Becksteinlab repositories

71 repositories

zarrtraj
Public
zarrtraj MDAKit for @MDAnalysis
streaming molecular-dynamics file-format
streaming molecular-dynamics file-format mdanalysis zarr
Jupyter Notebook
•
MIT License
•2•9•10•2•Updated Sep 17, 2026Sep 17, 2026
imdclient
Public
Streaming analysis from running MD simulations.
python science streaming
python science streaming md mdanalysis
Python
•
MIT License
•3•13•27•2•Updated Sep 7, 2026Sep 7, 2026
Prestin_Analysis
Public
Analysis scripts for prestin project
Python
•
MIT License
•0•0•0•0•Updated Aug 11, 2026Aug 11, 2026
ConfoState
Public
Categorizing functional states of transporters
Python
•
MIT License
•0•0•4•0•Updated Aug 10, 2026Aug 10, 2026
Protein_Area
Public
Calculation of cross sectional area profiles from MD simulations of membrane proteins.
molecular-dynamics-simulation mdanalysis membrane-proteins
molecular-dynamics-simulation mdanalysis membrane-proteins
Python
•
GNU General Public License v2.0
•1•2•5•0•Updated Aug 6, 2026Aug 6, 2026
TBC1D5-Rab7-NHE6-proton-diffusion-model
Public
Computational models and analyses for studying proton diffusion in the TBC1D5-Rab7-NHE6 protein complex
Jupyter Notebook
•
MIT License
•1•0•0•0•Updated Jul 28, 2026Jul 28, 2026
hollow
Public
Fork of Bosco Ho's and Franz Gruswitz's HOLLOW 1.1 (see http://hollow.sourceforge.net/).
python protein-structure
python protein-structure
Python
•2•6•4•0•Updated Jul 27, 2026Jul 27, 2026
propkatraj
Public
pKa estimates for proteins using an ensemble approach
pandas molecular-dynamics-simulation mdanalysis
pandas molecular-dynamics-simulation mdanalysis pka-predictions
Python
•
GNU General Public License v2.0
•8•31•7•1•Updated Jul 24, 2026Jul 24, 2026
ASBT_LB_analysis
Public
Analysis scripts for L. Biflexa ASBT
Jupyter Notebook
•
MIT License
•1•0•1•0•Updated Jul 6, 2026Jul 6, 2026
YiiP_OF_data
Public
Supplementary files for the YiiP OF paper.
Python
•0•0•3•0•Updated Jul 2, 2026Jul 2, 2026
basicrta
Public
Bayesian nonparametric inference of ligand binding kinetics from molecular dynamics simulations.
python bayesian-inference md
python bayesian-inference md mdanalysis moleculardynamics lipids
Python
•
GNU General Public License v3.0
•2•2•6•1•Updated Jun 18, 2026Jun 18, 2026
GromacsWrapper
Public
GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).
python science molecular-dynamics
python science molecular-dynamics gromacs gromacswrapper
Python
•
GNU General Public License v3.0
•54•192•13•0•Updated May 20, 2026May 20, 2026
lammps
Public
Public development project of the LAMMPS MD software package
C++
•
GNU General Public License v2.0
•2k•0•0•0•Updated May 11, 2026May 11, 2026
multibind
Public
A Python package for building thermodynamically consistent state graphs.
python thermodynamics mle
python thermodynamics mle freeenergy
Python
•
MIT License
•1•3•1•0•Updated Mar 20, 2026Mar 20, 2026
kda
Public
Python package used for the analysis of biochemical kinetic diagrams.
python graph kinetics
python graph kinetics
Python
•
GNU General Public License v3.0
•1•6•11•1•Updated Jan 8, 2026Jan 8, 2026
streaming-md-docker
Public
Docker images with MD packages that support streaming with IMD v3.
Dockerfile
•
MIT License
•0•1•5•0•Updated Nov 9, 2025Nov 9, 2025
mdpow-molconfgen
Public
torsional sampler
Jupyter Notebook
•
GNU General Public License v2.0
•1•0•2•1•Updated Jul 11, 2025Jul 11, 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
python science molecular-dynamics free-energy gromacs gromacswrapper
Python
•
GNU General Public License v3.0
•10•29•29•3•Updated Oct 14, 2024Oct 14, 2024
numkit
Public
Numerical first aid kit (with numpy/scipy).
python science gromacswrapper
python science gromacswrapper
Python
•
Other
•2•2•2•0•Updated Oct 10, 2024Oct 10, 2024
imdreader
Public archive
prototype IMDReader for MDAnalysis
streaming md 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
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

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Becksteinlab

All

71 repositories

zarrtraj

imdclient

Prestin_Analysis

ConfoState

Protein_Area

TBC1D5-Rab7-NHE6-proton-diffusion-model

hollow

propkatraj

ASBT_LB_analysis

YiiP_OF_data

basicrta

GromacsWrapper

lammps

multibind

kda

streaming-md-docker

mdpow-molconfgen

streaming-namd-docker

MDPOW

numkit

imdreader

kda-examples

mdaadb

napalib

pandas-example

yiip_analysis

multibind-publication-code

rmsfkit

scipy-2023-mdakits

SAMPL7_logP_data

Repositories list

71 repositories