XML to Pyrosetta: EvolutionaryDynamicsMover as an example

In the previous post I discuss the strategies to use a Pyrosetta class when the documentation lets you down. One topic discussed was the conversion of a Rosetta XML script to Pyrosetta. Here is an example, namely using the EvolutionaryDynamics mover as an example.

Pyrosetta scripting without a manual

I got recently asked how to figure out how to write a Pyrosetta script when there is no example. This is definitely the biggest weakness of Pyrosetta and Rosetta script, but it is not insurmountable. In fact, there is a wealth of information that is hidden that can be mined. Here is how and in the next post, I give an example.

The Freedom unit for molar energy: the foot-pound-force per pound-mole

In computational biochemistry the most commonly used unit is molar energy. The SI unit is kJ/mol (kilojoule per mole), but kcal/mol is also as frequently used —Google enumerates 5.3e6 and 3.8e6 pages for them respectively. Different programs use one or the other, GROMACS uses kJ/mol, while Rosetta uses kcal/mol. They differ by a factor of about 4, the latter has the advantage that 1 kcal/mol is the strength of a hydrogen bond and k_BT/N_A is 0.6 kcal/mol (25°C) or 1. kcal/mol (37°C), while the former being SI sounds more sciency ——and not in the overly obnoxious way as folk who use Kelvin for enzymology.

However, whereas it is not an SI unit, kcal/mol is still very metric and European, after all the unit calorie was introduced by a Frenchman. Therefore, a more American unit is clearly required. Hence the need for the foot–pound-force per pound-mole.

Rosetta/Pyrosetta on a cluster or in the cloud

Due to licensing Rosetta and Pyrosetta cannot be installed via apt-get/pip but has to be downloaded from the Rosetta Commons website. This makes things harder if you are in a colabs notebook, ssh'ed into a machine or running off a remote jupyter notebook. Luckily it actually is straightforward.

5-hydroxytryptophan biosynthesis

 

I was intrigued by a recent article in the journal Chem (link)  entitled "Creation of Bacterial Cells with 5-hydroxytryptophan as a 21st Amino Acid Building Block" by Chen et al. in the group of Han Xiao at Rice University, wherein they make a strain that metabolically produces 5-hydroxytryptophan for genetic code expansion. It is an interesting example of why metabolic engineering is non-trivial and how scientific research does not progress in a logical fashion.

Stay hydrated

Waters can be an integral part of a protein structure, in fact, it is common to find water crystallised tightly in an X-ray structure. These waters can change the calculated Gibbs free energy of a protein and give better experimental results. Explicit waters can be added in Rosetta/Pyrosetta thanks to the SPaDES algorithm described in Lai et al. 2017. Here is a guide to using it in Pyrosetta.

Switching ligand in a PDB with Fragmenstein

For the Covid Moonshot project, one question by Prof. Frank von Delft of Diamond XChem led to a series of events that culminated in Fragmenstein, a module to do fragment mergers when the followup is as faithful to the starting crystal hits as possible. Even if it's intended use is the hit-to-lead process, there is a nice use that make it rather handy for computational biochemistry in general: switching the ligand in a PDB to another in an energy minimised fashion that obeys the original ligand.