holeung

macvim

Vim - the text editor - for macOS

graphein

Protein Graph Library

neuromancer

Pytorch-based framework for solving parametric constrained optimization problems, physics-informed system identification, and parametric model predictive control.

biopandas

Working with molecular structures in pandas DataFrames

NonlinearSolve.jl

High-performance and differentiation-enabled nonlinear solvers (Newton methods), bracketed rootfinding (bisection, Falsi), with sparsity and Newton-Krylov support.

Uni-Dock

Uni-Dock: a GPU-accelerated molecular docking program

MolTrans

MolTrans: Molecular Interaction Transformer for Drug Target Interaction Prediction (Bioinformatics)

morfeus

A Python package for calculating molecular features

DeeplyTough

DeeplyTough: Learning Structural Comparison of Protein Binding Sites

PyAutoFEP

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

DrugAssist

DrugAssist: A Large Language Model for Molecule Optimization

ThermoNet

ThermoNet is a computational method for quantitative prediction of the impact of single-point mutations on protein thermodynamic stability. The core algorithm of ThermoNet is an ensemble of deep 3D convolutional neural networks.

DeepMol

DeepMol: A Machine and Deep Learning Framework for Computational Chemistry

PMDM

DeepImmuno

Deep-learning empowered prediction and generation of immunogenic epitopes for T cell immunity

rDock

rDock is a fast and versatile Open Source docking program that can be used to dock small molecules against proteins and nucleic acids. It is designed for High Throughput Virtual Screening (HTVS) campaigns and Binding Mode prediction studies.

LDNets

bigmhc

BigMHC predicts MHC-I (neo)epitope presentation and immunogenicity

awesome-conformal-prediction

A professionally curated list of awesome Conformal Prediction videos, tutorials, books, papers, PhD and MSc theses, articles and open-source libraries.

Large-Language-Models-in-Chemistry

Working collection of papers, repos and models of transformer based language models trained or tuned for the Chemical domain, from natural language to chemical modeling and property prediction

IGN

InteractionGraphNet: a Novel and Efficient Deep Graph Representation Learning Framework for Accurate Protein-Ligand Interaction Predictions

OnionNet-SFCT

Improving protein–ligand docking and screening accuracies by incorporating a scoring function correction term

deepQM

PL-REX

Data set of protein-ligand complexes with reliable experimental structures and affinities

DLpTCR

Predicting immunogenic peptide recognized by TCR through ensemble deep learning

3D-RISM-AI

DeepNetBim

DeepNetBim: Deep learning model for predicting HLA-epitope interaction based on Net work analysis by harnessing Binding and immunogenicity information

EPISOL

The Expanded Package for IET Solvation

SFE

The python script for the stepwise feature elimination in nonlinear SVR model

CNP14-WDR91