PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
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Updated
Mar 18, 2024 - Python
PDB2PQR - determining titration states, adding missing atoms, and assigning charges/radii to biomolecules.
The Open Free Energy toolkit
PENSA - a collection of python methods for exploratory analysis and comparison of biomolecular conformational ensembles.
A Python platform for Structural Bioinformatics
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
Oil Palm Growth and Yield Model
DeepDriveMD: Deep-Learning Driven Adaptive Molecular Simulations
Collection of Python scripts to setup and run simulations with OpenMM
genomics, biochemistry, biotechnology, cell biology, biophysics, ecology
Computational Biophysics for Medicine in 3D Slicer
python library for numerical focusing (refocusing, autofocusing) of complex wave fields
A CTF Simulation Web App
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.
Yet another version of PDBx/mmCIF Python implementation
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