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
☆25Updated 2 years 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☆44Updated 4 years ago
- A versatile workflow for the generation of receptor-based pharmacophore models for virtual screening☆27Updated last month
- Python package built on NAMD/OpenMM and OpenMMTools to perform binding free energy calculations using the TIES protocol.☆32Updated last year
- Cryptic pocket prediction using AlphaFold 2☆23Updated 2 years ago
- ☆25Updated last year
- 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
- Computational Chemistry Workflows☆53Updated 2 years ago
- EXPRORER: Rational cosolvents set construction method for cosolvent molecular dynamics (CMD) with large-scale computation☆11Updated 2 years ago
- Scripts for running alchemical, free-energy perturbation simulations using Gromacs☆14Updated 7 years ago
- ☆26Updated 2 years ago
- CosolvKit is a versatile tool for cosolvent MD preparation and analysis☆24Updated last month
- Tool to predict water molecules placement and energy in ligand binding sites☆28Updated last week
- PROTACable is an end-to-end in-silico design toolkit for novel PROTACs☆29Updated last year
- MSMD (mixed-solvent molecular dynamics) engine and analysis tools☆19Updated 2 months ago
- Fully automated high-throughput MD pipeline☆61Updated last week
- Machine Learning Boosted Docking (HASTEN): Accelerate Structure-based Virtual Screening☆39Updated last year
- Lightweight induced fit docking☆21Updated 2 years ago
- Pocket dynamics analysis tool☆14Updated last month
- ☆48Updated last month
- ☆39Updated 11 months ago
- ☆12Updated last year
- ☆21Updated 6 months ago
- ☆28Updated last month
- 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
- ☆16Updated 11 months ago
- Different run and analysis scripts as described in the research guides.☆13Updated 2 years ago
- ☆10Updated 5 years ago
- A repository for the development of data analysis tools for replica exchange molecular dynamics (REMD) simulations☆12Updated 2 years ago
- MD pharmacophores and virtual screening☆33Updated last year
- Virtual screening approach for fragments selection and merging to lead-like compounds☆13Updated 3 years ago