biophysics
There are 210 repositories under biophysics topic.
OpenFreeEnergy/openfe
The Open Free Energy toolkit
Electrostatics/pdb2pqr
PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
Electrostatics/apbs-pdb2pqr
APBS - software for biomolecular electrostatics and solvation
drorlab/pensa
PENSA - a collection of python methods for exploratory analysis and comparison of biomolecular conformational ensembles.
Electrostatics/apbs
Software for biomolecular electrostatics and solvation calculations
jaxleyverse/jaxley
Differentiable neuron simulations with biophysical detail on CPU, GPU, or TPU.
graik/biskit
A Python platform for Structural Bioinformatics
maxscheurer/pycontact
Analysis of non-covalent interactions in MD trajectories
RI-imaging/ODTbrain
Python library for diffraction tomography with the Born and Rytov approximations
bowman-lab/enspara
Modeling molecular ensembles with scalable data structures and parallel computing
Electrostatics/electrostatics.github.io
APBS & PDB2PQR - software for biomolecular electrostatics and solvation
weria-pezeshkian/FreeDTS
a package to simulate fluid surfaces and biomembranes
osita-sunday-nnyigide/Pras_Server
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
kamerlinlab/KIF
KIF - Key Interactions Finder. A python package to identify the key molecular interactions that regulate any conformational change.
cbsteh/PySawit
Oil Palm Growth and Yield Model
pylattice/pyLattice
A python library for advanced lattice light-sheet image analysis
martavarela/EP-PINNs
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.
moldyn/Clustering
Robust and stable clustering of molecular dynamics simulation trajectories.
flatironinstitute/aLENS
a Living ENsemble Simulator -- a lens to help you watch biophysics
DeepDriveMD/DeepDriveMD-pipeline
DeepDriveMD: Deep-Learning Driven Adaptive Molecular Simulations
JoaoRodrigues/openmm_scripts
Collection of Python scripts to setup and run simulations with OpenMM
HussainAther/biology
genomics, biochemistry, biotechnology, cell biology, biophysics, ecology
SlicerCBM/SlicerCBM
Computational Biophysics for Medicine in 3D Slicer
KULL-Centre/DEERpredict
Software for the prediction of DEER and PRE data from conformational ensembles.
simonguld/CellSegmentationTracker
A Python module intended to make cell segmentation, tracking and subsequent (mostly biophysical) statisticial analysis easy
alihashmiii/3D-Vertex-Model
vertex model implementation to simulate biological tissue in 3D
ctboughter/AIMS
AIMS - Automated Immune Molecule Separator: An analysis pipeline for distinguishing distinct subsets of Ig and MHC molecules. See below site for documentation
andim/evolimmune
Source code accompanying the paper "Diversity of immune strategies explained by adaptation to pathogen statistics"
christophmark/jointforces
A Python package to conduct 3D Traction Force Microscopy on multicellular aggregates (spheroids).
DavidEilenstein/ImageD
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
Nico-Curti/SysDyn
System Dynamics script utilities
RI-imaging/nrefocus
python library for numerical focusing (refocusing, autofocusing) of complex wave fields
alihashmiii/2D-vertex-model
vertex model for simulating two-dimensional epithelial tissues
Chaste/ApPredict
Cardiac Action Potential Prediction (ApPredict) under drug-induced block of ion channels. This is a Chaste extension/bolt-on project.
naotohori/vmd-scripts
VMD scripts
Sarah-Hesham-2022/BioPhysics-Molecular-Dynamics-Simulation
Using VMD and NAMD for molecular dynamics simulation of protein PDB files.