Software
hplusminus: Powerful statistical tests for ordered data
Description Sign-based statistical tests and combination with Pearson's chi-square test
Developers Jürgen Köfinger, Klaus Reuter
Reference Powerful Statistical Tests for Ordered Data, Jürgen Köfinger and Gerhard Hummer, preprint, https://doi.org/10.26434/chemrxiv.13373351.v1 (2020)
MDBenchmark: a toolkit to optimize the performance of molecular dynamics simulations
Description Tool to run benchmarks and scaling studies for molecular dynamics simulations
Developers Michael Gecht, Marc Siggel, Max Linke, Sebastian Kehl
Documentation https://mdbenchmark.readthedocs.io/
Reference MDBenchmark: a toolkit to optimize the performance of molecular dynamics simulations, Michael Gecht, Marc Siggel, Max Linke, Gerhard Hummer, and Jürgen Köfinger, J. Chem. Phys. 153 (2020)
BioEn: Bayesian Inference Of Ensembles
Description Integrating experiments and simulations via reweighing
Developers Cesar Allende, Jürgen Köfinger, Katrin Reichel, Klaus Reuter, Lukas Stelzl
Download https://github.com/bio-phys/bioen
Reference Bayesian ensemble refinement by replica simulations and reweighting, Gerhard Hummer and Jürgen Köfinger, J. Chem. Phys. 143 (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.
Documentation http://capriqorn.readthedocs.io
Reference Atomic-resolution structural information from scattering experiments on macromolecules in solution, Jürgen Köfinger and Gerhard Hummer, Phys. Rev. E 87 (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
Reference CADISHI: Fast parallel calculation of particle-pair distance histograms on CPUs and GPUs, Klaus Reuter and Jürgen Köfinger, Comp. Phys. Commun. 236 (2019)