zhenglz

openclaude. runs anywhere. uses anything

ProSolNet. ProSolNet and ProSolNet_mut are deep learning models based on multimodal features, designed to predict protein solubility and the changes in solubility caused by mutations, respectively.

zFold. Zelixir's light-weight protein folding framework

CataPro. A generalized enzyme kinetics parameter prediction model.

HybridSP. Distance and orientation based statistical potential for protein-ligand interaction modelling.

ProstT5. Bilingual Language Model for Protein Sequence and Structure

SeqGenerator. Python

IGModel. This is the first model that can simultaneously predict the RMSD of the ligand docking pose and the binding strength against the target.

DeepRMSD-Vina_Optimization. DeepRMSD+Vina is a computational framework that integrates ligand binding pose optimization and screening.

pymol-vis. PyMOL extensions for protein artification

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

pdbecif. A lightweight pure python package for reading, writing and manipulating mmCIF files distributed by the wwPDB"

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

DEPECT. Design and Engineering of Protein and Enzymes by Computational Tools

fep-benchmark. Benchmark set for relative free energy calculations.

OnionNet-2. OnionNet-2 is constructed based on convolutional neural network (CNN) to predict the protein-ligand binding affinity.

openmm_gamd. Gaussian accelerated Molecular Dynamics in OpenMM

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

gnina. A deep learning framework for molecular docking

opus_fold. OPUS-Fold: An Open-Source Protein Folding Framework Based on Torsion-Angle Sampling

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

fast-soft-sort. Fast Differentiable Sorting and Ranking

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

acpype. OFFICIAL: AnteChamber PYthon Parser interfacE

qm3. QMCube: An all-purpose suite for multiscale QM/MM calculations

CGCF-ConfGen. :test_tube: Learning Neural Generative Dynamics for Molecular Conformation Generation (ICLR 2021)

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

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

OptiMol. Optimization of binding affinities in chemical space for drug discovery

se3-transformer-public. code for the SE3 Transformers paper: https://arxiv.org/abs/2006.10503

skorch. A scikit-learn compatible neural network library that wraps PyTorch

GraphDTA. GraphDTA: Predicting drug-target binding affinity with graph neural networks

MONN. MONN: a Multi-Objective Neural Network for Predicting Pairwise Non-Covalent Interactions and Binding Affinities between Compounds and Proteins

DeepPurpose. A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)

cddd. Implementation of the Paper "Learning Continuous and Data-Driven Molecular Descriptors by Translating Equivalent Chemical Representations" by Robin Winter, Floriane Montanari, Frank Noe and Djork-Arne Clevert.

rmsd. Calculate Root-mean-square deviation (RMSD) of two molecules, using rotation, in xyz or pdb format

SPOT-RNA. RNA Secondary Structure Prediction using an Ensemble of Two-dimensional Deep Neural Networks and Transfer Learning.

deltaVinaXGB. This is a machine-learning based protein-ligand scoring function.

jax-md. Differentiable, Hardware Accelerated, Molecular Dynamics

QVina.github.io. The code for the QuickVina homepage.

dlwpt-code. Code for the book Deep Learning with PyTorch by Eli Stevens, Luca Antiga, and Thomas Viehmann.

pmx. Toolkit for free-energy calculation setup/analysis and biomolecular structure handling

oneflow. OneFlow is a deep learning framework designed to be user-friendly, scalable and efficient.

MiniFold. MiniFold: Deep Learning for Protein Structure Prediction inspired by DeepMind AlphaFold algorithm

ProteinSecondaryStructure-CNN. Protein Secondary Structure predictor using Convolutional Neural Networks

TensorFlow-Examples. TensorFlow Tutorial and Examples for Beginners (support TF v1 & v2)

openmm. OpenMM is a toolkit for molecular simulation using high performance GPU code.

prefmd. Shell

MD-TASK. Tool suite for analysing molecular dynamics trajectories using network analysis and PRS

PDB_Tool. Extract structural features from original PDB file

repex. Python replica-exchange simulation facility for OpenMM.

Amap. Python

meld. Modeling with limited data

chembl_webresource_client. Official Python client for accessing ChEMBL API

jpredapi. Python library and CLI for submitting jobs to JPred - A Protein Secondary Structure Prediction Server

openff-toolkit. The Open Forcefield Toolkit provides implementations of the SMIRNOFF format, parameterization engine, and other tools. Documentation available at http://open-forcefield-toolkit.readthedocs.io

psikit. psi4+RDKit

PaperRobot. Code for PaperRobot: Incremental Draft Generation of Scientific Ideas

no-ip. A shell script that works as Dynamic Update Client (DUC) for noip.com

tushare. TuShare is a utility for crawling historical data of China stocks

deep-learning-v2-pytorch. Projects and exercises for the latest Deep Learning ND program https://www.udacity.com/course/deep-learning-nanodegree--nd101

solubility. An implementation of Delaney's ESOL method using the RDKit

nma. Normal Mode Analysis for Macromolecules

pdbfixer. PDBFixer fixes problems in PDB files

scikit-learn. scikit-learn: machine learning in Python

onedrive. Free Client for OneDrive on Linux

LBTS. Ligand based target searching

qvina. Accurately speed up AutoDock Vina

AI_for_healthcare. This is the code for "AI for Healthcare" By Siraj Raval on Youtube

DrugAI. Generation and Classification of Drug Like molecule usings Neural Networks

gromacs-HREMD. Public/backup repository of the gromacs molecular simulation toolkit