Skip to content

@deargen deargen

Change the repository type filter

All

    Repositories list

    38 repositories

    • python-project-template-2024

      Public template
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Dec 21, 2024Dec 21, 2024

    • biotest

      Public
      Pytest utilities for bioinformatics
      Python
      •
      Apache License 2.0
      •0•0•0•1•Updated Dec 20, 2024Dec 20, 2024

    • workflows

      Public
      Reusable GitHub Actions workflows (CI) and a python project management tool `projector`
      Python
      •1•1•0•0•Updated Dec 17, 2024Dec 17, 2024

    • .github

      Public
      0•0•0•0•Updated Dec 13, 2024Dec 13, 2024

    • py-apbs-binary

      Public
      Install APBS with pip
      Python
      •0•0•0•0•Updated Dec 12, 2024Dec 12, 2024

    • py-reduce-binary

      Public
      Install reduce with pip
      Python
      •0•0•0•0•Updated Dec 12, 2024Dec 12, 2024

    • slack-helpers

      Public
      Send traceback, matplotlib, pillow, PDB etc. on Slack and preview them with ease.
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Dec 12, 2024Dec 12, 2024

    • bio-data-to-db

      Public
      Parse Bio data and make DB, fix string encodings, useful DB helpers etc.
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Dec 12, 2024Dec 12, 2024

    • rust-graph

      Public
      Graph algorithm implementations in Rust available as a Python package
      Python
      •
      Apache License 2.0
      •0•5•0•0•Updated Dec 12, 2024Dec 12, 2024

    • reduce-binary

      Public
      Automatically compile and release "reduce".
      Dockerfile
      •0•0•0•0•Updated Oct 17, 2024Oct 17, 2024

    • Pocket2Mol_RL_public

      Public
      Public repository of the paper <Fine-tuning Pocket-conditioned 3D Molecule Generation via Reinforcment Learning>
      Python
      •
      Other
      •2•6•0•0•Updated Sep 12, 2024Sep 12, 2024

    • bsp_public

      Public
      Python
      •0•0•0•0•Updated Sep 5, 2024Sep 5, 2024

    • pdb2pqr

      Public
      PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
      Python
      •
      Other
      •38•0•0•0•Updated Jun 17, 2024Jun 17, 2024

    • seldon-core

      Public
      Seldon-core v2 for local docker deployment
      Go
      •
      Other
      •834•0•0•0•Updated Mar 5, 2024Mar 5, 2024

    • 3D-Generative-SBDD

      Public
      💊 A 3D Generative Model for Structure-Based Drug Design (NeurIPS 2021)
      Python
      •
      MIT License
      •43•0•0•0•Updated Feb 1, 2024Feb 1, 2024

    • gypsum_dl

      Public
      Gypsum-DL is a free, open-source program that converts 1D and 2D small-molecule representations (SMILES strings or flat SDF files) into 3D models. It outputs models with alternate ionization, tautomeric, chiral, cis/trans isomeric, and ring-conformational states.
      Python
      •
      Apache License 2.0
      •12•0•0•0•Updated Dec 15, 2023Dec 15, 2023

    • 3Dmol.js

      Public
      WebGL accelerated JavaScript molecular graphics library
      Jupyter Notebook
      •
      Other
      •195•0•0•0•Updated Sep 13, 2023Sep 13, 2023

    • molskill

      Public
      Learning chemical intuition from humans in the loop. Supporting code.
      Python
      •
      MIT License
      •9•0•0•0•Updated Sep 6, 2023Sep 6, 2023

    • apex

      Public
      fixed version of nvidia apex
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Jul 24, 2023Jul 24, 2023

    • degpred

      Public
      A deep learning model to predict E3 binding sites (degrons) on protein substrates
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Jul 5, 2023Jul 5, 2023

    • GeoLDM

      Public
      Geometric Latent Diffusion Models for 3D Molecule Generation
      Python
      •
      MIT License
      •42•0•0•0•Updated Jun 15, 2023Jun 15, 2023

    • scscore

      Public
      Roff
      •
      MIT License
      •43•0•0•0•Updated Jun 12, 2023Jun 12, 2023

    • jtvae

      Public
      Junctional Tree Variational Auto-encoder
      Python
      •
      MIT License
      •3•0•0•0•Updated Jun 7, 2023Jun 7, 2023

    • Pocket2Mol

      Public
      Pocket2Mol: Efficient Molecular Sampling Based on 3D Protein Pockets
      Python
      •
      MIT License
      •72•0•0•0•Updated May 24, 2023May 24, 2023

    • DESERT

      Public
      Zero-Shot 3D Drug Design by Sketching and Generating (NeurIPS 2022)
      Python
      •9•0•0•0•Updated May 18, 2023May 18, 2023

    • PretrainYourLoss

      Public
      Python
      •13•0•0•0•Updated May 3, 2023May 3, 2023

    • DeepInteract

      Public
      Replicating DeepInteract for custom PPI
      Python
      •
      GNU General Public License v3.0
      •11•0•0•0•Updated Apr 18, 2023Apr 18, 2023

    • swag_original

      Public
      Code repo for "A Simple Baseline for Bayesian Uncertainty in Deep Learning"
      Jupyter Notebook
      •
      BSD 2-Clause "Simplified" License
      •82•0•0•0•Updated Jan 4, 2023Jan 4, 2023

    • react-clustergrammer

      Public
      React component for clustergrammer
      JavaScript
      •6•6•4•0•Updated Aug 3, 2022Aug 3, 2022

    • Reinvent

      Public
      Reinvent for Deargen
      Python
      •
      Apache License 2.0
      •110•0•0•0•Updated Aug 1, 2022Aug 1, 2022