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Showing posts with label rosetta. Show all posts
Showing posts with label rosetta. Show all posts
Saturday, 31 October 2020

XML to Pyrosetta: EvolutionaryDynamicsMover as an example

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In the previous post I discuss the strategies to use a Pyrosetta class when the documentation lets you down. One topic discussed was the co...
2 comments:
Tuesday, 27 October 2020

Pyrosetta scripting without a manual

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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...
Wednesday, 7 October 2020

Rosetta/Pyrosetta on a cluster or in the cloud

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Due to licensing Rosetta and Pyrosetta cannot be installed via apt-get/pip but has to be downloaded from the Rosetta Commons website. This m...
2 comments:
Saturday, 8 August 2020

Stay hydrated

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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. ...
Monday, 8 June 2020

Love thy neighbours, but select them with caution

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In Rosetta NeighborhoodResidueSelector behaves differently than PyMOL's expand selector and it is good to be aware of it. Namely, in P...
Monday, 21 October 2019

RDKit for Rosetta: PLP ligand space as an example

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Docking requires a molecule to dock. Preparing a ligand is often tricky, especially if the ligand is complicated, such as PLP. PLP is an in...
2 comments:
Tuesday, 18 September 2018

Everything you wanted to know about isopeptide bonds in Rosetta, but were too afraid to ask

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Rosetta is great at predicting (with some accuracy) the energies of variant proteins, however, to make the most out of it with proteins wit...
2 comments:
Monday, 19 March 2018

The curious case of fluorescein and implicit waters

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I recently was asked a straightforward task: get the energy scores of a given protein by itself, conjugated with fluorescein maleimide and i...
Friday, 18 August 2017

Rosetta easteregg

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The guide to use Rosetta may be a bit, ehm, flaky, but I think it is made up for by this rather amusing comment header I found in one of its...