Pinned Repositories
2023-1st-AI-assisted-drug-discovery-SNU
Lecture materials for AI-assissted-drug-discovery
3D-geometric-deep-learning-in-drugs
3D-geometric-deep-learning-in-drugs
Adan-pytorch
Implementation of the Adan (ADAptive Nesterov momentum algorithm) Optimizer in Pytorch
adaptiveumbrella
Adaptive umbrella sampling in Python
alignn
Atomistic Line Graph Neural Network
alphafold
Install alphafold on the local machine, get out of docker.
alphafold2
To eventually become an unofficial Pytorch implementation / replication of Alphafold2, as details of the architecture get released
alphafold2-multiprocessing
Use AlphaFold by Deep Mind in Batch Mode + Multiprocessing
educational
openmm-pulling
Pulling Simulation and Smoothing
Byun-jinyoung's Repositories
Byun-jinyoung/alphafold
Install alphafold on the local machine, get out of docker.
Byun-jinyoung/alphafold2-multiprocessing
Use AlphaFold by Deep Mind in Batch Mode + Multiprocessing
Byun-jinyoung/DeepDock
Code related to : O. Mendez-Lucio, M. Ahmad, E.A. del Rio-Chanona, J.K. Wegner, A Geometric Deep Learning Approach to Predict Binding Conformations of Bioactive Molecules
Byun-jinyoung/DesignBODIPY
ML on BODIPY molecules
Byun-jinyoung/difftre
Learning neural network potentials from experimental data via Differentiable Trajectory Reweighting
Byun-jinyoung/ECpH-MD
Byun-jinyoung/egnn_dgl
Implementation of EGNN (E(n) Equivariant Graph Neural Networks, https://arxiv.org/pdf/2102.09844.pdf) using DGL
Byun-jinyoung/gamd_we
Byun-jinyoung/GMT
Official Code Repository for the paper "Accurate Learning of Graph Representations with Graph Multiset Pooling" (ICLR 2021)
Byun-jinyoung/hgraph2graph
Hierarchical Generation of Molecular Graphs using Structural Motifs
Byun-jinyoung/Hydrogen-Bond-interaction-calculations-for-Gromacs-MD-simulations
Program to calculate hydrogen bond interactions in MD simulations in Gromacs 5.x or higher, for any system, independent of the Atomistic Force-filed used.
Byun-jinyoung/JAX-ReaxFF
JAX-ReaxFF: A Gradient Based Framework for Extremely Fast Optimization of Reactive Force Fields
Byun-jinyoung/jraph
A Graph Neural Network Library in Jax
Byun-jinyoung/keras2torch
Byun-jinyoung/lipophilicity-prediction
Code for "Lipophilicity Prediction with Multitask Learning and Molecular Substructures Representation" paper. Machine Learning for Molecules Workshop @ NeurIPS 2020
Byun-jinyoung/meld
Modeling with limited data
Byun-jinyoung/Modof
Molecule Optimization via Fragment-based Generative Models
Byun-jinyoung/openmm-atmmetaforce-plugin
An OpenMM plugin that implements the Alchemical Transfer Potential
Byun-jinyoung/openmm-cookbook
Proof-of-concept for the OpenMM Cookbook
Byun-jinyoung/pf-gnn_pli
Byun-jinyoung/pigvae
Byun-jinyoung/pmx
Toolkit for free-energy calculation setup/analysis and biomolecular structure handling
Byun-jinyoung/polyply_regression_tests
Regression tests and tutorial input files for the polyply software suite
Byun-jinyoung/PracticalSessions2021
Byun-jinyoung/RealVS
Reproducing of the paper entitled "RealVS: Towards Enhancing the Precision of Top Hits in Ligand-Based Virtual Screening of Drug Leads from Large Compound Databases" (Journal of Chemical Information and Modeling)
Byun-jinyoung/saltswap
Package to fluctuate the number of counterions in an OpenMM simulation
Byun-jinyoung/SARS-CoV-2-Modelling
Repo for SARS-CoV-2 Mpro modelling results; see https://bitly.com/peptibitors for the bioRxiv preprint.
Byun-jinyoung/seqdesign-pytorch
Protein design and variant prediction using autoregressive generative models
Byun-jinyoung/SINAPs
Byun-jinyoung/sPhysNet