mqcomplab / PRIMELinks
protein structure prediction with precision
☆26Updated last year
Alternatives and similar repositories for PRIME
Users that are interested in PRIME are comparing it to the libraries listed below
Sorting:
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆33Updated 2 years ago
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆58Updated 8 months ago
- The Guest HOst Affinity Tool (GHOAT.py) is a fully automated tool for absolute binding free energy calculations on guest-host systems.☆21Updated 6 months ago
- This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration fr…☆32Updated 6 months ago
- Python code for generating Boresch restraints from MD simulations☆22Updated 2 months ago
- ☆68Updated 2 years ago
- Computational Chemistry Workflows☆56Updated 3 years ago
- CosolvKit is a versatile tool for cosolvent MD preparation and analysis☆27Updated last month
- Fully automated high-throughput MD pipeline☆85Updated 3 months ago
- ☆25Updated last year
- Cryptic pocket prediction using AlphaFold 2☆24Updated 3 years ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆39Updated 2 years ago
- Free Parametrization for Small Molecules☆49Updated 2 months ago
- A tutorials suite for BioSimSpace.☆31Updated last month
- A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)☆10Updated 3 years ago
- Tool to predict water molecules placement and energy in ligand binding sites☆34Updated 2 months ago
- Pocket dynamics analysis tool☆16Updated 7 months ago
- ☆35Updated last year
- Workflow to clean up and fix structural problems in protein-ligand binding datasets☆60Updated last month
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆39Updated 2 years ago
- FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery☆77Updated 11 months ago
- Tutorial on the setup and simulation of a membrane protein with AMBER Lipid21 and PACKMOL-Memgen☆70Updated 2 years ago
- MDPath - A tool for calculating allosteric communication pathways in proteins by analyzing the mutual information of residue dihedral ang…☆26Updated last month
- ☆28Updated 7 months ago
- EXPRORER: Rational cosolvents set construction method for cosolvent molecular dynamics (CMD) with large-scale computation☆11Updated 3 years ago
- Full automation of relative protein-ligand binding free energy calculations in GROMACS☆46Updated 4 years ago
- Automated molecular dynamics simulations workflow for high-throughput assessment of protein-ligand dynamics☆19Updated last year
- Random Acceleration Molecular Dynamics in GROMACS☆40Updated last year
- ☆52Updated 7 months ago
- The public versio☆73Updated 2 years ago