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@NBDsoftware Nostrum Biodiscovery Software

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    32 repositories

    • MDDB-docker

      Public
      fork of MDDB-docker to freeze an specific version
      Python
      •
      Apache License 2.0
      •6•0•0•0•Updated Oct 15, 2026Oct 15, 2026

    • deep_cartograph

      Public
      Deep Cartograph - A library to analyze biomolecular conformational ensembles and enhance sampling of MD simulations using data-driven collective variables. Free…
      machine-learningmolecular-dynamicsmolecular-modeling
      machine-learningmolecular-dynamicsmolecular-modelingcollective-variables
      Python
      •
      Other
      •1•2•0•0•Updated Oct 9, 2026Oct 9, 2026

    • bdd

      Public
      Benchmark-driven development (BDD)
      MIT License
      •1•1•0•0•Updated Sep 29, 2026Sep 29, 2026

    • nostrum_calculations

      Public
      A version of the bsc_calculations (https://github.com/Martin-Floor/bsc_calculations) in order to be able to run in the Nostrum Biodiscovery (Bright) cluster the…
      Python
      •2•1•0•0•Updated Sep 29, 2026Sep 29, 2026

    • biobb_md_workflows

      Public
      BioBB workflow to run MD simulations with GROMACS including protein preparation, ligand parameterization and trajectory post-processing. Free for academic use.
      Jupyter Notebook
      •
      Other
      •1•1•19•0•Updated Sep 25, 2026Sep 25, 2026

    • biobb_vs_workflows

      Public
      BioBB workflow to run cavity analysis with Fpocket and virtual screening with Autodock. Free for academic use.
      Jupyter Notebook
      •
      Other
      •0•0•4•0•Updated Aug 4, 2026Aug 4, 2026

    • biobb_vs

      Public
      Biobb_vs is the Biobb module collection to perform virtual screening studies.
      Python
      •
      Apache License 2.0
      •3•0•0•0•Updated Aug 3, 2026Aug 3, 2026

    • biobb_analysis

      Public
      Biobb_analysis is the Biobb module collection to perform analysis of molecular dynamics simulations.
      Python
      •
      Apache License 2.0
      •3•0•0•0•Updated Aug 3, 2026Aug 3, 2026

    • biobb_gromacs

      Public
      Python
      •
      Apache License 2.0
      •3•0•0•0•Updated Jul 24, 2026Jul 24, 2026

    • horus_plugin_template

      Public template
      Template for creating Horus plugins
      TypeScript
      •0•0•0•0•Updated Jul 21, 2026Jul 21, 2026

    • peleffy

      Public
      The peleffy (PELE Force Field Yielder) is a Python package that builds PELE-compatible force field templates.
      Python
      •
      MIT License
      •9•0•0•0•Updated Jul 11, 2026Jul 11, 2026

    • mlcolvar

      Public
      A unified framework for machine learning collective variables for enhanced sampling simulations
      Python
      •
      MIT License
      •36•0•0•0•Updated Jun 5, 2026Jun 5, 2026

    • horus_plugin_dev_tutorial

      Public
      Understand how to work with Horus and how to develop your custom Plugins
      Python
      •0•0•0•0•Updated Apr 8, 2026Apr 8, 2026

    • custom_msas

      Public
      Custom MSA generation using public databases with HMMER software. Based on AlphaFold2 Data Pipeline.
      Python
      •
      Apache License 2.0
      •2•0•0•0•Updated Mar 18, 2026Mar 18, 2026

    • IndustryBenchmarks2024

      Public
      Repository for the 2024 OpenFE industry benchmark efforts
      Jupyter Notebook
      •
      MIT License
      •25•0•0•0•Updated Nov 18, 2025Nov 18, 2025

    • enterovirus

      Public
      Nextflow
      •2•0•0•0•Updated Nov 12, 2025Nov 12, 2025

    • md_utils

      Public
      Scripts to analyze RAVE-related results and produce bias potential for subsequent rounds
      Python
      •
      Other
      •0•0•0•0•Updated Oct 12, 2025Oct 12, 2025

    • MDDB-loader

      Public
      JavaScript
      •2•0•0•0•Updated Aug 18, 2025Aug 18, 2025

    • GDD

      Public
      Python
      •1•8•0•0•Updated Jun 27, 2025Jun 27, 2025

    • cinnabar

      Public
      Package for consistent reporting of relative free energy results
      Python
      •
      MIT License
      •16•0•0•0•Updated Mar 31, 2025Mar 31, 2025

    • webapp_demo1

      Public
      This package contains the analysis script and the raw data to reproduce the results from the first demo of Nostrum's web app
      Python
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Nov 9, 2023Nov 9, 2023

    • nbdsuite_issues

      Public
      Issue tracker of the NBDSuite web app
      engineeringbioinformaticsenzyme
      engineeringbioinformaticsenzymechemistryproteinsdiscoverysoftwaredrugsmilespharma
      0•1•1•0•Updated Oct 6, 2023Oct 6, 2023

    • biobb_pydock

      Public
      C
      •
      Apache License 2.0
      •0•0•0•0•Updated May 18, 2023May 18, 2023

    • wjelement

      Public
      C++ librayr for PELE
      C
      •
      MIT License
      •0•0•0•0•Updated Oct 11, 2022Oct 11, 2022

    • nbd_suite_fe

      Public
      Python
      •0•0•0•0•Updated Sep 21, 2022Sep 21, 2022

    • frag_pele

      Public
      FrAG, a new tool for in silico hit-to-lead drug design, capable of growing a fragment into a core while exploring the protein-ligand conformational space
      Python
      •
      MIT License
      •16•1•0•0•Updated Sep 5, 2022Sep 5, 2022

    • alphafold

      Public
      Open source code for AlphaFold.
      Python
      •
      Apache License 2.0
      •3k•0•0•0•Updated Aug 12, 2022Aug 12, 2022

    • p38alpha

      Public
      R
      •0•0•0•0•Updated Apr 22, 2022Apr 22, 2022

    • PELEpharmacophore

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 17, 2021Nov 17, 2021

    • masif

      Public
      MaSIF- Molecular surface interaction fingerprints. Geometric deep learning to decipher patterns in molecular surfaces.
      Python
      •
      Apache License 2.0
      •175•0•0•0•Updated Sep 14, 2021Sep 14, 2021
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