UCL-CCS / TIES_MDLinks
Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.
☆32Updated last year
Alternatives and similar repositories for TIES_MD
Users that are interested in TIES_MD are comparing it to the libraries listed below
Sorting:
- ☆25Updated last year
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated last week
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆50Updated 3 months ago
- This pipeline is executing a RE-EDS run for relative free energy calculations. It can be used for example for calculation of hydration fr…☆31Updated last month
- A tutorials suite for BioSimSpace.☆25Updated 2 months ago
- A Deep Neural Network to predict small molecule torsion energy profiles with the accuracy of QM☆39Updated 2 years ago
- Set of tools for input preparation for conserved water search from MD trajectories (gromacs, amber) and their analysis☆17Updated 2 weeks ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆40Updated 2 years ago
- ☆15Updated 8 years ago
- A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)☆10Updated 3 years ago
- EXPRORER: Rational cosolvents set construction method for cosolvent molecular dynamics (CMD) with large-scale computation☆11Updated 2 years ago
- ☆28Updated 2 months ago
- Full automation of relative protein-ligand binding free energy calculations in GROMACS☆44Updated 4 years ago
- Computation of the drug-target relative residence times from RAMD simulations☆16Updated 10 months ago
- Computational Chemistry Workflows☆53Updated 2 years ago
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆37Updated last year
- FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery☆67Updated 6 months ago
- Funnel maker is a set of scripts that sets up funnel metadynamics simulations for protein-ligand binding with PLUMED and OpenMM.☆14Updated last year
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆30Updated 3 years ago
- ☆16Updated last year
- 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
- ☆27Updated last year
- The Guest HOst Affinity Tool (GHOAT.py) is a fully automated tool for absolute binding free energy calculations on guest-host systems.☆18Updated 2 months ago
- Implementation of Shape and Electrostatic similarity metric in deepFMPO.☆44Updated 3 years ago
- Machine Learning model for molecular micro-pKa prediction☆42Updated 9 months ago
- Cryptic pocket prediction using AlphaFold 2☆23Updated 2 years ago
- Simulation-Enabled Estimation of Kinetic Rates - Version 2☆29Updated 4 months ago
- Alchemical mutation scoring map☆39Updated 4 months ago
- Python code for generating Boresch restraints from MD simulations☆22Updated 2 years ago
- AI-augmented R-group exploration in medicinal chemistry☆17Updated 9 months ago