MobleyLab / alchemical-setup
☆15Updated 7 years ago
Related projects ⓘ
Alternatives and complementary repositories for alchemical-setup
- This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration fr…☆30Updated 9 months ago
- ☆25Updated 10 months ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated 11 months ago
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆22Updated this week
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆34Updated last year
- Set up relative free energy calculations using a common scaffold☆22Updated 3 months ago
- EXPRORER: Rational cosolvents set construction method for cosolvent molecular dynamics (CMD) with large-scale computation☆10Updated 2 years ago
- Implementation of Shape and Electrostatic similarity metric in deepFMPO.☆43Updated 2 years ago
- ☆26Updated last month
- Python code for generating Boresch restraints from MD simulations☆18Updated 2 years ago
- ☆41Updated 2 years ago
- ☆27Updated 5 months ago
- Tool to predict water molecules placement and energy in ligand binding sites☆27Updated 4 months ago
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆43Updated 2 weeks ago
- Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.☆13Updated last year
- Restraintmaker is a tool intended to build Position or Distance restraints for Molecular Dynamics simulations (or any other simulation te…☆17Updated 2 years ago
- A package to identify matched molecular pairs and use them to predict property changes.☆24Updated 6 months ago
- ☆44Updated 4 years ago
- Different run and analysis scripts as described in the research guides.☆10Updated 2 years ago
- Full automation of relative protein-ligand binding free energy calculations in GROMACS☆43Updated 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
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆15Updated 2 weeks ago
- ☆26Updated 10 months ago
- A tutorials suite for BioSimSpace.☆16Updated this week
- An OpenMM plugin that implements the Alchemical Transfer Potential☆37Updated last year
- ☆17Updated 9 months ago
- This package contains tools for setting up hybrid-topology FE calculations☆25Updated this week
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆27Updated 2 years ago
- Cryptic pocket prediction using AlphaFold 2☆22Updated last year