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    63 repositories

    • MDPOW

      Public
      Calculation of water/solvent partition coefficients with Gromacs.
      pythonsciencemolecular-dynamicsfree-energygromacsgromacswrapper
      Python
      •
      GNU General Public License v3.0
      •10•25•31•4•Updated Oct 11, 2024Oct 11, 2024

    • imdclient

      Public
      Python
      •
      MIT License
      •0•0•10•2•Updated Oct 10, 2024Oct 10, 2024

    • numkit

      Public
      Numerical first aid kit (with numpy/scipy).
      pythonsciencegromacswrapper
      Python
      •
      Other
      •2•2•1•0•Updated Oct 10, 2024Oct 10, 2024

    • GromacsWrapper

      Public
      GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).
      pythonsciencemolecular-dynamicsgromacsgromacswrapper
      Python
      •
      GNU General Public License v3.0
      •53•168•13•2•Updated Oct 7, 2024Oct 7, 2024

    • zarrtraj

      Public
      zarrtraj MDAKit for @MDAnalysis
      streamingmolecular-dynamicsfile-formatmdanalysiszarr
      Python
      •
      GNU General Public License v3.0
      •1•5•13•1•Updated Oct 3, 2024Oct 3, 2024

    • basicrta

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 2, 2024Oct 2, 2024

    • streaming-md-docker

      Public
      Docker images with MD packages that support streaming with IMD v3.
      Shell
      •0•1•0•0•Updated Oct 2, 2024Oct 2, 2024

    • mdpow-molconfgen

      Public
      torsional sampler
      Jupyter Notebook
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Oct 1, 2024Oct 1, 2024

    • imdreader

      Public archive
      prototype IMDReader for MDAnalysis
      streamingmdmdanalysis
      Python
      •
      GNU General Public License v2.0
      •0•1•1•0•Updated Aug 29, 2024Aug 29, 2024

    • kda

      Public
      Python package used for the analysis of biochemical kinetic diagrams.
      Python
      •
      GNU General Public License v3.0
      •1•3•11•0•Updated Aug 22, 2024Aug 22, 2024

    • kda-examples

      Public
      Kinetic Diagram Analysis Examples
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•2•0•Updated Aug 10, 2024Aug 10, 2024

    • mdaadb

      Public
      A package that interfaces SQLite database IO with MDAnalysis analysis results.
      Python
      •
      GNU General Public License v2.0
      •0•1•0•0•Updated Jul 29, 2024Jul 29, 2024

    • propkatraj

      Public
      pKa estimates for proteins using an ensemble approach
      molecular-dynamics-simulationmdanalysispka-predictionspandas
      Python
      •
      GNU General Public License v2.0
      •7•25•4•1•Updated Jul 22, 2024Jul 22, 2024

    • napalib

      Public
      Python
      •
      GNU General Public License v3.0
      •1•0•1•0•Updated Mar 28, 2024Mar 28, 2024

    • pandas-example

      Public
      jupyter notebook with some basic pandas examples
      Jupyter Notebook
      •1•0•0•0•Updated Mar 11, 2024Mar 11, 2024

    • multibind

      Public
      A Python package for building thermodynamically consistent state graphs.
      Python
      •
      MIT License
      •1•4•2•0•Updated Dec 18, 2023Dec 18, 2023

    • yiip_analysis

      Public
      Analysis package for YiiP projects
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Oct 16, 2023Oct 16, 2023

    • multibind-publication-code

      Public
      Repository for the code used in the multibind paper
      Jupyter Notebook
      •0•1•0•0•Updated Jul 6, 2023Jul 6, 2023

    • rmsfkit

      Public
      Python
      •
      GNU General Public License v2.0
      •0•0•0•0•Updated Apr 13, 2023Apr 13, 2023

    • scipy-2023-mdakits

      Public
      0•0•0•0•Updated Feb 28, 2023Feb 28, 2023

    • SAMPL7_logP_data

      Public
      Supplementary Information for SAMPL7 Physical Properties challenge
      Rich Text Format
      •
      MIT License
      •0•0•0•0•Updated Aug 5, 2022Aug 5, 2022

    • hollow

      Public
      Fork of Bosco Ho's and Franz Gruswitz's HOLLOW 1.1 (see http://hollow.sourceforge.net/).
      pythonprotein-structure
      Python
      •1•6•3•0•Updated Jul 30, 2022Jul 30, 2022

    • .github

      Public
      Becksteinlab profile
      0•0•0•0•Updated Jul 27, 2022Jul 27, 2022

    • PDB_Ion_Survey_data

      Public
      Data for PDB_Ion_Survey
      0•0•0•0•Updated Jun 17, 2022Jun 17, 2022

    • PDB_Ion_Survey

      Public
      A survey of ion coordination geometries in proteins.
      scienceprotein-structureproteins
      Python
      •
      GNU General Public License v3.0
      •1•1•5•0•Updated Jun 17, 2022Jun 17, 2022

    • BornProfiler

      Public
      A small Python package to set up electrostatic solvation free energy ("Born energy") calculations of an ion in a membrane protein and calculate the electrostatic free energy with APBS .
      scienceelectrostaticsmembrane-proteinsapbspoisson-boltzmannpython
      Python
      •
      GNU General Public License v3.0
      •2•2•6•4•Updated Mar 1, 2022Mar 1, 2022

    • gmx_first_aid

      Public
      A command line utility intended to assist in recovering data from corrupted gromacs trajectories.
      gromacs
      C
      •
      GNU General Public License v2.0
      •1•1•1•0•Updated Nov 29, 2021Nov 29, 2021

    • CpHMD-Analysis

      Public
      Jack Henderson's CpHMD analysis scripts
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •4•1•0•0•Updated Oct 22, 2021Oct 22, 2021

    • alchemical_conformational_analysis

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Sep 11, 2021Sep 11, 2021

    • OBscripts

      Public
      Old and new scripts for working with simulations and molecular structures.
      Python
      •
      MIT License
      •0•0•0•0•Updated Aug 12, 2021Aug 12, 2021