bio-phys

All

41 repositories

asyncmd
Public
asyncmd is a library to write concurrent code for setup, run and analysis of molecular dynamics simulations using pythons async/await synthax.
molecular-dynamics slurm molecular-dynamics-simulation slurm-cluster enhanced-sampling
Python
•
GNU General Public License v3.0
•3•9•2•0•Updated Nov 21, 2024Nov 21, 2024
pydiffusion
Public
Analyse Rotational Diffusion Tensor from MD Simulations
python simulation molecular-dynamics rotation mdanalysis diffusion brownian-dynamics
Jupyter Notebook
•
Other
•3•16•0•0•Updated Oct 31, 2024Oct 31, 2024
af2_lir_screen
Public
Python
•
GNU General Public License v3.0
•0•1•0•0•Updated Sep 12, 2024Sep 12, 2024
MDBenchmark
Public
Quickly generate, start and analyze benchmarks for molecular dynamics simulations.
python cli benchmark simulation molecular-dynamics computational-chemistry high-performance-computing namd gromacs
Python
•
Other
•17•76•10•4•Updated Sep 5, 2024Sep 5, 2024
aimmd
Public
Python
•
GNU General Public License v3.0
•1•10•0•1•Updated Jul 25, 2024Jul 25, 2024
hierarchical-chain-growth
Public
Grow ensembles of disordered biomolecules from fragment libraries
Python
•
GNU General Public License v3.0
•1•8•1•0•Updated Jul 24, 2024Jul 24, 2024
trimem
Public
Monte Carlo sampling of the Helfrich bending energy.
C++
•
GNU General Public License v3.0
•4•5•0•2•Updated May 29, 2024May 29, 2024
BioEn.jl
Public
BioEn optimization
Julia
•
MIT License
•0•0•0•0•Updated Apr 19, 2024Apr 19, 2024
BioEn
Public
BioEn - Bayesian Inference Of ENsembles
structural-biology molecular-dynamics biological-simulations nmr data-integration bayesian-inference deer xray-scattering-experiments electron-paramagnetic-resonance saxs
Python
•
Other
•8•16•0•5•Updated Feb 6, 2024Feb 6, 2024
RefinementModels.jl
Public
Julia
•
MIT License
•0•0•0•0•Updated Oct 12, 2023Oct 12, 2023
VantHoffFitting
Public
Nonlinear least squares fitting of van 't Hoff plots via cubic splines, which makes the extraction of heat capacity and thermodynamic potentials possible.
Julia
•
MIT License
•0•0•0•5•Updated Aug 7, 2023Aug 7, 2023
ForceSpectroscopyMLE
Public
Analyze rupture force spectra from single-molecule force spectroscopy experiments to extract disassociation rates and parameters characterizing the free-energy profile underlying the bond.
julia maximum-likelihood-estimation single-molecule-force-spectroscopy forcible-bond-rupture
Julia
•
GNU General Public License v3.0
•1•2•0•5•Updated Aug 7, 2023Aug 7, 2023
complexespp
Public
Coarse-grained simulations of biomolecular complexes
C++
•
Other
•4•9•10•1•Updated Aug 2, 2023Aug 2, 2023
SAXS_BioEn
Public
Jupyter Notebook
•
MIT License
•0•2•0•0•Updated Jul 11, 2023Jul 11, 2023
ForceFieldsMC3
Public
0•1•0•0•Updated Jun 23, 2023Jun 23, 2023
BioEM
Public
GPU accelerating computing for Bayesian inference of electron microscopy images. BioEM is a publicly available software that enables the characterization of structural models with respect to individual electron microscopy images.
C++
•
Other
•3•11•2•1•Updated Apr 7, 2023Apr 7, 2023
constraint-coupling-analysis
Public
Python
•0•2•0•0•Updated Oct 17, 2022Oct 17, 2022
cnt-clusters
Public
Simulation parameters and results for lipid-mediated self-assembly of CNT membranes.
OpenEdge ABL
•1•0•0•0•Updated Aug 21, 2022Aug 21, 2022
DiffusionGLS
Public
Estimate the self-diffusion coefficient of a trajectory with a Generalized Least Squares (GLS) optimization procedure.
Jupyter Notebook
•
GNU General Public License v3.0
•7•13•2•2•Updated Aug 12, 2022Aug 12, 2022
memdiff
Public
Implementation of corrections for diffusion coefficients in membrane simulations.
diffusion-coefficient membrane-simulations lipid-membranes
Python
•
MIT License
•1•10•0•0•Updated Aug 2, 2022Aug 2, 2022
RebindingKineticsMLE
Public
Analyze pulling traces from single-molecule force spectroscopy experiments close to equilibrium to extract on and off rates and parameters characterizing the free-energy profile underlying the bond.
Julia
•
GNU General Public License v3.0
•1•1•0•1•Updated Jul 18, 2022Jul 18, 2022
ff-Mg-Ca-NucleicAcids
Public
Extension for the interactions with DNA and RNA of our previously bulk-optimized force field parameters (https://doi.org/10.1063/1.5017694)
0•0•1•0•Updated Jun 23, 2022Jun 23, 2022
BioFF
Public
Bayesian inference of force fields
Jupyter Notebook
•0•1•0•0•Updated Dec 22, 2021Dec 22, 2021
MgFF_OPC
Public
Magnesium Force Fields for OPC Water with Accurate Solvation, Ion-Binding, and Water-Exchange Properties: Successful Transfer from SPC/E
0•1•0•0•Updated Dec 9, 2021Dec 9, 2021
optimizedMgFFs
Public
Optimized force field parameters for Magnesium in combination with the SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, or TIP4P-D water model for all-atom MD simulations.
0•3•2•0•Updated Dec 9, 2021Dec 9, 2021
Magnesium-FFs
Public
Optimized force field parameters for Magnesium in combination with the TIP3P water model for all-atom MD simulations.
Makefile
•0•4•1•0•Updated Dec 2, 2021Dec 2, 2021
cnt-martini
Public
Generates Martini models for open carbon nanotubes to use with Gromacs.
Python
•
MIT License
•4•13•1•0•Updated Nov 24, 2021Nov 24, 2021
DiffusionMLE
Public
Analyze experimental tracking data using a maximum likelihood estimator (MLE) to extract translational diffusion coefficients.
julia expectation-maximization-algorithm diffusion-coefficient maximum-likelihood-estimation
Julia
•
GNU General Public License v3.0
•2•2•0•5•Updated Sep 28, 2021Sep 28, 2021
hplusminus
Public
Statistical tests to detect and quantify correlations in residuals when fitting models to one-dimensional data.
Python
•
MIT License
•0•1•1•0•Updated Jan 25, 2021Jan 25, 2021
capriqorn
Public
Capriqorn: CAlculation of P(R) and I(Q) Of macRomolecules in solutioN
python science dynamics simulations molecular saxs waxs
Python
•
Other
•1•10•2•0•Updated Sep 17, 2020Sep 17, 2020