UCL-CCS / TIES_MDLinks
Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.
☆33Updated 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 2 weeks 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…☆32Updated 4 months ago
- A tutorials suite for BioSimSpace.☆27Updated 5 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.☆53Updated 6 months ago
- ☆28Updated 5 months ago
- ☆16Updated 8 years ago
- Computational Chemistry Workflows☆55Updated 3 years ago
- EXPRORER: Rational cosolvents set construction method for cosolvent molecular dynamics (CMD) with large-scale computation☆11Updated 3 years 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 last month
- ☆28Updated last year
- Cryptic pocket prediction using AlphaFold 2☆24Updated 2 years ago
- Codes to use funnel-metadynamics and funnel metadynamics automated protocol☆30Updated 3 years ago
- Full automation of relative protein-ligand binding free energy calculations in GROMACS☆45Updated 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 2 years ago
- An OpenMM plugin that implements the Alchemical Transfer Potential☆39Updated 2 years ago
- A tool for the analysis of pathways sampled in molecular dynamics simulations based on Self-Organizing Maps (SOM)☆10Updated 3 years ago
- CosolvKit is a versatile tool for cosolvent MD preparation and analysis☆25Updated 5 months ago
- ☆35Updated last year
- ☆30Updated 2 months ago
- The Guest HOst Affinity Tool (GHOAT.py) is a fully automated tool for absolute binding free energy calculations on guest-host systems.☆20Updated 4 months ago
- Cloud GPU supported NAMD3-based binding free energy difference between two small molecules against the same protein target. This is prob…☆26Updated 2 years ago
- ☆22Updated last month
- Dynamic pharmacophore modeling of molecular interactions☆36Updated last year
- CReM-dock: generation of chemically reasonable molecules guided by molecular docking☆27Updated last month
- Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane☆37Updated 2 years ago
- ☆44Updated 3 years ago
- Implementation of Shape and Electrostatic similarity metric in deepFMPO.☆45Updated 3 years ago
- A package to identify matched molecular pairs and use them to predict property changes.☆24Updated last year