MobleyLab / Lomap
Alchemical mutation scoring map
☆37Updated 2 years ago
Related projects ⓘ
Alternatives and complementary repositories for Lomap
- A tool for setting up free energy simulations.☆34Updated 2 years ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆37Updated 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…☆30Updated 9 months ago
- ☆41Updated 2 years ago
- Set up relative free energy calculations using a common scaffold☆22Updated 3 months ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated 11 months ago
- A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism☆55Updated 9 months ago
- Applications of nonequilibrium candidate Monte Carlo (NCMC) to ligand binding mode sampling☆33Updated 2 years ago
- Alchemical mutation scoring map☆33Updated 4 months ago
- ☆27Updated 5 months ago
- ☆25Updated 10 months ago
- Gaussian Accelerated Molecular Dynamics (GaMD) is a computational method for both unconstrained enhanced sampling and free energy calcula…☆70Updated 5 months ago
- ☆29Updated last month
- Benchmark sets for binding free energy calculations: Perpetual review paper, discussion, datasets, and standards☆42Updated 3 years ago
- Tutorials of few enhanced sampling methods along with bash script to run the method in a single shot..☆41Updated 3 years ago
- ☆53Updated last year
- Toolkit for free-energy calculation setup/analysis and biomolecular structure handling☆57Updated 3 years ago
- ☆47Updated 4 months ago
- Solvation Structure and Thermodynamic Mapping☆38Updated 7 months ago
- Tool to predict water molecules placement and energy in ligand binding sites☆27Updated 4 months ago
- ☆71Updated last year
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆34Updated last year
- Full automation of relative protein-ligand binding free energy calculations in GROMACS☆43Updated 3 years ago
- Random Acceleration Molecular Dynamics in GROMACS☆32Updated 4 months ago
- Analysis of non-covalent interactions in MD trajectories☆51Updated last year
- The public versio☆36Updated last year
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆30Updated last year
- Materials for 2023 workshop at CCPBioSim Training Week https://www.ccpbiosim.ac.uk/events/upcoming-events/eventdetail/104/-/training-week☆30Updated last year
- Python code for generating Boresch restraints from MD simulations☆18Updated 2 years ago
- Exploratory work on free energy calculations with GROMACS using "separated topologies" approach (Rocklin et al., 2013).☆22Updated this week