quantaosun / NAMD-FEPLinks
Cloud GPU supported NAMD3-based binding free energy difference between two small molecules against the same protein target. This is probably one of the fastest FEP simulation with FREE GPU hardwares that the genearl public could have access to
☆26Updated 2 weeks ago
Alternatives and similar repositories for NAMD-FEP
Users that are interested in NAMD-FEP are comparing it to the libraries listed below
Sorting:
- Full automation of relative protein-ligand binding free energy calculations in GROMACS☆45Updated 4 years ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆33Updated last year
- Cryptic pocket prediction using AlphaFold 2☆24Updated 2 years ago
- This script is designed for evaluating the binding affinity between a protein target and a small molecule, by calculating the binding fre…☆13Updated 2 years ago
- A versatile workflow for the generation of receptor-based pharmacophore models for virtual screening☆31Updated 5 months ago
- ☆52Updated 6 months ago
- Computational Chemistry Workflows☆56Updated 3 years ago
- ☆25Updated last year
- A tutorials suite for BioSimSpace.☆30Updated 3 weeks ago
- A toolkit developed to predict and analyze PROTAC-mediated ternary complexes using AlphaFold3 and Boltz-1.☆35Updated 4 months ago
- ☆21Updated 11 months ago
- PROTACable is an end-to-end in-silico design toolkit for novel PROTACs☆29Updated last year
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆57Updated 7 months ago
- CosolvKit is a versatile tool for cosolvent MD preparation and analysis☆26Updated 3 weeks ago
- ☆10Updated 5 years ago
- Fully automated high-throughput MD pipeline☆84Updated 2 months ago
- Machine Learning Boosted Docking (HASTEN): Accelerate Structure-based Virtual Screening☆39Updated 2 years 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…☆17Updated last year
- The Guest HOst Affinity Tool (GHOAT.py) is a fully automated tool for absolute binding free energy calculations on guest-host systems.☆20Updated 6 months ago
- ☆12Updated 2 years ago
- ☆32Updated 3 months ago
- CReM-dock: generation of chemically reasonable molecules guided by molecular docking☆28Updated 2 months ago
- Pocket dynamics analysis tool☆16Updated 6 months ago
- EXPRORER: Rational cosolvents set construction method for cosolvent molecular dynamics (CMD) with large-scale computation☆11Updated 3 years ago
- Implementation of Shape and Electrostatic similarity metric in deepFMPO.☆45Updated 3 years ago
- ☆26Updated 2 years ago
- ☆28Updated 6 months ago
- DeepFrag is a deep convolutional neural network that guides ligand optimization by extending a ligand with a molecular fragment, such tha…☆28Updated 4 months ago
- ☆35Updated last year
- MSMD (mixed-solvent molecular dynamics) engine and analysis tools☆19Updated 7 months ago