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:
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- ☆25Updated last year
- 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
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated last week
- 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
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆17Updated last month
- Computation of the drug-target relative residence times from RAMD simulations☆16Updated 11 months ago
- AI-augmented R-group exploration in medicinal chemistry☆18Updated 11 months ago
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆30Updated 3 years ago
- Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.☆15Updated 2 years ago
- The Guest HOst Affinity Tool (GHOAT.py) is a fully automated tool for absolute binding free energy calculations on guest-host systems.☆19Updated 3 months ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆39Updated 2 years ago
- A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)☆11Updated 3 years ago
- ☆28Updated last year
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆37Updated 2 years ago
- CReM-dock: generation of chemically reasonable molecules guided by molecular docking☆26Updated 2 months ago
- Code and notebook for our paper "Assessing interaction recovery of predicted protein-ligand poses"☆18Updated 10 months ago
- Cryptic pocket prediction using AlphaFold 2☆24Updated 2 years ago
- A package to identify matched molecular pairs and use them to predict property changes.☆24Updated last year
- ☆28Updated 3 months ago
- Machine Learning model for molecular micro-pKa prediction☆42Updated 10 months ago
- Contributed and additional nodes for maize☆16Updated 4 months ago
- ☆34Updated last year
- ☆31Updated last year
- CosolvKit is a versatile tool for cosolvent MD preparation and analysis☆25Updated 3 months ago
- EXPRORER: Rational cosolvents set construction method for cosolvent molecular dynamics (CMD) with large-scale computation☆11Updated 3 years ago
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆30Updated last year
- Different run and analysis scripts as described in the research guides.☆13Updated 3 years ago
- ☆29Updated 2 weeks ago
- ☆16Updated 6 months ago