jhenin / SAFEP_tutorialLinks
A tutorial for Streamlined Alchemical Free Energy Perturbations with NAMD
☆12Updated 3 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:
- Input files and binding free energy values from our benchmark with QuantumBind-RBFE☆15Updated 3 months ago
- MSMD (mixed-solvent molecular dynamics) engine and analysis tools☆19Updated 3 months ago
- Multiscale Simulation Tool for Backmapping☆17Updated last week
- CReM-dock: generation of chemically reasonable molecules guided by molecular docking☆25Updated last month
- SubPEx (Sub-Pocket Explorer) is a tool to enhance ensemble (multiple-receptor/relaxed-complex) virtual screening. It uses weighted ensemb…☆16Updated 2 weeks ago
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆17Updated 2 weeks ago
- A repository of the analysis and simulation tools for biomolecular modeling, simulations and drug discovery☆12Updated 4 months ago
- Implementation of the Paper "iScore: A ML-Based Scoring Function for de novo Drug Discovery" by S.J. Mahdizadeh, and L.A. Eriksson (https…☆16Updated last year
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- ☆21Updated 5 months ago
- ☆18Updated 3 years ago
- To run metadynamics simulations using openMM (based on Peter Eastman's script)☆13Updated 6 years ago
- ☆12Updated 2 years ago
- Cryptic pocket prediction using AlphaFold 2☆23Updated 2 years ago
- Weighted Ensemble Data Analysis and Plotting☆24Updated 3 weeks ago
- ☆11Updated last year
- A tutorials suite for BioSimSpace.☆25Updated 2 months ago
- ☆17Updated last month
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated last week
- ☆25Updated last year
- Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.☆14Updated last year
- Deep Learning-based Bioisosteric Replacements for Optimization of Multiple Molecular Properties☆18Updated 2 weeks ago
- ☆9Updated 4 years ago
- Code and notebook for our paper "Assessing interaction recovery of predicted protein-ligand poses"☆18Updated 9 months ago
- ☆16Updated last year
- SIEVE-Score: interaction energy-based virtual screening method based on random forest.☆15Updated last year
- ☆12Updated last year
- Tools to build coarse grained models and perform simulations with OpenMM☆24Updated 2 years ago
- Simulation-Enabled Estimation of Kinetic Rates - Version 2☆29Updated 4 months ago
- ☆27Updated last year