relates to the concept of the reading frame, which is the point at which you start dividing 3-letter sequences into codons. As you point out, there are multiple ways to divide a string of amino ...
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3 votes

How to convert amino acid sequence to SMILES format

SMILES are meant for machines, but reading up on the format is very handy and one totally can read and write them —I do it often and could not recommend it enough. You can have SMILES written ...
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  • 3,719
3 votes

general cheminformatics references

The definition of cheminformatics has been covered in Difference between bioinformatics and cheminformatics For a reference, simply citing Essentials of Computational Chemistry by C. Cramer will do ...
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3 votes

How to download the whole genome of an organism from NCBI using R or Python?

I'd suggest the bit-dl-ncbi-assemblies from the Bioinformatics Tools package. ...
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2 votes
Accepted

How to specify input resfile for Rosetta?

The problem is my pack.xml specified a resfile.txt location which over-wrote my command-line option. ...
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  • 153
2 votes
Accepted

How many models should be generated by rosetta for denovo protein structure prediction?

Unfortunately you do in general increase your chance of success by going to the 50k range of models or higher. Projects like Rosetta@home exist because even large research groups can't access as much ...
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  • 901
1 vote
Accepted

Parsing pre-2007 SMILES string

I couldn't find a way to directly convert these SMILES strings to a more canonical format. However, thanks to @Matteo Ferla, I was able to get around the problem entirely by looking up the chemical ...
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1 vote

Building small molecules de novo

Most universities have a ChemDraw site lincence, so you may want to check that for drawing a non–3D-embedded molecule. Alternatively there are many other programs. PyMOL is not really a good choice. ...
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  • 3,719
1 vote

Are codons in RNA layered? Are we misinterpreting RNA codons?

To add complexity to this discussion, there are examples in some mitochondrial genomes where the stop point of a gene is based on the polyA-attached transcript, rather than the genomic sequence. I ...
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  • 11.8k
1 vote

How are different forcefields developed/evaluated?

The Rosetta ref2015 is well described in two papers, which I wish I had read much earlier, see this JChIM paper. It's a statistical forcefield, where the terms are weighted to best match the empirical ...
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1 vote

How are different forcefields developed/evaluated?

Some force-fields rely solely on theoretical physical principles, while others are tweaked specifically for the goal of accurately depicting certain structures like sheets and helices or movement/...
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  • 151
1 vote

B-factor analysis in nanobodies

So B-factors, for "blur factors", are how much movement an atom has in the crystal structure. They are not reliable. B-factor putty in PyMOL is the most you should push them. B-factors bad ...
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1 vote

How do I convert an Excel file (.xlsx) to an .smi file format?

So a smi file is simply a text file formatted SMILES tab name newline. Therefore what you need to do is save for safety make a ...
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