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:
- ☆31Updated 2 years ago
- A tutorials suite for BioSimSpace.☆31Updated last month
- Cryptic pocket prediction using AlphaFold 2☆24Updated 3 years ago
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆18Updated 2 months ago
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆30Updated 3 years ago
- Tools to build coarse grained models and perform simulations with OpenMM☆24Updated 2 years ago
- Free Parametrization for Small Molecules☆49Updated last month
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆57Updated 8 months ago
- COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3☆42Updated last week
- ☆14Updated 11 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
- Several QM/MM tutorials for biological simulations adapted to CP2K. Tutorials adapted from AMBER, GMX, NAMD and CPMD softwares.☆22Updated 6 years ago
- A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)☆10Updated 3 years ago
- ☆34Updated last year
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆33Updated last year
- ☆25Updated last year
- ☆39Updated last year
- An OpenMM plugin that implements the Alchemical Transfer Potential☆39Updated 2 years ago
- Tool to predict water molecules placement and energy in ligand binding sites☆34Updated 2 months ago
- Random Acceleration Molecular Dynamics in GROMACS☆40Updated last year
- ☆28Updated 7 months ago
- Multiscale Simulation Tool for Backmapping☆21Updated 2 months ago
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆88Updated 4 months ago
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆31Updated 2 years ago
- Deep Boosted Molecular Dynamics☆13Updated last year
- Analysis of non-covalent interactions in MD trajectories☆65Updated 11 months ago
- CReM-dock: generation of chemically reasonable molecules guided by molecular docking☆28Updated 3 months ago
- Temperature generator for Replica Exchange MD simulations☆29Updated 2 years ago
- Standalone charge assignment from Espaloma framework.☆44Updated last month
- 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