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Resources for the BioML Challenge 2024: Bits to Binders
Making Protein folding accessible to all!
Predict multiple protein conformations using sequence clustering and AlphaFold2.
Pymol-open-source wheels for Python on Windows
List of papers about Proteins Design using Deep Learning
Automated Adaptive Absolute alchemical Free Energy calculator
Generate intrinsically disordered peptide conformations via machine learning
Causal Learning: A new ML framework utilizing cooperative networks
High-Performance Symbolic Regression in Python and Julia
Interface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes
InteractionGraphNet: a Novel and Efficient Deep Graph Representation Learning Framework for Accurate Protein-Ligand Interaction Predictions
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) ca…
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
Improving protein–ligand docking and screening accuracies by incorporating a scoring function correction term
Uni-Dock: a GPU-accelerated molecular docking program
High-performance and differentiation-enabled nonlinear solvers (Newton methods), bracketed rootfinding (bisection, Falsi), with sparsity and Newton-Krylov support.
Pytorch-based framework for solving parametric constrained optimization problems, physics-informed system identification, and parametric model predictive control.
MolTrans: Molecular Interaction Transformer for Drug Target Interaction Prediction (Bioinformatics)
DeeplyTough: Learning Structural Comparison of Protein Binding Sites
Working with molecular structures in pandas DataFrames
DeepMol: A Machine and Deep Learning Framework for Computational Chemistry
A Python package for calculating molecular features
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…