mdavari Goto Github PK

acid

Auto in silico Consensus Inverse Docking(ACID) is a web server mainly for drug repurposing based on the consensus inverse docking method, which is designed to evaluate the binding affinities between each protein and the given small molecule. ACID is open to the public and shows great potential.

bglb_family

Quantitative prediction of mutant function across an enzyme family

chemicaltagger

ChemicalTagger is a tool for semantic text-mining in chemistry.

deepchem

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

deepdock

An experimental package for deep learning for molecular docking

deeplearninglifesciences

Example code from the book "Deep Learning for the Life Sciences"

deepsequence

A generative latent variable model for biological sequence families.

enlighten

Protocols and tools to run (automated) atomistic simulations of enzyme-ligand systems

epp

Code for the paper "Enzyme Promiscuity Prediction using hierarchy-informed multi-label classification"

evcouplings-1

Evolutionary couplings from protein and RNA sequence alignments

evmutation

Mutation effects predicted from sequence co-variation

evzoom

Visually explore covariation in protein families

jax-unirep

Reimplementation of the UniRep protein featurization model.

km_prediction

low-n-protein-engineering

Code and data to reproduce analyses in Biswas et al. (2020) "Low-N protein engineering with data-efficient deep learning".

low-n-protein-engineering-1

A complete, open-source, end-to-end re-implementation of the Church Lab's low-N eUniRep in silico protein engineering pipeline presented in Biswas et al.

machine-learning-for-proteins

Listing of papers about machine learning for proteins.

mlcodelab

This introduces basics of machine learning packages

neurips19-graph-protein-design

Generative Models for Graph-Based Protein Design

plmc

Inference of couplings in proteins and RNAs from sequence variation

protein-dihedral-angles-prediction

A hybrid approach to protein structure (dihedral / torsional angles) prediction using techniques from Mohammed AlQuraishi's work on End-to-end differentiable learning of protein structure and Gao et al. on RaptorX.

pymol-script-repo

Collected scripts for Pymol

pypef

PyPEF – Pythonic Protein Engineering Framework

qmmm_practical_short

Files and info for a practical session in the MSc Biophysics course run by Biochemistry

retropathrl

Reinforcement Learning based bioretrosynthesis tool

tape

Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.

taxyl

TAXyl (Thermal activity prediction for xylanase)

unirep

UniRep model, usage, and examples.