yuriychen

yuriychen's Stars

• instadeepai/nucleotide-transformer

  🧬 Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics

  Language:Python54361

• mat10d/EvolvePro

  This is the offical codebase to reproduce and use EVOLVEpro, a model for in silico directed evolution of protein activities using few-shot active learning.

  Language:Python15636

• oxpig/CaLM

  Protein language model trained on coding DNA

  Language:Python4210

• ml4bio/RNA-FM

  Nature Methods: RNA foundation model (together with RhoFold)

  Language:Jupyter Notebook23024

• yikunpku/RNA-MSM

  Nucleic Acids Research 2024：RNA-MSM model is an unsupervised RNA language model based on multiple sequences that outputs both embedding and attention map to match different types of downstream tasks.

  Language:Python555

• lbcb-sci/RiNALMo

  RiboNucleic Acid (RNA) Language Model

  Language:Python7813

• CatIIIIIIII/RNAErnie

  Official implement of paper "Multi-purpose RNA Language Modeling with Motif-aware Pre-training and Type-guided Fine-tuning"

  Language:Python408

• ShintaroMinami/PyDSSP

  A simplified implementation of DSSP algorithm for PyTorch and NumPy

  Language:Python759

• cmbi/hssp

  Create DSSP and HSSP files

  Language:C++8618

• pyg-team/pytorch_geometric

  Graph Neural Network Library for PyTorch

  Language:Python21.7k3.7k

• daattali/advanced-shiny

  🤹 Shiny tips & tricks for improving your apps and solving common problems

  Language:R1.2k388

• Kortemme-Lab/flex_ddG_tutorial

  Language:Python9429

• BCLCommons/bcl

  The Biochemical Library (BCL) integrates traditional small molecule cheminformatics tools with machine learning-based quantitative structure-activity/property relationship (QSAR/QSPR) modeling. The cheminformatics toolkit contains customizable tools for the design, processing, and analysis of small molecules for computer-aided drug discovery.

  Language:C++2319

• rifdock/rifdock

  Rifdock Library for Conformational Search

  Language:C++14541

• nrbennet/dl_binder_design

  Language:Python26765

• Homebrew/brew

  🍺 The missing package manager for macOS (or Linux)

  Language:Ruby42k9.9k

• sokrypton/ColabDesign

  Making Protein Design accessible to all via Google Colab!

  Language:Python658153

• RosettaCommons/RFDesign

  Protein hallucination and inpainting with RoseTTAFold

  Language:Python25067

• RosettaCommons/RFdiffusion

  Code for running RFdiffusion

  Language:Python1.9k365

• wangleiofficial/DSSPparser

  DSSPparser is an easy tool to parse dssp file, and can transform PDB format file to dssp format file by xssp,also support the tansfrom between the PDB id and dssp format, hssp format and sequence.

  Language:Python125

• PDB-REDO/dssp

  Application to assign secondary structure to proteins

  Language:C++17519

• systemsomicslab/MsdialWorkbench

  Universal workbench incorporating msdial, msfinder, and mrmprobs

  Language:C#5819

• jackfrued/Python-100-Days

  Python - 100天从新手到大师

  Language:Python160k52.7k

• DDoSolitary/LxRunOffline

  A full-featured utility for managing Windows Subsystem for Linux (WSL)

  Language:C++4.2k250

• bathyg/Prolucid_gui

  Prolucid GUI, accelerate your bottom-up proteomics workflow.

  32

• JinjunGao/SESTAR

  Selenium-Encoded Isotopic Signature Targeted Profiling

  Language:R2

• cgob/codonDT_snakemake

  Ribo-DT is a snakemake pipeline to infer single-codon and codon-pair dwell times as well as gene flux from ribosome profiling data using generalized linear model (GLM) with negative binomial noise model (Gobet et al., PNAS, 2020).

  Language:R44

• williamgilpin/pypdb

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

  Language:Python31777

• Pymol-Scripts/Pymol-script-repo

  Collected scripts for Pymol

  Language:Python457258

• sarisabban/RosettaDesign

  RosettaDesign using PyRosetta

  Language:Python307