All

68 repositories

imdclient
Public
Streaming analysis from running MD simulations.
python science streaming
python science streaming md mdanalysis
Python
•
MIT License
•3•12•24•2•Updated Jul 13, 2026Jul 13, 2026
ASBT_LB_analysis
Public
Analysis scripts for L. Biflexa ASBT
Jupyter Notebook
•
MIT License
•0•0•1•0•Updated Jul 6, 2026Jul 6, 2026
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•3•Updated Jul 2, 2026Jul 2, 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 Jun 26, 2026Jun 26, 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•1•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•190•14•1•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
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•4•0•Updated Apr 21, 2026Apr 21, 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
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
•0•0•0•0•Updated Mar 14, 2026Mar 14, 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
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 May 2, 2025May 2, 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
.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 proteins protein-structure
science proteins protein-structure
Python
•
GNU General Public License v3.0
•1•1•5•0•Updated Jun 17, 2022Jun 17, 2022

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Becksteinlab

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68 repositories

imdclient

ASBT_LB_analysis

zarrtraj

propkatraj

basicrta

GromacsWrapper

lammps

Protein_Area

multibind

TBC1D5-Rab7-NHE6-proton-diffusion-model

kda

streaming-md-docker

mdpow-molconfgen

hollow

streaming-namd-docker

MDPOW

numkit

imdreader

kda-examples

mdaadb

napalib

pandas-example

yiip_analysis

multibind-publication-code

rmsfkit

scipy-2023-mdakits

SAMPL7_logP_data

.github

PDB_Ion_Survey_data

PDB_Ion_Survey

All

All

Repositories list

68 repositories