Becksteinlab/zarrtraj

zarrtraj MDAKit for @MDAnalysis

Language: Jupyter Notebook - Size: 27 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 9 - Forks: 2

Becksteinlab/GromacsWrapper

GromacsWrapper wraps system calls to GROMACS tools into thin Python classes (GROMACS 4.6.5 - 2024 supported).

Language: Python - Size: 11.9 MB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 178 - Forks: 54

Becksteinlab/basicrta

Bayesian nonparametric inference of ligand binding kinetics from molecular dynamics simulations.

Language: Python - Size: 11.1 MB - Last synced at: 8 days ago - Pushed at: 8 days ago - Stars: 0 - Forks: 2

Becksteinlab/mdpow-molconfgen

torsional sampler

Language: Jupyter Notebook - Size: 3.36 MB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 0 - Forks: 1

Becksteinlab/imdclient

Streaming analysis from running MD simulations.

Language: Python - Size: 373 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 7 - Forks: 1

Becksteinlab/MDPOW

Calculation of water/solvent partition coefficients with Gromacs.

Language: Python - Size: 739 MB - Last synced at: 27 days ago - Pushed at: 10 months ago - Stars: 28 - Forks: 9

Becksteinlab/Protein_Area

Language: Python - Size: 87.9 KB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 0 - Forks: 1

Becksteinlab/streaming-md-docker

Docker images with MD packages that support streaming with IMD v3.

Language: Dockerfile - Size: 127 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 1 - Forks: 0

Becksteinlab/hollow

Fork of Bosco Ho's and Franz Gruswitz's HOLLOW 1.1 (see http://hollow.sourceforge.net/).

Language: Python - Size: 2.58 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 6 - Forks: 1

Becksteinlab/lammps Fork of lammps/lammps

Public development project of the LAMMPS MD software package

Language: C++ - Size: 758 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

Becksteinlab/kda

Python package used for the analysis of biochemical kinetic diagrams.

Language: Python - Size: 6.26 MB - Last synced at: 2 months ago - Pushed at: 3 months ago - Stars: 5 - Forks: 1

Becksteinlab/propkatraj

pKa estimates for proteins using an ensemble approach

Language: Python - Size: 9.4 MB - Last synced at: 8 days ago - Pushed at: 16 days ago - Stars: 28 - Forks: 6

Becksteinlab/BornProfiler

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 .

Language: Python - Size: 1.09 GB - Last synced at: 23 days ago - Pushed at: over 3 years ago - Stars: 3 - Forks: 2

Becksteinlab/Parallel-analysis-in-the-MDAnalysis-Library

Benchmarking MDAnalysis with Dask (and MPI). Supplementary Information for SciPy 2017 paper.

Language: Python - Size: 78.1 KB - Last synced at: 3 months ago - Pushed at: almost 8 years ago - Stars: 3 - Forks: 4

Becksteinlab/making-prettier-plots

a quick primer on making prettier (and more impactful) plots

Size: 652 KB - Last synced at: 5 months ago - Pushed at: almost 10 years ago - Stars: 14 - Forks: 1

Becksteinlab/numkit

Numerical first aid kit (with numpy/scipy).

Language: Python - Size: 303 KB - Last synced at: 1 day ago - Pushed at: 10 months ago - Stars: 2 - Forks: 2

Becksteinlab/imdreader 📦

prototype IMDReader for MDAnalysis

Language: Python - Size: 6.91 MB - Last synced at: 4 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 0

Becksteinlab/hop

Solvent network analysis. Hop is a python package based on MDAnalysis to analyze solvation dynamics.

Language: Python - Size: 16.9 MB - Last synced at: 3 months ago - Pushed at: almost 7 years ago - Stars: 14 - Forks: 5

Becksteinlab/kda-examples

Kinetic Diagram Analysis Examples

Language: Jupyter Notebook - Size: 11.1 MB - Last synced at: 5 months ago - Pushed at: 12 months ago - Stars: 0 - Forks: 0

Becksteinlab/mdaadb

A package that interfaces SQLite database IO with MDAnalysis analysis results.

Language: Python - Size: 142 KB - Last synced at: 5 months ago - Pushed at: 12 months ago - Stars: 1 - Forks: 0

Becksteinlab/vesicle_library

library of vesicles with the Dry Martini force field

Size: 52.4 MB - Last synced at: about 2 months ago - Pushed at: about 9 years ago - Stars: 6 - Forks: 1

Becksteinlab/AdKGromacsTutorial

Basic tutorial for running and analyzing a Gromacs MD simulation of AdK

Language: Shell - Size: 22 MB - Last synced at: 3 months ago - Pushed at: about 7 years ago - Stars: 9 - Forks: 7

Becksteinlab/MDAnalysis-workshop

MDAnalysis Tutorial at the 2015 CECAM Macromolecular simulation software workshop

Language: Jupyter Notebook - Size: 22.3 MB - Last synced at: 3 months ago - Pushed at: about 9 years ago - Stars: 12 - Forks: 7

Becksteinlab/PSAnalysisTutorial

Examples and data for performing path similarity analysis (PSA).

Language: Python - Size: 159 MB - Last synced at: 3 months ago - Pushed at: almost 10 years ago - Stars: 16 - Forks: 5

Becksteinlab/gmx_first_aid

A command line utility intended to assist in recovering data from corrupted gromacs trajectories.

Language: C - Size: 15.6 KB - Last synced at: 5 months ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 1

Becksteinlab/SPIDAL-www Fork of DSC-SPIDAL/www

DSC-Spidal Web Page

Language: Makefile - Size: 3.56 MB - Last synced at: over 1 year ago - Pushed at: about 9 years ago - Stars: 0 - Forks: 0

Becksteinlab/propka Fork of jensengroup/propka

PROPKA predicts the pKa values of ionizable groups in proteins and protein-ligand complexes based in the 3D structure.

Language: Python - Size: 3.57 MB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 0

Becksteinlab/pandas-example Fork of l-repa/pandas-example

jupyter notebook with some basic pandas examples

Size: 582 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 1

Becksteinlab/rmsfkit

Language: Python - Size: 55.7 KB - Last synced at: 5 months ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

Becksteinlab/vesicle_analysis_methods

Language: Jupyter Notebook - Size: 145 KB - Last synced at: 1 day ago - Pushed at: over 9 years ago - Stars: 1 - Forks: 0

Becksteinlab/CpHMD-Analysis Fork of Hendejac/CpHMD-Analysis

Jack Henderson's CpHMD analysis scripts

Size: 2.95 MB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 1 - Forks: 0

Becksteinlab/multibind

A Python package for building thermodynamically consistent state graphs.

Language: Python - Size: 404 KB - Last synced at: 3 months ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 1

Becksteinlab/yiip_analysis

Analysis package for YiiP projects

Language: Jupyter Notebook - Size: 1.21 MB - Last synced at: 5 months ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 0

Becksteinlab/MDAnalysis-with-Dask

Benchmarking MDAnalysis with dask.

Language: Python - Size: 1.15 MB - Last synced at: 8 days ago - Pushed at: almost 8 years ago - Stars: 5 - Forks: 1

Becksteinlab/scipy-2023-mdakits

Size: 5.86 KB - Last synced at: 5 months ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

Becksteinlab/multibind-publication-code

Repository for the code used in the multibind paper

Language: Jupyter Notebook - Size: 9.37 MB - Last synced at: 5 months ago - Pushed at: about 2 years ago - Stars: 1 - Forks: 0

Becksteinlab/SAMPL7_logP_data

Supplementary Information for SAMPL7 Physical Properties challenge

Language: Rich Text Format - Size: 1.71 MB - Last synced at: 5 months ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

Becksteinlab/.github

Becksteinlab profile

Size: 1000 Bytes - Last synced at: about 1 month ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

Becksteinlab/alchemical_conformational_analysis

Language: Jupyter Notebook - Size: 5.57 MB - Last synced at: 5 months ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0

Becksteinlab/PDB_Ion_Survey_data

Data for PDB_Ion_Survey

Size: 1.65 MB - Last synced at: 5 months ago - Pushed at: about 3 years ago - Stars: 0 - Forks: 0

Becksteinlab/PDB_Ion_Survey

A survey of ion coordination geometries in proteins.

Language: Python - Size: 2.74 MB - Last synced at: 5 months ago - Pushed at: about 3 years ago - Stars: 1 - Forks: 1

Becksteinlab/workflows-talk

Materials for workflows/automation talks.

Size: 9.59 MB - Last synced at: 5 months ago - Pushed at: over 6 years ago - Stars: 2 - Forks: 0

Becksteinlab/mdworks

molecular dynamics, with Fireworks!

