There are 15 repositories under biophysics topic.
APBS - software for biomolecular electrostatics and solvation
PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
The Open Free Energy toolkit
Software for biomolecular electrostatics and solvation calculations
Analysis of non-covalent interactions in MD trajectories
Python library for diffraction tomography with the Born and Rytov approximations
Modeling molecular ensembles with scalable data structures and parallel computing
APBS & PDB2PQR - software for biomolecular electrostatics and solvation
KIF - Key Interactions Finder. A python package to identify the key molecular interactions that regulate any conformational change.
Pras Server is a library to repair PDB or mmCIF structures, add missing heavy atoms and hydrogen atoms and assign secondary structure by amide-amide interactions of the backbone
a Living ENsemble Simulator -- a lens to help you watch biophysics
a package to simulate biomembranes at mesoscale
Robust and stable clustering of molecular dynamics simulation trajectories.
DeepDriveMD: Deep-Learning Driven Adaptive Molecular Simulations
genomics, biochemistry, biotechnology, cell biology, biophysics, ecology
Collection of Python scripts to setup and run simulations with OpenMM
EP-PINNs implementation for 1D and 2D forward and inverse solvers for the Aliev-Panfilov cardiac electrophysiology model. Also includes Matlab finite-differences solver for data generation.
vertex model implementation to simulate biological tissue in 3D
AIMS - Automated Immune Molecule Separator: An analysis pipeline for distinguishing distinct subsets of Ig and MHC molecules. See below site for documentation
Source code accompanying the paper "Diversity of immune strategies explained by adaptation to pathogen statistics"
ImageD is an image processing software designed for rapid prototyping and implementing algorithms and solutions for science, research and teaching. For more information see: https://davideilenstein.github.io/ImageD/index.html
Software for the prediction of DEER and PRE data from conformational ensembles.
A Python package to conduct 3D Traction Force Microscopy on multicellular aggregates (spheroids).
Evaluates the fiber orientation and intensity around cells that compact collagen tissue as measure of contractile strength.
A CTF Simulation Web App
System Dynamics script utilities
python library for numerical focusing (refocusing, autofocusing) of complex wave fields
Manuscript repository for our research paper, including reproducibility packages for all results, and latex source files.
Introductory Git Repository for the Biophysics Research Group at BYU
A Python module intended to make cell segmentation, tracking and subsequent (mostly biophysical) statisticial analysis easy