Matteo Ferla

Fragmenstein. Merging, linking and placing compounds by stitching bound compounds together like a reanimated corpse

DnD-battler. A 5e D&D encounter simulator written for my own amusement to test some hypotheses.

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

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

pyrosetta-help. Some scripts that I keep using over and over.

Christmas_tree_protein. A Christmas tree protein

pyfurby. Raspberry Pi Zero W controlled Furby

Display-of-preset-Rosetta-NCAAs. What exactly are the non-canonical amino acids in the Rosetta database folder?

Fragment-hit-follow-up-chemistry. A collection of notebooks and scripts for the prediction of follow-up compounds in

Snippets-for-ColabFold. A collections of snippets for working with ColabFold

Epistasis_Calculator. Python

Pyrosetta-documentarian. A class to help reverse engineer what what a Pyrosetta class does...

PLIP-PyRosetta-hotspots-test. A proof-of-principle of using PLIP and PyRosetta as a substitute to Hotspot API and CCDC Gold

AtomicRenamer. Given a molecule label the atoms (names/labels) according to a reference ligand from the PDB

JSME_notebook. JSME molecular editor in a Jupyter or Colab notebook in a hacky way

DnD-encounter-simulator-site. The site for the DnD encounter similator

validation_of_venus_ddG. Tests to assess the accuracy of Venus ddG calculations

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

MichelaNGLo-protein-analysis. protein module for Michelanglo and VENUS (handles the actual protein analysis)

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?

Arthorian-Quest. An experiment in using Arthor (arthor.docking.org) by NextMove and filtering the results with Fragmenstein

MichelaNGLo-api. A python module to interact with Michelaɴɢʟo programmatically

protein_fuser. A py3 script to fuse structures together

Michelanglo-and-Venus. Topmost repository for the Michelanglo webapp, including the Venus functionality.

mutagenesis. Python DNA mutagenesis model and more

ConsurfDB-client-API. A Python3 module to requests information from the ConsurfDB server and perform several operations (_e.g._ reindexing) with grade files and PDB files :snake::left_right_arrow::surfer:

notebook-error-reporter. An idea on how to collect errors generated by other users using a notebook that was shared.

Wikipedian-compounds. Parsing Wikipedia Chembox data for fun

viral-chembl. Brief survey of virus binding affinity data and crystallographic data

MEF2C_analysis. Analysis of variants of MEF2C

tangents. Python

mutant_calculator. Now live on www.mutanalyst.com

Sociable-fragment-library-design. The design of a fragment library that is sociably poised for the XChem in house synthesis robot

Replace-ligand. Example of how to replace a ligand with a similar in Rdkit and Pyrosetta

MichelaNGLo-human-protein-data. pickled files containing protein data for humans

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

protein-design-analysis. A toolkit to analyse complicated de novo protein designs in PyRosetta

crysalin. Engineering crysalin lattice

EV-D68-3C-protease. Follow-up suggestions for EV-D68 3C protease fragment-based drug-discovery campaign of ASAP consortium

PRKG2_analysis. In silico analysis of the cGMP-dependent protein kinase 2 (PRKG2 encoded)

GCN2-open-state. De novo design for GCN2 in the open state

SLC38A3_analysis. SLC38A3 protein modelling

protein_alphabet_dropcaps. A JS/CSS library to add protein structure dropcaps