byun-jinyoung Goto Github PK

openmm-tutorial-msbs

OpenMM tutorial for the MSBS course

openmm-tutorials

Quickstart Python tutorials helping molecular dynamics practitioners get up to speed with OpenMM

openmmenergycomparisons

Comparisons of energies and forces between OpenMM and other packages

ownmy-software-installation-guide

Trial and errors of software installation

paddlehelix

Bio-Computing Platform Featuring Large-Scale Representation Learning and Multi-Task Deep Learning “螺旋桨”生物计算工具集

peg

pf-gnn_pli

pigvae

pmx

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

practicalsessions2021

pypdb

A Python API for the RCSB Protein Data Bank (PDB)

pytorch

Deep Learning Zero to All - Pytorch

pytorch_geometric

Graph Neural Network Library for PyTorch

pytorch_geometric_temporal

PyTorch Geometric Temporal: Spatiotemporal Signal Processing with Neural Machine Learning Models (CIKM 2021)

pytorchgeometrictutorial

Pytorch Geometric Tutorials

quicksom

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)

reweight

Reimplementation of aMD reweighting protocol

saltswap

Package to fluctuate the number of counterions in an OpenMM simulation

sars-cov-2-modelling

Repo for SARS-CoV-2 Mpro modelling results; see https://bitly.com/peptibitors for the bioRxiv preprint.

seqdesign-pytorch

Protein design and variant prediction using autoregressive generative models

sinaps

smina

sml_cv

Using supervised machine learning to build collective variables for accelerated sampling

spyrmsd

📐 Symmetry-corrected RMSD in Python

torsional-diffusion

Implementation of Torsional Diffusion for Molecular Conformer Generation (NeurIPS 2022)

transformer

Implementation of "Attention Is All You Need" using pytorch

trimnet

Code for paper "TrimNet: learning molecular representation from triplet messages for biomedicine "

tutorial_dctmd

Tutorial for the usage of the dcTMD approach and Langevin simulations employing the trypsin-benzamidine complex as example.

waterkit

Tool to predict water molecules placement and energy in ligand binding sites