Dept. Theoretical Biophysics - Available Software

PyDiffusion

Description: PyDiffusion is a python library to analyze the rotational and translational diffusion of molecules in molecular dynamics simulation or rigid body simulations.
Developers
: Max Linke, Gerhard Hummer
Download: https://github.com/bio-phys/pydiffusion
Documentation: https://github.com/bio-phys/pydiffusion
Reference: Fully Anisotropic Rotational Diffusion Tensor from Molecular Dynamics Simulations, M. Linke, Jürgen Köfinger and Gerhard Hummer, J. Phys. Chem. B. (accepted)

CNT-GAFF

Description: Build atomistic structures of carbon nanotubes with the possibility to add functional groups (OH, COOH, COO-) and assigns generalized Amber (GAFF) parameters to them.
Developers
: Martin Vögele
Download
: https://github.com/bio-phys/cnt-gaff
Documentation
: -
Reference
: Simulations of Carbon Nanotube Porins in Lipid Bilayers. M. Vögele, J. Köfinger, G. Hummer, Faraday Discussions (in preparation, February 2018)

CAPRIQORN

CAlculation of P(R) and I(Q) Of macRomolecules in solutioN

Description: Calculation SAXS/WAXS scattering intensities and pair-distance distribution functions directly from the output trajectories of molecular dynamics simulations using explicit solvent.
Developers
: Jürgen Köfinger, Klaus Reuter, and contributers.
Download: https://github.com/bio-phys/capriqorn
Documentation: http://capriqorn.readthedocs.io/en/latest/
Reference:
Atomic-resolution structural information from scattering experiments on macromolecules in solution. Jürgen Köfinger and Gerhard Hummer. Phys.   Rev. E 87, 052712 (2013)

Cadishi

CAlculation of DIStance HIstograms

Description: Fast computations of histograms of the (Euclidean) distances between objects.
Developers: Klaus Reuter and Jürgen Köfinger
Download: https://github.com/bio-phys/cadishi
Documentation: http://cadishi.readthedocs.io/en/latest/
Reference: -

PyDHAMed

Description: Dynamic Histogram Analysis extended to detailed balance
Developers: Lukas S. Stelzl, Gerhard Hummer, and contributors.
Download: https://github.com/bio-phys/PyDHAMed
Reference:
Dynamic Histogram Analysis To Determine Free Energies and Rates from Biased Simulations. Lukas S. Stelzl, Adam Kells, Edina Rosta, and Gerhard Hummer. J. Chem. Theory Comput.,  13 (12), 6328–6342 (2017)
 

MDBenchmark

Description: Benchmark and scaling studies for MD simulations
Developers: Max Linke, Michael Gecht, and contributors.
Download: https://github.com/bio-phys/MDBenchmark
Reference: -

BioEM

Bayesian Inference Of Electron Microscopy

Description: The method enables the characterization of structural models by calculating their posterior probability with respect to individual electron microscopy images.
Developers: Pilar Cossio, David Rohr, Luka Stanisic, Fabio Barruffa, Markus Rampp, Volker Lindenstruth, Gerhard Hummer
Download
: https://github.com/bio-phys/BioEM
Documentation: http://bioem.readthedocs.io/en/latest/
References:
Towards structures of dynamic and heterogeneous biomolecular assemblies. Pilar Cossio and Gerhard Hummer. J Struct Biolo, 184, 427-437 (2013)

BioEM: GPU-accelerated computing of Bayesian inference of electron microscopy images. Pilar Cossio, David Rohr,  Fabio Barruffa, Markus Rampp, Volker Lindenstruth, Gerhard Hummer. Comput Phys Commun, 210, 163-171 (2017)

Contact:

Max Planck Institute of Biophysics

Dr. Jürgen Köfinger, project leader
Department Theoretical Biophysics

Tel.: +49 (0) 69 6303-2503
E-Mail: juergen.koefinger(at)biophys.mpg.de