delemottelab / allosteric-pathways
Building and analyzing residue interaction networks with cofactors (includes tutorial).
☆17Updated 4 years ago
Alternatives and similar repositories for allosteric-pathways:
Users that are interested in allosteric-pathways are comparing it to the libraries listed below
- KIF - Key Interactions Finder. A python package to identify the key molecular interactions that regulate any conformational change.☆29Updated 11 months ago
- Repo for the publication titled: "Key Interaction Networks: Identifying Evolutionarily Conserved Non-Covalent Interaction Networks Across…☆17Updated last year
- Cryptic pocket prediction using AlphaFold 2☆22Updated 2 years ago
- development repository for PyInteraph2☆22Updated last month
- Input files for GROMACS tutorials written for the Journal of Physical Chemistry B☆19Updated 9 months ago
- Pocket to Concavity is a tool for refinement of Protein-Ligand binding site shape from alpha-spheres☆16Updated 7 months ago
- Weighted Ensemble Data Analysis and Plotting☆24Updated 7 months ago
- ☆28Updated last year
- MSMD (mixed-solvent molecular dynamics) engine and analysis tools☆18Updated last month
- Utilities to assist with Amber Molecular Dynamics structure preparation and MMPBSA.py energy methods☆20Updated 5 years ago
- We provide a set of scripts to calculate native contacts from a MD. Native contacts are determined according to the overlap and rCSU appr…☆16Updated 10 months ago
- Cloud-based Drug Binding Structure Prediction☆37Updated last month
- example demonstrating a free energy estimation starting from OFF and OpenMM☆11Updated 4 years ago
- A repository of the analysis and simulation tools for biomolecular modeling, simulations and drug discovery☆12Updated 2 months ago
- ☆18Updated 3 years ago
- Tools to build coarse grained models and perform simulations with OpenMM☆23Updated 2 years ago
- Pras Server is a library to repair PDB or mmCIF structures, add missing heavy atoms and hydrogen atoms and assign secondary structure by …☆27Updated 10 months ago
- A collections of scripts for working molecular dynamics simulations☆43Updated 11 months ago
- The OpenMM Cookbook and Tutorials☆43Updated last year
- Collection of Python scripts to setup and run simulations with OpenMM☆17Updated 4 years ago
- Fully automated high-throughput MD pipeline☆60Updated this week
- Boltzmann-ranked alternative protein conformations from reduced-MSA AlphaFold2☆46Updated 2 weeks ago
- ☆14Updated 2 months ago
- MMTSB Tool Set☆31Updated 6 months ago
- Scores for Hydrophobicity and Charges based on SASAs☆31Updated last month
- Protocols and tools to run (automated) atomistic simulations of enzyme-ligand systems☆19Updated 3 years ago
- Code to accompany "Practical Cheminformatics With Open Source Software"☆16Updated 3 years ago
- ☆21Updated 2 months ago
- A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)☆10Updated 3 years ago
- Clustering of SES virtual probes for pocket generation and ranking via Isolation Forest☆12Updated 2 years ago