Projects in Awesome Lists by bio-phys
A curated list of projects in awesome lists by bio-phys .
https://github.com/bio-phys/cnt-gaff
Build atomistic structures of carbon nanotubes with the possibility to add functional groups (OH, COOH, COO-) and assigns generalized Amber (GAFF) parameters to them.
amber carbon-nanotubes force-field gaff molecular-dynamics
Last synced: 16 Jan 2026
https://github.com/bio-phys/pydiffusion
Analyse Rotational Diffusion Tensor from MD Simulations
brownian-dynamics diffusion mdanalysis molecular-dynamics python rotation simulation
Last synced: 16 Jan 2026
https://github.com/bio-phys/asyncmd
asyncmd is a library to write concurrent code to run and analyze molecular dynamics simulations using pythons async/await syntax. Computationally costly operations can be performed locally or submitted to a queuing system.
enhanced-sampling molecular-dynamics molecular-dynamics-simulation slurm slurm-cluster
Last synced: 14 Jan 2026
https://github.com/bio-phys/cadishi
Cadishi: CAlculation of DIStance HIstograms
astrophysics capriqorn correlation cuda distance-histogram distribution function gpgpu gpu high-performance histogram molecular-dynamics openmp openmp-parallelization orthorhombic periodic-box python rdf triclinic vectorization
Last synced: 16 Jan 2026
https://github.com/bio-phys/cnt-martini
Generates Martini models for open carbon nanotubes to use with Gromacs.
Last synced: 16 Jan 2026
https://github.com/bio-phys/complexespp
Coarse-grained simulations of biomolecular complexes
Last synced: 16 Jan 2026
https://github.com/bio-phys/bioem
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.
Last synced: 16 Jan 2026
https://github.com/bio-phys/memdiff
Implementation of corrections for diffusion coefficients in membrane simulations.
diffusion-coefficient lipid-membranes membrane-simulations
Last synced: 16 Jan 2026
https://github.com/bio-phys/capriqorn
Capriqorn: CAlculation of P(R) and I(Q) Of macRomolecules in solutioN
dynamics molecular python saxs science simulations waxs
Last synced: 16 Jan 2026
https://github.com/bio-phys/hierarchical-chain-growth
Grow ensembles of disordered biomolecules from fragment libraries
Last synced: 16 Jan 2026
https://github.com/bio-phys/trimem
Monte Carlo sampling of the Helfrich bending energy.
Last synced: 16 Jan 2026
https://github.com/bio-phys/force-fields-for-metal-cations
Optimized force field parameters for metal cations (Li+, Na+, K+, Cs+, Mg2+, Ca2+, Sr2+, and Ba2+) in combination with the TIP3P water model for all-atom MD simulations.
Last synced: 16 Jan 2026
https://github.com/bio-phys/cnt-martini-analysis
Analysis tools for Martini simulations of a single carbon nanotube porin in a lipid membrane. Mostly also work for membrane proteins.
Last synced: 16 Jan 2026
https://github.com/bio-phys/kinetics-remd
Extracting kinetics from replica exchange molecular dynamics and related methods that produce discontinuous trajectories.
extracting-kinetics kinetics kinetics-remd md-simulations python remd-simulations science
Last synced: 16 Jan 2026
https://github.com/bio-phys/optimizedmgffs
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.
Last synced: 16 Jan 2026
https://github.com/bio-phys/magnesium-ffs
Optimized force field parameters for Magnesium in combination with the TIP3P water model for all-atom MD simulations.
Last synced: 16 Jan 2026
https://github.com/bio-phys/binless-wham
Binless weighted histogram analysis
Last synced: 16 Jan 2026
https://github.com/bio-phys/cnt-lipid14-analysis
Analysis tools for simulations of carbon nanotubes (CNTs) in lipid membranes modeled with the Lipid14 force field.
Last synced: 16 Jan 2026
https://github.com/bio-phys/forcespectroscopymle
Analyze rupture force spectra from single-molecule force spectroscopy experiments to extract disassociation rates and parameters characterizing the free-energy profile underlying the bond.
forcible-bond-rupture julia maximum-likelihood-estimation single-molecule-force-spectroscopy
Last synced: 16 Jan 2026
https://github.com/bio-phys/diffusionmle
Analyze experimental tracking data using a maximum likelihood estimator (MLE) to extract translational diffusion coefficients.
diffusion-coefficient expectation-maximization-algorithm julia maximum-likelihood-estimation
Last synced: 16 Jan 2026
https://github.com/bio-phys/hplusminus
Statistical tests to detect and quantify correlations in residuals when fitting models to one-dimensional data.
Last synced: 16 Jan 2026
https://github.com/bio-phys/af2_lir_screen
AlphaFold2 Multimer pipeline to identify candidate LIR motifs
Last synced: 16 Jan 2026
https://github.com/bio-phys/rebindingkineticsmle
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.
Last synced: 16 Jan 2026
https://github.com/bio-phys/rotmemdiff
Study on finite-size effects on rotational diffusion in membranes: simulation parameter files, results and analysis scripts.
Last synced: 16 Jan 2026
https://github.com/bio-phys/vanthofffitting
Nonlinear least squares fitting of van 't Hoff plots via cubic splines, which makes the extraction of heat capacity and thermodynamic potentials possible.
Last synced: 16 Jan 2026
https://github.com/bio-phys/nix-lir-binding-to-wipi2d
analysis-scripts md-simulations
Last synced: 16 Jan 2026
https://github.com/bio-phys/cnt-clusters
Simulation parameters and results for lipid-mediated self-assembly of CNT membranes.
Last synced: 16 Jan 2026
https://github.com/bio-phys/ff-mg-ca-nucleicacids
Extension for the interactions with DNA and RNA of our previously bulk-optimized force field parameters (https://doi.org/10.1063/1.5017694)
Last synced: 16 Jan 2026