LQCT / MDScanLinks
An efficient approach to RMSD-Based HDBSCAN Clustering of long Molecular Dynamics
☆17Updated 3 years ago
Alternatives and similar repositories for MDScan
Users that are interested in MDScan are comparing it to the libraries listed below
Sorting:
- A tutorials suite for BioSimSpace.☆34Updated 3 months ago
- ☆32Updated 2 years ago
- ☆31Updated last week
- Free Parametrization for Small Molecules☆50Updated 3 months ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆40Updated 2 years ago
- Computation of the drug-target relative residence times from RAMD simulations☆21Updated last year
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆31Updated 4 years ago
- ☆15Updated 3 weeks ago
- ☆29Updated 9 months 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 last year
- A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)☆10Updated 4 years ago
- Temperature generator for Replica Exchange MD simulations☆30Updated 3 years ago
- Analysis framework of dissipation-corrected targeted molecular dynamics (dcTMD) simulations.☆16Updated last month
- COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3☆43Updated 2 months ago
- ☆43Updated last year
- Tools to build coarse grained models and perform simulations with OpenMM☆25Updated 3 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.☆60Updated last month
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆18Updated this week
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆34Updated 2 years 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 8 months ago
- ☆36Updated last year
- Useful Collective Variables for OpenMM☆17Updated last year
- Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation te…☆19Updated 3 years ago
- ☆34Updated last year
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆31Updated 2 years ago
- Cryptic pocket prediction using AlphaFold 2☆24Updated 3 years ago
- Random Acceleration Molecular Dynamics in GROMACS☆43Updated last year
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆40Updated 2 years ago
- Set up relative free energy calculations using a common scaffold☆24Updated 5 months ago
- Python code for generating Boresch restraints from MD simulations☆22Updated 3 months ago