wolberlab / mdpathLinks
MDPath - A tool for calculating allosteric communication pathways in proteins by analyzing the mutual information of residue dihedral angle movements throughout an MD simulation.
☆26Updated 2 months ago
Alternatives and similar repositories for mdpath
Users that are interested in mdpath are comparing it to the libraries listed below
Sorting:
- 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
- ☆70Updated last year
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆18Updated last week
- Fully automated high-throughput MD pipeline☆88Updated this week
- Simulation-Enabled Estimation of Kinetic Rates - Version 2☆34Updated last month
- Boltzmann-ranked alternative protein conformations from reduced-MSA AlphaFold2☆60Updated this week
- ☆69Updated 2 years ago
- Free Parametrization for Small Molecules☆50Updated 3 months ago
- FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery☆80Updated last year
- CosolvKit is a versatile tool for cosolvent MD preparation and analysis☆28Updated 3 months ago
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆60Updated last month
- ☆15Updated 2 weeks ago
- Random Acceleration Molecular Dynamics in GROMACS☆43Updated last year
- A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)☆10Updated 4 years ago
- A tutorials suite for BioSimSpace.☆34Updated 3 months ago
- ☆40Updated last year
- Cryptic pocket prediction using AlphaFold 2☆24Updated 3 years ago
- Automated molecular dynamics simulations workflow for high-throughput assessment of protein-ligand dynamics☆19Updated last year
- ☆34Updated last year
- Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen☆72Updated 2 years ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆34Updated 2 years ago
- ☆25Updated 2 years ago
- Entropy from PDB conformational ensembles☆13Updated last year
- protein structure prediction with precision☆26Updated last year
- 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
- ☆32Updated 2 years ago
- ☆22Updated 9 months ago
- ☆29Updated 8 months ago
- Python code to run Thermal Titration Molecular Dynamics (TTMD) simulations☆20Updated last year
- Workflow to clean up and fix structural problems in protein-ligand binding datasets☆68Updated 2 months ago