delemottelab / allosteric-pathwaysLinks
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
Sorting:
- Utilities to assist with Amber Molecular Dynamics structure preparation and MMPBSA.py energy methods☆19Updated 6 years ago
- KIF - Key Interactions Finder. A python package to identify the key molecular interactions that regulate any conformational change.☆32Updated last week
- Cryptic pocket prediction using AlphaFold 2☆24Updated 3 years ago
- A repository of the analysis and simulation tools for biomolecular modeling, simulations and drug discovery☆13Updated 10 months ago
- MSMD (mixed-solvent molecular dynamics) engine and analysis tools☆19Updated 9 months ago
- ☆32Updated 2 years ago
- Rapid Generation of Rare Event Pathways Using Direction Guided Adaptive Sampling: From Ligand Unbinding to Protein (Un)Folding☆38Updated last month
- ☆18Updated 4 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 …☆28Updated 5 months ago
- Weighted Ensemble Data Analysis and Plotting☆25Updated last month
- Input files for GROMACS tutorials written for the Journal of Physical Chemistry B☆24Updated last year
- ☆13Updated 2 years ago
- Binding pocket optimization based on force fields and docking scoring functions☆37Updated 10 months ago
- Analysis of non-covalent interactions in MD trajectories☆65Updated last year
- ☆21Updated last year
- A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)☆10Updated 3 years ago
- Collection of Python scripts to setup and run simulations with OpenMM☆17Updated 5 years ago
- Free Parametrization for Small Molecules☆50Updated 3 months ago
- This script makes a cyclic peptide or cyclic nucleotide topology file for GROMACS out of (specially prepared) linear molecule topology fi…☆14Updated 5 years ago
- Pocket to Concavity is a tool for refinement of Protein-Ligand binding site shape from alpha-spheres☆16Updated last year
- ☆28Updated 8 months ago
- MD pharmacophores and virtual screening☆34Updated 2 years ago
- Cloud-based Drug Binding Structure Prediction☆46Updated 2 months ago
- A tutorials suite for BioSimSpace.☆33Updated 2 months ago
- Repo for the publication titled: "Key Interaction Networks: Identifying Evolutionarily Conserved Non-Covalent Interaction Networks Across…☆18Updated 2 years ago
- MDPath - A tool for calculating allosteric communication pathways in proteins by analyzing the mutual information of residue dihedral ang…☆26Updated 2 months ago
- Tools to build coarse grained models and perform simulations with OpenMM☆25Updated 3 years ago
- Boltzmann-ranked alternative protein conformations from reduced-MSA AlphaFold2☆60Updated last month
- The Guest HOst Affinity Tool (GHOAT.py) is a fully automated tool for absolute binding free energy calculations on guest-host systems.☆21Updated 8 months ago
- pyCHARMM tutorial, documentation and examples. This repository contains materials originally from the pyCHARMM Workshop run at the Univer…☆72Updated this week