zhenglz's repositories
OnionNet-SFCT
Improving protein–ligand docking and screening accuracies by incorporating a scoring function correction term
DECIMER-Image-Segmentation
https://decimer.ai
DNAWorks
Automatic oligonucleotide design for PCR-based gene synthesis
DLKcat
Deep learning and Bayesian approach applied to enzyme turnover number for the improvement of enzyme-constrained genome-scale metabolic models (ecGEMs) reconstruction
PyRosetta.notebooks
Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design
rel_ddG_MerckDataSet_JCIM
Relative free energy calculation data for the Merck protein-ligand set
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.
CAMP
predicting peptide-protein interactions
DockQ
DockQ is a single continuous quality measure for protein docked models based on the CAPRI evaluation protocol
202109-QHL
2021全球抗体亲和力预测大赛
esm
Evolutionary Scale Modeling (esm): Pretrained language models for proteins
opus_x
OPUS-X: An Open-Source Toolkit for Protein Torsion Angles, Secondary Structure, Solvent Accessibility, Contact Map Predictions, and 3D Folding
janus
Python library for adaptive QM/MM methods
qm3
QMCube: An all-purpose suite for multiscale QM/MM calculations
torchmd
End-To-End Molecular Dynamics (MD) Engine using PyTorch
ProtoCaller
Full automation of relative protein-ligand binding free energy calculations in GROMACS
selfies
Robust representation of semantically constrained graphs, in particular for molecules in chemistry
DEPECT
Design and Engineering of Protein and Enzymes by Computational Tools
deepmd-kit
A deep learning package for many-body potential energy representation and molecular dynamics
onionnet_featurize
OnionNet Featurize
se3-transformer-public
code for the SE3 Transformers paper: https://arxiv.org/abs/2006.10503
binanceapi
Binance REST API