Pinned Repositories
3D-Generative-SBDD
💊 A 3D Generative Model for Structure-Based Drug Design (NeurIPS 2021)
alchemical-analysis
An open tool implementing some recommended practices for analyzing alchemical free energy calculations
Autofinger
This script automatically takes the csv file from schrodinger-maestro and converts it into a table for data analysis and publication
BAR-FEP
BAR and FEP method for free energy calculation
BAT.py
The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy calculations on protein-ligand systems, compatible with the AMBER20 and OpenMM 7 simulation packages.
benchmarksets
Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards
bio_embeddings
Get protein embeddings from protein sequences
DeepFE-PPI
gromacs_cp2k_tutorial
Example systems for Gromacs-CP2K QMMM Interface
vdwp
vdwp method test
bwang-ecnu's Repositories
bwang-ecnu/3D-Generative-SBDD
💊 A 3D Generative Model for Structure-Based Drug Design (NeurIPS 2021)
bwang-ecnu/BAT.py
The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy calculations on protein-ligand systems, compatible with the AMBER20 and OpenMM 7 simulation packages.
bwang-ecnu/BioGPT
bwang-ecnu/dash_web
bwang-ecnu/DeepPROTACs
bwang-ecnu/DrugOOD
OOD Dataset Curator and Benchmark for AI-aided Drug Discovery
bwang-ecnu/fpocket
fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation. The platform is suited for the scientific community willing to develop new scoring functions and extract pocket descriptors on a large scale level. fpocket is distributed as free open source software. If you are interested in integrating fpocket in
bwang-ecnu/getting-started-with-genomics-tools-and-resources
Unix, R and python tools for genomics and data science
bwang-ecnu/GraphBP
Official implementation of "Generating 3D Molecules for Target Protein Binding" [ICML2022 Long Presentation]
bwang-ecnu/gromacs
Public/backup repository of the GROMACS molecular simulation toolkit. Please do not mine the metadata blindly; we use https://gitlab.com/gromacs/gromacs for code review and issue tracking.
bwang-ecnu/guacamol
Benchmarks for generative chemistry
bwang-ecnu/libmolgrid
Comprehensive library for fast, GPU accelerated molecular gridding for deep learning workflows
bwang-ecnu/LiGAN
Deep generative models of 3D grids for structure-based drug discovery
bwang-ecnu/LinearDesign
The LinearDesign mRNA design software.
bwang-ecnu/llama
Inference code for Llama models
bwang-ecnu/llama3
The official Meta Llama 3 GitHub site
bwang-ecnu/mlflow
Open source platform for the machine learning lifecycle
bwang-ecnu/molecule-generation
Implementation of MoLeR: a generative model of molecular graphs which supports scaffold-constrained generation
bwang-ecnu/MolRep
MolRep: A Deep Representation Learning Library for Molecular Property Prediction
bwang-ecnu/OpenBioMed
bwang-ecnu/PaddleHelix
Bio-Computing Platform Featuring Large-Scale Representation Learning and Multi-Task Deep Learning “螺旋桨”生物计算工具集
bwang-ecnu/Pocket2Mol
Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets
bwang-ecnu/Protac-Design
UROP Project @ Coley Group
bwang-ecnu/PROTAC-RL
bwang-ecnu/py-MCMD
This python code creates hybrid MD/MC (NAMD/GOMC) simulations for the NVT, NPT, GCMC, and GEMC-NVT ensembles
bwang-ecnu/PyAutoFEP
PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods
bwang-ecnu/Reinvent
bwang-ecnu/REINVENT4
AI molecular design tool for de novo design, scaffold hopping, R-group replacement, linker design and molecule optimization.
bwang-ecnu/SurfGen
SurfGen: Learning on Topological Surface and Geometric Structure for 3D Molecular Generation
bwang-ecnu/torchdrug
A powerful and flexible machine learning platform for drug discovery