OpenBioSim / biosimspace_tutorialsLinks
A tutorials suite for BioSimSpace.
☆34Updated 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.☆34Updated 2 years ago
- ☆25Updated 2 years ago
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆18Updated this week
- Free Parametrization for Small Molecules☆50Updated this week
- Computation of the drug-target relative residence times from RAMD simulations☆21Updated 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 8 months ago
- AI-augmented R-group exploration in medicinal chemistry☆20Updated last year
- Cryptic pocket prediction using AlphaFold 2☆24Updated 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
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆40Updated 2 years ago
- Tutorials on doing AMBER based Metadynamics and Gaussian Accelerated MD (GaMD)☆11Updated 2 months ago
- CReM-dock: generation of chemically reasonable molecules guided by molecular docking☆28Updated 2 weeks ago
- ☆31Updated last week
- Rapid construction of chemical pipelines in interactive notebooks and cli usage☆12Updated last year
- Tool to predict water molecules placement and energy in ligand binding sites☆35Updated 4 months ago
- A package to identify matched molecular pairs and use them to predict property changes.☆24Updated last year
- Entropy from PDB conformational ensembles☆13Updated last year
- ☆41Updated 3 weeks ago
- Contributed and additional nodes for maize☆20Updated 3 months ago
- Code and notebook for our paper "Assessing interaction recovery of predicted protein-ligand poses"☆19Updated last year
- Computational Chemistry Workflows☆56Updated 3 years ago
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆40Updated 2 years ago
- ☆13Updated 2 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 month
- EXPRORER: Rational cosolvents set construction method for cosolvent molecular dynamics (CMD) with large-scale computation☆11Updated 3 years ago
- COBY (Coarse Grained System Builder) can be used to create coarse-grained systems in Martini 3☆43Updated 2 months ago
- ☆13Updated last year