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@Becksteinlab

Becksteinlab

Computational Biophysics at Arizona State University

Beckstein Lab at Arizona State University 👋

The Beckstein Lab is part of the Center for Biological Physics and the Department of Physics at Arizona State University. It is headed by Oliver Beckstein.

The lab uses computational approaches such as molecular dynamics simulations in order to understand the function of biomolecules, in particular membrane proteins, at the molecular level.

Our work belongs to the area of computational biophysics. We aim to quantitatively predict the function and activity of proteins from the knowledge of their structures alone and so to better understand biological phenomena at the molecular level, in particular transmembrane transport processess catalyzed by membrane proteins such as secondary active transporters and ion channels. This works contributes to the fields of structural biology, physiology, nanobiotechnology as well as ultimately to the development of new drugs.

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  1. GromacsWrapper GromacsWrapper Public

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

    Python 171 54

  2. kda kda Public

    Python package used for the analysis of biochemical kinetic diagrams.

    Python 5 1

  3. multibind multibind Public

    A Python package for building thermodynamically consistent state graphs.

    Python 4 1

  4. MDPOW MDPOW Public

    Calculation of water/solvent partition coefficients with Gromacs.

    Python 25 10

  5. propkatraj propkatraj Public

    pKa estimates for proteins using an ensemble approach

    Python 27 7

  6. zarrtraj zarrtraj Public

    zarrtraj MDAKit for @MDAnalysis

    Jupyter Notebook 7 2

Repositories

Showing 10 of 63 repositories
  • streaming-md-docker Public

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

    Becksteinlab/streaming-md-docker’s past year of commit activity
    Dockerfile 1 MIT 0 4 0 Updated Nov 29, 2024
  • basicrta Public

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

    Becksteinlab/basicrta’s past year of commit activity
    Python 0 GPL-3.0 0 1 0 Updated Nov 29, 2024
  • imdclient Public

    Streaming analysis from running MD simulations.

    Becksteinlab/imdclient’s past year of commit activity
    Python 5 0 9 3 Updated Nov 29, 2024
  • zarrtraj Public

    zarrtraj MDAKit for @MDAnalysis

    Becksteinlab/zarrtraj’s past year of commit activity
    Jupyter Notebook 7 GPL-3.0 2 14 1 Updated Nov 9, 2024
  • MDPOW Public

    Calculation of water/solvent partition coefficients with Gromacs.

    Becksteinlab/MDPOW’s past year of commit activity
    Python 25 GPL-3.0 10 29 (1 issue needs help) 3 Updated Oct 14, 2024
  • propkatraj Public

    pKa estimates for proteins using an ensemble approach

    Becksteinlab/propkatraj’s past year of commit activity
    Python 27 GPL-2.0 7 6 1 Updated Oct 13, 2024
  • numkit Public

    Numerical first aid kit (with numpy/scipy).

    Becksteinlab/numkit’s past year of commit activity
    Python 2 2 1 0 Updated Oct 10, 2024
  • GromacsWrapper Public

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

    Becksteinlab/GromacsWrapper’s past year of commit activity
    Python 171 GPL-3.0 54 13 2 Updated Oct 7, 2024
  • mdpow-molconfgen Public

    torsional sampler

    Becksteinlab/mdpow-molconfgen’s past year of commit activity
    Jupyter Notebook 0 GPL-2.0 0 0 0 Updated Oct 1, 2024
  • imdreader Public archive

    prototype IMDReader for MDAnalysis

    Becksteinlab/imdreader’s past year of commit activity
    Python 1 GPL-2.0 0 1 0 Updated Aug 29, 2024