zhenglz

onionnet

A multiple-layer inter-molecular contact features based deep neural network for protein-ligand binding affinity prediction

OnionNet-SFCT

Improving protein–ligand docking and screening accuracies by incorporating a scoring function correction term

onionnet_featurize

OnionNet Featurize

PyAutoFEP

PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods

GASA

Synthetic Accessible Prediction of Organic Compounds based on Graph Attention Mechanism

gnina

A deep learning framework for molecular docking

mso

Implementation of the method proposed in the paper "Efficient Multi-Objective Molecular Optimization in a Continuous Latent Space" by Robin Winter, Floriane Montanari, Andreas Steffen, Hans Briem, Frank Noé and Djork-Arné Clevert

pymol-vis

PyMOL extension to color AlphaFold structures by confidence (pLDDT).

rel_ddG_MerckDataSet_JCIM

Relative free energy calculation data for the Merck protein-ligand set

202109-QHL

2021全球抗体亲和力预测大赛

alphafill

AlphaFill is an algorithm based on sequence and structure similarity that “transplants” missing compounds to the AlphaFold models. By adding the molecular context to the protein structures, the models can be more easily appreciated in terms of function and structure integrity.

binanceapi

Binance REST API

CAMP

predicting peptide-protein interactions

DECIMER-Image-Segmentation

https://decimer.ai

deepmd-kit

A deep learning package for many-body potential energy representation and molecular dynamics

DEPECT

Design and Engineering of Protein and Enzymes by Computational Tools

DLKcat

Deep learning and Bayesian approach applied to enzyme turnover number for the improvement of enzyme-constrained genome-scale metabolic models (ecGEMs) reconstruction

DNAWorks

Automatic oligonucleotide design for PCR-based gene synthesis

DockQ

DockQ is a single continuous quality measure for protein docked models based on the CAPRI evaluation protocol

esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

janus

Python library for adaptive QM/MM methods

opus_x

OPUS-X: An Open-Source Toolkit for Protein Torsion Angles, Secondary Structure, Solvent Accessibility, Contact Map Predictions, and 3D Folding

prefmd2

ProtoCaller

Full automation of relative protein-ligand binding free energy calculations in GROMACS

PyRosetta.notebooks

Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design

qm3

QMCube: An all-purpose suite for multiscale QM/MM calculations

RAbinding

se3-transformer-public

code for the SE3 Transformers paper: https://arxiv.org/abs/2006.10503

selfies

Robust representation of semantically constrained graphs, in particular for molecules in chemistry

torchmd

End-To-End Molecular Dynamics (MD) Engine using PyTorch