benf549

benf549's Stars

• hrsh7th/nvim-cmp

  A completion plugin for neovim coded in Lua.

  Language:Lua8.1k491.3k406

• vwxyzjn/cleanrl

  High-quality single file implementation of Deep Reinforcement Learning algorithms with research-friendly features (PPO, DQN, C51, DDPG, TD3, SAC, PPG)

  Language:Python5.8k38185651

• google-deepmind/alphafold3

  AlphaFold 3 inference pipeline.

  Language:Python5.2k586

• h5py/h5py

  HDF5 for Python -- The h5py package is a Pythonic interface to the HDF5 binary data format.

  Language:Python2.1k581.5k531

• chaidiscovery/chai-lab

  Chai-1, SOTA model for biomolecular structure prediction

  Language:Python1.3k1691159

• jwohlwend/boltz

  Official repository for the Boltz-1 biomolecular interaction model

  Language:Python1.2k123

• PaddlePaddle/PaddleHelix

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

  Language:Python1k24120225

• Ligo-Biosciences/AlphaFold3

  Open source implementation of AlphaFold3

  Language:Python932221381

• rusty1s/pytorch_cluster

  PyTorch Extension Library of Optimized Graph Cluster Algorithms

  Language:C++82815171148

• ericyangyu/PPO-for-Beginners

  A simple and well styled PPO implementation. Based on my Medium series: https://medium.com/@eyyu/coding-ppo-from-scratch-with-pytorch-part-1-4-613dfc1b14c8.

  Language:Python780119118

• biotite-dev/biotite

  A comprehensive library for computational molecular biology

  Language:Python68516189102

• bytedance/Protenix

  A trainable PyTorch reproduction of AlphaFold 3.

  Language:Python678162254

• brentyi/tyro

  CLI interfaces & config objects, from types

  Language:Python534712427

• zrqiao/NeuralPLexer

  NeuralPLexer: State-specific protein-ligand complex structure prediction with a multi-scale deep generative model

  Language:Jupyter Notebook26765071

• drorlab/gvp-pytorch

  Geometric Vector Perceptrons --- a rotation-equivariant GNN for learning from biomolecular structure

  Language:Python250131048

• LukeDitria/pytorch_tutorials

  Beginner Level Deep Learning Tutorials in Pytorch with Youtube Videos!

  Language:Jupyter Notebook2423155

• choderalab/espaloma

  Extensible Surrogate Potential of Ab initio Learned and Optimized by Message-passing Algorithm 🍹https://arxiv.org/abs/2010.01196

  Language:Python216168925

• plinder-org/plinder

  Protein Ligand INteraction Dataset and Evaluation Resource

  Language:Python16910179

• openmm/spice-dataset

  A collection of QM data for training potential functions

  Language:Python15517689

• EBjerrum/rdeditor

  Simple RDKit molecule editor GUI using PySide

  Language:Python135101532

• rlabduke/reduce

  Reduce - tool for adding and correcting hydrogens in PDB files

  Language:C++12482136

• biotite-dev/hydride

  Adding hydrogens to molecular models

  Language:Python36295

• matteoferla/rdkit_to_params

  Create or modify Rosetta params files (topology files) from scratch, RDKit mols or another params file

  Language:Python27325

• psipred/Merizo

  Fast and accurate protein domain segmentation using Invariant Point Attention

  Language:Python26555

• LDeng0205/confidence-bootstrapping

  Implementation of the Confidence Bootstrapping procedure for protein-ligand docking.

  Language:Python25213

• menhguin/minp_paper

  Code Implementation, Evaluations, Documentation, Links and Resources for Min P paper

  Language:Jupyter Notebook18101

• atisor73/chromatose

  Personal palette collection & mini-palette visualization

  Language:Python17100

• rlabduke/probe

  Evaluate and visualize protein interatomic packing

  Language:C10754

• benf549/REINFORCEmers

  Final Project for Harvard CS184: Introduction to Reinforcement Learning

  Language:Python1300

• dgazgalis/Workflows-Python-Scripts

  General purpose modeling scripts

  Language:Python1