MDPath - A tool for calculating allosteric communication pathways in proteins by analyzing the mutual information of residue dihedral angle movements throughout an MD simulation.
☆28Feb 22, 2026Updated last week
Alternatives and similar repositories for mdpath
Users that are interested in mdpath are comparing it to the libraries listed below
Sorting:
- A tool for 2D protein visualization aimed at improving the comparability of protein structures through standardized 2D visualizations.☆21Jul 31, 2025Updated 7 months ago
- ☆46Nov 19, 2025Updated 3 months ago
- code for SeqDance/ESMDance, biophysics-informed protein language models☆54Jan 28, 2026Updated last month
- Interface to OpenMM for easy setup of molecular dynamic simulations of protein-ligand complexes☆164Feb 1, 2026Updated 3 weeks ago
- Protein representation and design under a single training scheme☆24Updated this week
- ☆21Jan 1, 2026Updated last month
- DyNoPy☆11Sep 5, 2024Updated last year
- Free Parametrization for Small Molecules☆50Feb 18, 2026Updated last week
- MDANCE: O(N) clustering for molecular dynamics. Process 1.5M frames in 40min. 8 specialized algorithms.☆106Feb 17, 2026Updated last week
- QM/MM Study Group☆15Jan 22, 2019Updated 7 years ago
- Simulation-Enabled Estimation of Kinetic Rates - Version 2☆35Dec 10, 2025Updated 2 months ago
- EvolveX, a de novo antibody computational design pipeline.☆22Sep 18, 2025Updated 5 months ago
- code and source data for de novo design of Kemp elimination paper☆24Sep 18, 2025Updated 5 months ago
- Utility scripts to generate and evaluate parametrically guided beta barrel protein backbone structures.☆14Nov 14, 2025Updated 3 months ago
- Input files and binding free energy values from our benchmark with QuantumBind-RBFE☆16Apr 16, 2025Updated 10 months ago
- A collection of tutorials for the python implementation of Dynamical Network Analysis☆15Aug 6, 2025Updated 6 months ago
- Computation of the drug-target relative residence times from RAMD simulations☆21Aug 29, 2024Updated last year
- ☆20Aug 25, 2025Updated 6 months ago
- Building and analyzing residue interaction networks with cofactors (includes tutorial).☆18Mar 31, 2021Updated 4 years ago
- A Python library for constructing polymer topologies and coordinates☆18Sep 23, 2025Updated 5 months ago
- ☆14Jul 5, 2022Updated 3 years ago
- ☆37Aug 28, 2023Updated 2 years ago
- Official implementation of RuSH (Scaffold Hopping with Generative Reinforcement Learning). Includes ScaffoldFinder algorithm for 2D decor…☆20Feb 20, 2025Updated last year
- Visualization tool for changing networks☆20May 11, 2018Updated 7 years ago
- Fast, gene-specific joint humanisation of antibody heavy and light chains.☆18Nov 11, 2025Updated 3 months ago
- EnzyHTP is a python library that automates the complete life-cycle of enzyme modeling☆31Feb 12, 2026Updated 2 weeks ago
- STARLING - conSTruction of intrinsicAlly disoRdered proteins ensembles efficientLy vIa multi-dimeNsional Generative models☆38Dec 23, 2025Updated 2 months ago
- The gmx_rrcs script is designed to calculate the residues-residues contact scores (rrcs) from a trajectory file generated by GROMACS.☆18Jun 16, 2025Updated 8 months ago
- ☆70Feb 13, 2026Updated 2 weeks ago
- GRACE: Generative Renaissance in Artificial Computational Enzyme Design☆19Jan 8, 2025Updated last year
- A Tutorial for quasi Markov State Model(qMSM) developed by Huang Group, Dept of Chemistry at UW-Madison☆19Jun 6, 2023Updated 2 years ago
- A pipeline that used ML model based on Rosetta descriptors to predict the binding affinity of protein-protein complexes☆51Oct 27, 2025Updated 4 months ago
- protein conformational spaces meet machine learning☆50Updated this week
- ☆22Updated this week
- Official open-source of Accurate structure prediction of immune proteins using parameter-efficient transfer learning☆23Mar 19, 2025Updated 11 months ago
- ChemSpaceAL: An Efficient Active Learning Methodology Applied to Protein-Specific Molecular Generation☆16Dec 14, 2023Updated 2 years ago
- Code for AlphaFold Distillation for Protein Design☆25Sep 18, 2025Updated 5 months ago
- High level API for using machine learning models in OpenMM simulations☆149Feb 20, 2026Updated last week
- Learning the language of protein-protein interactions☆135Jan 12, 2026Updated last month