Becksteinlab

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66 repositories

basicrta
Public
Bayesian nonparametric inference of ligand binding kinetics from molecular dynamics simulations.
python bayesian-inference md mdanalysis moleculardynamics lipids
Python
•
GNU General Public License v3.0
•2•0•7•2•Updated Jul 31, 2025Jul 31, 2025
kda
Public
Python package used for the analysis of biochemical kinetic diagrams.
python graph kinetics
Python
•
GNU General Public License v3.0
•1•5•10•1•Updated Jul 22, 2025Jul 22, 2025
zarrtraj
Public
zarrtraj MDAKit for @MDAnalysis
streaming molecular-dynamics file-format mdanalysis zarr
Jupyter Notebook
•
MIT License
•2•9•11•0•Updated Jul 21, 2025Jul 21, 2025
imdclient
Public
Streaming analysis from running MD simulations.
python science streaming md mdanalysis
Python
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MIT License
•1•7•15•0•Updated Jul 21, 2025Jul 21, 2025
GromacsWrapper
Public
GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).
python science molecular-dynamics gromacs gromacswrapper
Python
•
GNU General Public License v3.0
•54•178•12•1•Updated Jul 12, 2025Jul 12, 2025
propkatraj
Public
pKa estimates for proteins using an ensemble approach
molecular-dynamics-simulation mdanalysis pka-predictions pandas
Python
•
GNU General Public License v2.0
•6•28•6•2•Updated Jul 11, 2025Jul 11, 2025
mdpow-molconfgen
Public
torsional sampler
Jupyter Notebook
•
GNU General Public License v2.0
•1•0•2•1•Updated Jul 11, 2025Jul 11, 2025
Protein_Area
Public
Calculation of cross sectional area profiles from MD simulations of membrane proteins.
molecular-dynamics-simulation mdanalysis membrane-proteins
Python
•
GNU General Public License v2.0
•1•0•3•2•Updated Jun 4, 2025Jun 4, 2025
streaming-md-docker
Public
Docker images with MD packages that support streaming with IMD v3.
Dockerfile
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MIT License
•0•1•4•0•Updated May 23, 2025May 23, 2025
hollow
Public
Fork of Bosco Ho's and Franz Gruswitz's HOLLOW 1.1 (see http://hollow.sourceforge.net/).
python protein-structure
Python
•2•6•4•0•Updated May 2, 2025May 2, 2025
lammps
Public
Public development project of the LAMMPS MD software package
C++
•
GNU General Public License v2.0
•1.9k•0•0•0•Updated Apr 22, 2025Apr 22, 2025
streaming-namd-docker
Public
0•0•0•0•Updated Dec 17, 2024Dec 17, 2024
MDPOW
Public
Calculation of water/solvent partition coefficients with Gromacs.
python science molecular-dynamics free-energy gromacs gromacswrapper
Python
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GNU General Public License v3.0
•9•28•29•3•Updated Oct 14, 2024Oct 14, 2024
numkit
Public
Numerical first aid kit (with numpy/scipy).
python science gromacswrapper
Python
•
Other
•2•2•1•0•Updated Oct 10, 2024Oct 10, 2024
imdreader
Public archive
prototype IMDReader for MDAnalysis
streaming md mdanalysis
Python
•
GNU General Public License v2.0
•0•1•1•0•Updated Aug 29, 2024Aug 29, 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
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
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MIT License
•0•0•0•0•Updated Aug 5, 2022Aug 5, 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.
science protein-structure proteins
Python
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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 .
science electrostatics membrane-proteins apbs poisson-boltzmann python
Python
•
GNU General Public License v3.0
•2•3•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