jhenin / SAFEP_tutorialLinks
A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD
☆15Updated 10 months ago
Alternatives and similar repositories for SAFEP_tutorial
Users that are interested in SAFEP_tutorial are comparing it to the libraries listed below
Sorting:
- MSMD (mixed-solvent molecular dynamics) engine and analysis tools☆19Updated 10 months ago
- Multiscale Simulation Tool for Backmapping☆22Updated this week
- Free Parametrization for Small Molecules☆50Updated this week
- ☆27Updated 11 months ago
- Input files and binding free energy values from our benchmark with QuantumBind-RBFE☆16Updated 9 months ago
- ☆13Updated last year
- CReM-dock: generation of chemically reasonable molecules guided by molecular docking☆28Updated 2 weeks ago
- Weighted Ensemble Data Analysis and Plotting☆25Updated last month
- Implementation of the Paper "iScore: A ML-Based Scoring Function for de novo Drug Discovery" by S.J. Mahdizadeh, and L.A. Eriksson (https…☆17Updated last year
- ☆13Updated 2 years ago
- Consensus pharmacophore for Drug Design☆14Updated 5 months ago
- A tutorials suite for BioSimSpace.☆34Updated 3 months ago
- A repository of the analysis and simulation tools for biomolecular modeling, simulations and drug discovery☆13Updated 11 months ago
- Cryptic pocket prediction using AlphaFold 2☆24Updated 3 years ago
- ☆18Updated 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 month
- WaterDock-2.0 implementation with Akshay Sridhar☆21Updated 2 years ago
- A versatile workflow for the generation of receptor-based pharmacophore models for virtual screening☆31Updated 8 months ago
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆18Updated this week
- AI-augmented R-group exploration in medicinal chemistry☆20Updated last year
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆34Updated 2 years ago
- ML-guided visual inspection for molecular docking☆21Updated 8 months ago
- ☆12Updated last year
- Scaffold decoration and fragment linking with chemical language models and RL☆26Updated 10 months ago
- ☆13Updated last year
- Code and notebook for our paper "Assessing interaction recovery of predicted protein-ligand poses"☆19Updated last year
- PairMap: An Intermediate Insertion Approach for Improving the Accuracy of Relative Free Energy Perturbation Calculations for Distant Comp…☆16Updated 3 months ago
- example demonstrating a free energy estimation starting from OFF and OpenMM☆12Updated 5 years ago
- Deep Learning-based Bioisosteric Replacements for Optimization of Multiple Molecular Properties☆27Updated 2 months ago
- ☆17Updated last year