narubi2

narubi2's Stars

• meilerlab/HyperMPNN

  HyperMPNN ‒ A general strategy to design thermostable proteins learned from hyperthermophiles

  Language:Jupyter Notebook438

• dauparas/LigandMPNN

  Language:Python25351

• patrickbryant1/EvoBind

  In silico directed evolution of peptide binders with AlphaFold

  Language:Jupyter Notebook13529

• baker-laboratory/rf_diffusion_all_atom

  Public RFDiffusionAA repo

  Language:Python33456

• google-deepmind/alphafold3

  AlphaFold 3 inference pipeline.

  Language:Python5.7k669

• microsoft/AI2BMD

  AI-powered ab initio biomolecular dynamics simulation

  Language:Python43151

• martinpacesa/BindCraft

  User friendly and accurate binder design pipeline

  Language:Python36366

• PDB-REDO/dssp

  Application to assign secondary structure to proteins

  Language:C++17419

• jensengroup/propka

  PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.

  Language:Python27559

• Becksteinlab/propkatraj

  pKa estimates for proteins using an ensemble approach

  Language:Python277

• YuzheWangPKU/DiffPepBuilder

  Official repository for Target-Specific De Novo Peptide Binder Design with DiffPepBuilder

  Language:Python687

• sokrypton/ColabDesign

  Making Protein Design accessible to all via Google Colab!

  Language:Python651151

• supernova4869/s_mmpbsa

  Supernova's MM-PBSA binding free energy calculation tool.

  Language:Rust111

• bjing2016/alphaflow

  AlphaFold Meets Flow Matching for Generating Protein Ensembles

  Language:Python39051

• michellab/a3fe

  Automated Adaptive Absolute alchemical Free Energy calculator

  Language:Python737

• Layne-Huang/PMDM

  Language:Python11423

• Zuricho/ProteinDesignLabs

  List of computational protein design research labs

  14310

• AstraZeneca/peptide-tools

  Programs to calculate phys-chem properties of synthetic peptides and proteins: isoelectric point and extinction coefficients.

  Language:Python265

• Adibvafa/CodonTransformer

  CodonTransformer: The ultimate tool for codon optimization, optimizing DNA sequences for heterologous protein expression across 164 species.

  Language:Python1094

• lucidrains/alphafold3-pytorch

  Implementation of Alphafold 3 from Google Deepmind in Pytorch

  Language:Python1.3k157

• schrodinger/pymol-open-source

  Open-source foundation of the user-sponsored PyMOL molecular visualization system.

  Language:C1.2k287

• sokrypton/ColabFold

  Making Protein folding accessible to all!

  Language:Jupyter Notebook2k507

• SadeghHayeri/GreenTunnel

  GreenTunnel is an anti-censorship utility designed to bypass the DPI system that is put in place by various ISPs to block access to certain websites.

  Language:JavaScript4.4k279

• dauparas/ProteinMPNN

  Code for the ProteinMPNN paper

  Language:Jupyter Notebook1.1k316

• matteoferla/Display-of-preset-Rosetta-NCAAs

  What exactly are the non-canonical amino acids in the Rosetta database folder?

  Language:Python93

• Peldom/papers_for_protein_design_using_DL

  List of papers about Proteins Design using Deep Learning

  1.5k182

• Valdes-Tresanco-MS/gmx_MMPBSA

  gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.

  Language:Python23268

• RosettaCommons/RFdiffusion

  Code for running RFdiffusion

  Language:Python1.9k359

• gcorso/DiffDock

  Implementation of DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking

  Language:Python1.1k271

• gnina/gnina

  A deep learning framework for molecular docking

  Language:C++646149