Sibbe Bakker's repositories
complex-prediction
Complex prediction using combfold
Luke-ebbis.github.io
Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes
protein-structure-comparison
A quick pipeline for protein structure comparison
snakemake-pixi
Building snakemake workflows with pixi ✨
CombFold
With pixi to manage dependencies
combfold-benchmark
Benchmarking the combfold pipeline
contact_map
Contact map analysis for biomolecules; based on MDTraj
containers
Bioinformatics containers
DiffDock
Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
distance-map
Calculating distance maps between subunits of PDB or mCIF files
DockQ
DockQ is a single continuous quality measure for protein docked models based on the CAPRI evaluation protocol
EMBER3D
Ultra-fast in-silico structure mutation
enpkg_full
The full enpkg workflow
fisher-lisp
Fisher exact test implemented in lisp
Is-Prime
O(1) Algorithm to check if number is prime that works in 95%+ cases.
mpi-snakemake-overview
snakemake presentation
nemo
A fast in-memory rule engine
NeuralPLexer
NeuralPLexer: State-specific protein-ligand complex structure prediction with a multi-scale deep generative model
neuralplexer-workflow
A workflow for predicting ligands and protein interactions with NeuralPlexer
nplinker
A python framework for data mining microbial natural products by integrating genomics and metabolomics data
PoseBench
Comprehensive benchmarking of protein-ligand structure generation methods
snakemake-tutorial
An example workflow with snakemake
snakemake-wrappers
This is the development home of the Snakemake wrapper repository, see
Stereochemical-Assesments
A repository to perform stereochemical assesments on PDB models generated by X-Ray Diffraction