matteoferla/MichelaNGLo-protein-analysis

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Python
License
MIT License
Created over 5 years ago
Updated over 2 years ago

matteoferla/MichelaNGLo-protein-analysis

matteoferla

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

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.

molecular_rectifier

Given an RDKit molecule that does not sanitise, correct it until it does

Python_SmallWorld_API

An (unofficial) Python3 module to query the SmallWorld chemical space search server (https://sw.docking.org/search.html)

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

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

Jupyter Notebook

Display-of-preset-Rosetta-NCAAs

What exactly are the non-canonical amino acids in the Rosetta database folder?

Snippets-for-ColabFold

A collections of snippets for working with ColabFold

pyfurby

Raspberry Pi Zero W controlled Furby

Christmas_tree_protein

A Christmas tree protein

Pyrosetta-documentarian

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

JSME_notebook

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

DTC-compchem-practical

Compchem practical for the University of Oxford Doctoral Training Centre

Jupyter Notebook

PLIP-PyRosetta-hotspots-test

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

DnD-encounter-simulator-site

The site for the DnD encounter similator

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?

protein_fuser

A py3 script to fuse structures together

DirEvo_tools

The new and improved server combining Pedel, Mutanalyst and much more

AtomicRenamer

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

Michelanglo-and-Venus

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

validation_of_venus_ddG

Tests to assess the accuracy of Venus ddG calculations

And-the-protein-ligand-went-boom

A collection of various computational chemistry/biochemistry fails

mutant_calculator

Now live on www.mutanalyst.com

Replace-ligand

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

MichelaNGLo-api

A python module to interact with Michelaɴɢʟo programmatically

Wikipedian-compounds

Parsing Wikipedia Chembox data for fun

notebook-error-reporter

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

tangents

mutational_scanning

Analysis of variants generated by mutational scanning for Carlos G Acevedo-Rocha et al 2017

MED27_analysis

Analysis of variants of MED27 (no mutant data is stored here)

Various-scripts-rosetta-pymol

scripts for Rosetta and PyMol stuff

MichelaNGLo-human-protein-data

pickled files containing protein data for humans

mutagenesis

Python DNA mutagenesis model and more

SLC38A3_analysis

SLC38A3 protein modelling

Epistasis_Calculator

PrettyFastaJS

Script to embed in a pretty way a fasta file in a website, such as blog

EV-D68-3C-protease

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

Jupyter Notebook

PRKG2_analysis

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

MEF2C_analysis

Analysis of variants of MEF2C

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 🐍↔️🏄

SARS-CoV-2_CL3_covalent_docking

This is junk a junkyard for code salvaging. Please see Fragmenstein instead

Arthorian-Quest

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

Poised-Fragment-library-design

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

Jupyter Notebook

crysalin

Engineering crysalin lattice