3

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 acids into triplets - in fact, there are six unique ways, found by shifting the start letter by one three times, and doing the same but reading in reverse. ...


3

I'd suggest the bit-dl-ncbi-assemblies from the Bioinformatics Tools package. $ bit-dl-ncbi-assemblies -------------------------------- HELP INFO --------------------------------- This program downloads assembly files for NCBI genomes. It takes as input assembly accessions (either GCA_* or GCF_*) and optionally a specification of which format to ...


2

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 it. I do not know if the newer Clayden (nitrile cover) deals with computational methods, but the old one (water+formaldehyde on cover) did not. In generally, a ...


2

The problem is my pack.xml specified a resfile.txt location which over-wrote my command-line option. <TASKOPERATIONS> <ReadResfile name="Design_Resfile" filename="resfile.txt"/> </TASKOPERATIONS> If you remove the filename option in the XML file, you are then able to specify the path. <TASKOPERATIONS> <...


2

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 compute power as they'd like. In this case the long time arises from the combinatorial explosion of possible fragment combinations that need to be explored. ...


1

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. Also there are online drawing tools everywhere, where you can download a SMILES (see below). Chemical formula is the wrong way to go, unless you are "...


1

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 worked on a paper about Nippostrongylus brasiliensis mtDNA, and needed polyA completion to explain the transcript expression I observed: https://doi.org/10.12688/...


1

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 total energy in kcal/mol and the paper does a swell job at explaining what they do. For several Rosetta experiments, you switch between full-atom and centroid (...


1

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/diffusion aspects at different theoretical temperatures of a set of well-studied proteins. (Top-Down vs. Bottom-Up) I haven't done MD myself but I am in an MD group ...


1

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 This is partly a result of flexibility, but it is highly influenced by crystal packing, which is not natural. Many enzymes, for example, are seen with an active ...


1

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 new sheet copy the SMILES column and the name column save as tab separated file in Finder/Nautilus/File Explorer rename the file extension to .smi


Only top voted, non community-wiki answers of a minimum length are eligible