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 ...
- 246
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 ...
- 4,234
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.
...
- 810
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.
...
- 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 ...
- 931
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 ...
- 41
1
vote
Do you know any virtual screening libraries with small, soluble compounds?
ZINC20 is a free database of commercially-available compounds for virtual screening. It contains 1.3M compounds with molecular weight less than 200.
https://zinc20.docking.org/
Cartblanche22 is an ...
- 118
1
vote
Do you know any virtual screening libraries with small, soluble compounds?
Lipinski and logP
Most datasets will be filtered by the Lipinski rule, plus in the some cases, such as Enamine Real whether they can be bought.
One criterion in the Lipinski rule filter is the logP, ...
- 4,234
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. ...
- 4,234
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 ...
- 13.8k
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 ...
- 4,234
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/...
- 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
...
- 4,234
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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