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Showing posts with label protein. Show all posts
Showing posts with label protein. Show all posts
Sunday, 31 December 2023

A possible BioB bipass route

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Nearly a decade ago there was something bugging me and I believe I have figured it out —although it's pointless now. Namely, is another ...
Saturday, 1 October 2022

Move aside coIP Westerns, ColabFold has got this!

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Recently AlphaFold2 released a new batch of models, this time covering all of the Trembl sequences in Uniprot, resulting in a h...
Sunday, 19 June 2022

Top 10 silliest PDB residue names for ligands!

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UPDATE: The PDB will finish 3 letter chemical component IDs sometime before 2024 at which point they will switch to 5 letter codes, which wi...
Tuesday, 10 May 2022

Show neighbours in nglview

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Nglview is a really nice Python library which encodes a widget to show a NGL viewport, a JS 3D protein viewer used until recently by the PDB...
Sunday, 31 October 2021

Multiple sequence alignments

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A sequence alignment is a rather important tool. Sequence conservation is a key ingredient in most nucleotide mutation severity predictors. ...
Sunday, 17 October 2021

Filling missing loops by cannibalising AlphaFold2

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I could not resist this Photoshop. But the process is not as dramatic and the results not as bad as Temple of Doom... If done right. AlphaFo...
Tuesday, 27 July 2021

What to look out for with an AlphaFold2 model

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There is nothing more disheartening than telling someone "Sorry, I cannot help you with your protein, because no homologue structures o...
Wednesday, 7 July 2021

Per residue RMSD

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Recently I calculated the local RMSD caused by each residue and I thought I'd share the methods I used using PyRosetta —it is nothing at...
Monday, 26 April 2021

Remodel in Pyrosetta

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The Rosetta binary Remodel is a great tool as it allows interesting designs to be made. However, it is rather incompatible with Rosetta Scri...
Monday, 22 February 2021

Multiple poses in NGLView

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As mentioned previously , most of my Pyrosetta operations are done in a Jupyter notebook run in a cluster node. As a result, I am heavily de...
Tuesday, 21 July 2020

Switching ligand in a PDB with Fragmenstein

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For the Covid Moonshot project, one question by Prof. Frank von Delft of Diamond XChem led to a series of events that culminated in Fragmens...
Saturday, 4 July 2020

Filling missing loops —the proper way

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Previously, I posted about how to join proteins and add missing loops the shoddy way . Now I'll address how to do it correctly, using Ro...
1 comment:
Sunday, 19 April 2020

How to set up an electron density scorefunction in Pyrosetta

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Energy minimising structures in Rosetta/Pyrosetta is essential to avoid artifactual results. Say a mutation is introduced and in the protoco...
Wednesday, 18 March 2020

Atom names purely in RDKit

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For some applications, such as PyMOL scripts or Rosetta, atom names are really important, say CA is the standard name for the α-carbon. Exa...
Thursday, 7 November 2019

Go away glycerol!!

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Due to the nature of crystallisation additives are often found in PDB structures. These are generally unwelcome, especially if you want to e...
Wednesday, 4 September 2019

PDB numbering rollercoaster

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The position in a crystal structure and the protein sequence rarely match. In fact, there are four parts of start-end: position in whole p...
Saturday, 3 August 2019

When will the PDB run out of 4-letter codes?

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The PDB ids are really nice and short: 4 letter codes. But when will all the combinations run out? Actually, not for a long long time. The ...
Friday, 31 May 2019

A note on the Linux PyMOL C01 atom oddity

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This weird bug has been haunting me for ages. The PyMOL 1.8 (not 2 in Win or Mac) and Linux PyMOL 2 builder creates residues with a Cα calle...
Tuesday, 15 January 2019

Phosphorylated PDB files

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Sometime in human protein, a residue is phosphorylated, yet the model one gets from I-TASSER, Phyre etc. or the actual PDB structure lacks t...
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: