Becksteinlab

GromacsWrapper

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

propkatraj

pKa estimates for proteins using an ensemble approach

MDPOW

Calculation of water/solvent partition coefficients with Gromacs.

hollow

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

multibind

A Python package for building thermodynamically consistent state graphs.

kda

Python package used for the analysis of biochemical kinetic diagrams.

zarrtraj

zarrtraj MDAKit for @MDAnalysis

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 .

numkit

Numerical first aid kit (with numpy/scipy).

CpHMD-Analysis

Jack Henderson's CpHMD analysis scripts

gmx_first_aid

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

imdreader

multibind-publication-code

Repository for the code used in the multibind paper

PDB_Ion_Survey

A survey of ion coordination geometries in proteins.

alchemical_conformational_analysis

SAMPL7_logP_data

Supplementary Information for SAMPL7 Physical Properties challenge

.github

Becksteinlab profile

basicrta

h5md_examples

kda-examples

Kinetic Diagram Analysis Examples

mdpow-molconfgen

torsional sampler

napalib

OBscripts

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

pandas-example

jupyter notebook with some basic pandas examples

PDB_Ion_Survey_data

Data for PDB_Ion_Survey

rmsfkit

scipy-2023-mdakits

scipy2021-mpiH5MD-data

scipy_proceedings

Tools used to generate the SciPy conference proceedings

yiip_analysis

Analysis package for YiiP projects