Language: Python - Size: 33.2 KB - Last synced at: 3 months ago - Pushed at: over 7 years ago - Stars: 7 - Forks: 1

Becksteinlab/napalib

Language: Python - Size: 6.76 MB - Last synced at: about 2 months ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 1

Becksteinlab/OBscripts

Old and new scripts for working with simulations and molecular structures.

Language: Python - Size: 9.77 KB - Last synced at: 5 months ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0

Becksteinlab/scipy_proceedings Fork of scipy-conference/scipy_proceedings

Tools used to generate the SciPy conference proceedings

Language: Python - Size: 197 MB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 2

Becksteinlab/scipy2021-mpiH5MD-data

Language: Jupyter Notebook - Size: 11.8 MB - Last synced at: about 2 months ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 0

Becksteinlab/conda-gromacs-5.1.2

Conda package of gromacs 5.1.2 intended for testing purposes.

Language: Shell - Size: 10.7 KB - Last synced at: 5 months ago - Pushed at: over 8 years ago - Stars: 1 - Forks: 1

Becksteinlab/h5md_examples

Language: Python - Size: 6.82 MB - Last synced at: 5 months ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0

Becksteinlab/remote-vmd

Python client for the VMD server.

Language: Python - Size: 13.7 KB - Last synced at: 5 months ago - Pushed at: over 8 years ago - Stars: 1 - Forks: 0

Becksteinlab/SAMPL6_logP_data

Supplementary data for SAMPL6 Part II (logP) calculations.

Language: Jupyter Notebook - Size: 1.09 MB - Last synced at: 5 months ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

Becksteinlab/lipidbook

Lipidbook force field repository (public issue tracker and wiki).

Size: 0 Bytes - Last synced at: 5 months ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

Becksteinlab/scipy2019-pmda-data

data and abstract for PMDA paper (SciPy 2019)

Language: Python - Size: 80.9 MB - Last synced at: 5 months ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 2

Becksteinlab/conda-gromacs-4.6.7

Conda package of gromacs 4.6.7 intended for testing purposes.

Language: Shell - Size: 6.84 KB - Last synced at: 5 months ago - Pushed at: over 8 years ago - Stars: 0 - Forks: 0

Becksteinlab/workshop_testing

Files for the summer workshop for tests and CI

Language: Python - Size: 12.1 MB - Last synced at: 5 months ago - Pushed at: almost 7 years ago - Stars: 0 - Forks: 0

Becksteinlab/timeseries-analysis-example

A brief example showing the basics of writing efficient timeseries analyses in python, and efficiently storing and exploring the resulting data

Language: Python - Size: 176 KB - Last synced at: 5 months ago - Pushed at: over 10 years ago - Stars: 2 - Forks: 0

Becksteinlab/queuetools

a collection of tools that make a distributed, heterogeneous workstation queue easier to leverage

Language: Python - Size: 17.6 KB - Last synced at: 5 months ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 1

Becksteinlab/Bash_workshop

Language: Jupyter Notebook - Size: 10.9 MB - Last synced at: 5 months ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 0

Becksteinlab/queuing-systems

Demo files for queuing systems talk

Language: Shell - Size: 3.18 MB - Last synced at: 5 months ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 0

Becksteinlab/gromacswrapper.analysis

Legacy code from GromacsWrapper: gromacs.analysis module

Language: Python - Size: 345 KB - Last synced at: 5 months ago - Pushed at: over 8 years ago - Stars: 0 - Forks: 0

Becksteinlab/Scipy2017

Size: 90.8 KB - Last synced at: 5 months ago - Pushed at: over 8 years ago - Stars: 0 - Forks: 1

Becksteinlab/conda-gromacs-2016

Conda package of gromacs 2016 intended for testing purposes.

Language: Shell - Size: 5.86 KB - Last synced at: 5 months ago - Pushed at: over 8 years ago - Stars: 0 - Forks: 0

Becksteinlab/minlatex

A minimal working example for an article written in LaTeX

Language: TeX - Size: 29.3 KB - Last synced at: 5 months ago - Pushed at: over 8 years ago - Stars: 0 - Forks: 0

Becksteinlab/ComputationalPhysics_PHY494

Materials for PHY 494

Language: Shell - Size: 2.93 KB - Last synced at: 5 months ago - Pushed at: over 9 years ago - Stars: 0 - Forks: 0

Becksteinlab/beckernels

A repository of radical.ensemblemd kernels used by the Beckstein Lab

Language: Python - Size: 11.7 KB - Last synced at: 5 months ago - Pushed at: over 9 years ago - Stars: 0 - Forks: 0