matteoferla
Computational biochemist in University of Oxford OPIG/XChem groups
University of OxfordOxford, United Kingdom
Pinned Repositories
DirEvo_tools
The new and improved server combining Pedel, Mutanalyst and much more
DnD-battler
A 5e D&D encounter simulator written for my own amusement to test some hypotheses.
Fragmenstein
Merging, linking and placing compounds by stitching bound compounds together like a reanimated corpse
Fragment-hit-follow-up-chemistry
A collection of notebooks and scripts for the prediction of follow-up compounds in
Michelanglo-and-Venus
Topmost repository for the Michelanglo webapp, including the Venus functionality.
MichelaNGLo-app
A web app to convert a PyMOL PSE file or PDB file to a easy to implement NGL.js view that can be implemented easily on any site
molecular_rectifier
Given an RDKit molecule that does not sanitise, correct it until it does
pyrosetta-help
Some scripts that I keep using over and over.
Python_SmallWorld_API
An (unofficial) Python3 module to query the SmallWorld chemical space search server (https://sw.docking.org/search.html)
rdkit_to_params
Create or modify Rosetta params files (topology files) from scratch, RDKit mols or another params file
matteoferla's Repositories
matteoferla/Fragmenstein
Merging, linking and placing compounds by stitching bound compounds together like a reanimated corpse
matteoferla/Python_SmallWorld_API
An (unofficial) Python3 module to query the SmallWorld chemical space search server (https://sw.docking.org/search.html)
matteoferla/molecular_rectifier
Given an RDKit molecule that does not sanitise, correct it until it does
matteoferla/rdkit_to_params
Create or modify Rosetta params files (topology files) from scratch, RDKit mols or another params file
matteoferla/pyrosetta-help
Some scripts that I keep using over and over.
matteoferla/Fragment-hit-follow-up-chemistry
A collection of notebooks and scripts for the prediction of follow-up compounds in
matteoferla/DirEvo_tools
The new and improved server combining Pedel, Mutanalyst and much more
matteoferla/DTC-compchem-practical
Compchem practical for the University of Oxford Doctoral Training Centre
matteoferla/JSME_notebook
JSME molecular editor in a Jupyter or Colab notebook in a hacky way
matteoferla/And-the-protein-ligand-went-boom
A collection of various computational chemistry/biochemistry fails
matteoferla/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?
matteoferla/Arthorian-Quest
An experiment in using Arthor (arthor.docking.org) by NextMove and filtering the results with Fragmenstein
matteoferla/Sociable-fragment-library-design
The design of a fragment library that is sociably poised for the XChem in house synthesis robot
matteoferla/crysalin
Engineering crysalin lattice
matteoferla/EV-D68-3C-protease
Follow-up suggestions for EV-D68 3C protease fragment-based drug-discovery campaign of ASAP consortium
matteoferla/A-thaliana-FatA-modelling
Native ligand modelling (phosphopantetheine (PNS) and oleic acid (OLA) bound to carrier protein) for FatA
matteoferla/Analysis-of-Fragalysis-historical-hits
An analysis of what makes stuff stick
matteoferla/aprotinin_engineering
Improve the interface between aprotinin and Zika protease
matteoferla/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
matteoferla/COVID-Moonshot-metadata-analysis
In the Postera wesbite users can write a rationale for their submission
matteoferla/EV-A71-2A-elaborations
Elaborations for the XChem fragment hits against EV A71 2A protease
matteoferla/Fragmenstein-manuscript-data
Analyses and figures for the Fragmenstein manuscript
matteoferla/Functional-subsets-of-Enamine-BB
Subsets of Enamine Real good for T3P amidation, Suzuki, etc or by number of rotatable bonds
matteoferla/Idea-for-Fragalysis-job-modularization
A barebone hypothetical example for Fragalysis jobs for discussion purposes of how a modularised job could look like to avoid continual reinvention and training
matteoferla/matteoferla
Config files for my GitHub profile.
matteoferla/munged-Fragalysis-targets
An small crosstabulation of what the public Fragalysis targets are
matteoferla/Q6ZUT9-analyses
matteoferla/Sindarin-character-sheet
A character sheet for Dungeons and Dragons 5e written in Sindarin (Tolkien modern elvish)
matteoferla/Somewhat-Smart-Home
Integrating the Raspberry pi across the house
matteoferla/Zika-NS2B-NS3-elaborations
Elaborations based on the initial fragments of Zika protease (ASAP project)