quantaosun / Gromacs-ABFLinks
This script is designed for evaluating the binding affinity between a protein target and a small molecule, by calculating the binding free energy, supporting both gmx and gmx_mpi, with or without GPU
☆14Updated 2 years ago
Alternatives and similar repositories for Gromacs-ABF
Users that are interested in Gromacs-ABF are comparing it to the libraries listed below
Sorting:
- Cloud GPU supported NAMD3-based binding free energy difference between two small molecules against the same protein target. This is prob…☆26Updated 2 months ago
- Pocket dynamics analysis tool☆16Updated 8 months ago
- CosolvKit is a versatile tool for cosolvent MD preparation and analysis☆28Updated 2 months ago
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆34Updated 2 years ago
- ☆53Updated 8 months ago
- Efficient Sampling of PROTAC-Induced Ternary Complexes☆11Updated 7 months ago
- DeepFrag is a deep convolutional neural network that guides ligand optimization by extending a ligand with a molecular fragment, such tha…☆29Updated 6 months ago
- EXPRORER: Rational cosolvents set construction method for cosolvent molecular dynamics (CMD) with large-scale computation☆11Updated 3 years ago
- This is a SnakeMake based workflow for ABFE calculations that can be easily scaled in a high-throughput manner via Slurm for example.☆60Updated last month
- OnionNet-2 is constructed based on convolutional neural network (CNN) to predict the protein-ligand binding affinity.☆23Updated last year
- PROTACable is an end-to-end in-silico design toolkit for novel PROTACs☆29Updated last year
- ☆40Updated last year
- Official implementation of RuSH (Scaffold Hopping with Generative Reinforcement Learning). Includes ScaffoldFinder algorithm for 2D decor…☆19Updated 10 months ago
- Lightweight induced fit docking☆21Updated 2 years ago
- ☆39Updated 5 months ago
- Code used to mine surfaces.☆25Updated 10 months ago
- A versatile workflow for the generation of receptor-based pharmacophore models for virtual screening☆31Updated 7 months ago
- The Guest HOst Affinity Tool (GHOAT.py) is a fully automated tool for absolute binding free energy calculations on guest-host systems.☆21Updated 8 months ago
- Scripts for running alchemical, free-energy perturbation simulations using Gromacs☆16Updated 7 years ago
- Binding pocket optimization based on force fields and docking scoring functions☆37Updated 9 months 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
- ☆19Updated 3 years ago
- Open Source, Automated free binding free energy calculation between protein and small molecule. An all-in-one workflow, free energy pertu…☆59Updated 8 months ago
- ☆13Updated 2 years ago
- ☆26Updated last year
- FEP-SPell-ABFE: An Open Source Alchemical Absolute Binding Free Energy Calculation Workflow for Drug Discovery☆79Updated last year
- ☆69Updated 2 years ago
- ☆18Updated last year
- Cryptic pocket prediction using AlphaFold 2☆24Updated 3 years ago
- ☆29Updated 2 years ago