OpenBioSim / biosimspace_tutorialsLinks
A tutorials suite for BioSimSpace.
☆25Updated 3 months ago
Alternatives and similar repositories for biosimspace_tutorials
Users that are interested in biosimspace_tutorials are comparing it to the libraries listed below
Sorting:
- ☆25Updated last year
- 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 2 months ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- Different run and analysis scripts as described in the research guides.☆13Updated 3 years ago
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated last week
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆50Updated 4 months ago
- ☆29Updated this week
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆17Updated last month
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆39Updated 2 years ago
- Alchemical mutation scoring map☆39Updated 4 months ago
- AI-augmented R-group exploration in medicinal chemistry☆17Updated 10 months ago
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆30Updated 3 years ago
- ☆16Updated last year
- The Guest HOst Affinity Tool (GHOAT.py) is a fully automated tool for absolute binding free energy calculations on guest-host systems.☆19Updated 2 months ago
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆37Updated last year
- Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation te…☆19Updated 2 years ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆40Updated 2 years ago
- ☆67Updated 2 years ago
- Cryptic pocket prediction using AlphaFold 2☆24Updated 2 years ago
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆48Updated 4 years ago
- Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.☆15Updated last year
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆27Updated 8 months ago
- A package to identify matched molecular pairs and use them to predict property changes.☆24Updated last year
- This package contains tools for setting up hybrid-topology FE calculations☆29Updated last month
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆30Updated last year
- Temperature generator for Replica Exchange MD simulations☆28Updated 2 years ago
- Machine Learning model for molecular micro-pKa prediction☆43Updated 10 months ago
- Examples of applications of pymbar to various problems in simulation and experiment☆22Updated 10 years ago
- ☆32Updated last year
- 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