Matteo Ferla's repositories
Fragmenstein
Merging, linking and placing compounds by stitching bound compounds together like a reanimated corpse
Python_SmallWorld_API
An (unofficial) Python3 module to query the SmallWorld chemical space search server (https://sw.docking.org/search.html)
molecular_rectifier
Given an RDKit molecule that does not sanitise, correct it until it does
rdkit_to_params
Create or modify Rosetta params files (topology files) from scratch, RDKit mols or another params file
pyrosetta-help
Some scripts that I keep using over and over.
Fragment-hit-follow-up-chemistry
A collection of notebooks and scripts for the prediction of follow-up compounds in
Christmas_tree_protein
A Christmas tree protein
JSME_notebook
JSME molecular editor in a Jupyter or Colab notebook in a hacky way
DirEvo_tools
The new and improved server combining Pedel, Mutanalyst and much more
DTC-compchem-practical
Compchem practical for the University of Oxford Doctoral Training Centre
And-the-protein-ligand-went-boom
A collection of various computational chemistry/biochemistry fails
Arthorian-Quest
An experiment in using Arthor (arthor.docking.org) by NextMove and filtering the results with Fragmenstein
gist-import
GitHub Gist are handy snippets, which are meant to be copy-pasted into one's code... but what if you could import them?
Sociable-fragment-library-design
The design of a fragment library that is sociably poised for the XChem in house synthesis robot
protein-design-analysis
A toolkit to analyse complicated de novo protein designs in PyRosetta
A-thaliana-FatA-modelling
Native ligand modelling (phosphopantetheine (PNS) and oleic acid (OLA) bound to carrier protein) for FatA
aprotinin_engineering
Improve the interface between aprotinin and Zika protease
ASAP-dataset-matching
Matching an alphabet soup of compounds is not trivial. This my attempt at matching Postera and multiple Fragalysis sources for metadata presevation
COVID-Moonshot-metadata-analysis
In the Postera wesbite users can write a rationale for their submission
Dengue-NS2B-NS3-closed-state-design
Wild type Dengue NS2B-NS3 protease refuses to crystallise in the closed/reaction-ready state: designs to the rescue
DogCatcher
Engineering of a orthogonal pair of catcher–tag
EV-A71-2A-elaborations
Elaborations for the XChem fragment hits against EV A71 2A protease
Fragmenstein-manuscript-data
Analyses and figures for the Fragmenstein manuscript
isopeptide-builder
Given a protein without an isopeptide predict where one would work best
matteoferla
Config files for my GitHub profile.
Sindarin-character-sheet
A character sheet for Dungeons and Dragons 5e written in Sindarin (Tolkien modern elvish)
Zika-NS2B-NS3-elaborations
Elaborations based on the initial fragments of Zika protease (ASAP project)