Project ID: plumID:23.017
Name: How and When Does an Enzyme React? Unraveling α-Amylase Catalytic Activity with Enhanced Sampling Techniques
Archive: https://github.com/sudipdas789/Reaction_discovery/archive/refs/heads/main.zip
Category: bio
Keywords: enzymatic reaction discovery, reaction mechanism, catalysis, ligand-binding modes, water, alpha-amylase, sugar, QM/MM MD, OPES, OPES explore, graph CV, machine learning, Deep TDA CV, path CV
PLUMED version: 2.9
Contributor: Sudip Das
Submitted on: 10 May 2023
Publication: S. Das, U. Raucci, R. P. P. Neves, M. J. Ramos, M. Parrinello, How and When Does an Enzyme React? Unraveling α-Amylase Catalytic Activity with Enhanced Sampling Techniques. ACS Catalysis. 13, 8092–8098 (2023)
PLUMED input files
| File | Compatible with |
|---|---|
| QM-MM_MD/34atomsCV/plumed.dat |   |
| QM-MM_MD/8atomsCV/plumed.dat | |
| classical_biased_MD/plumed.dat | |
| classical_unbiased_MD/unbiasedCVs/plumed.dat | |
Last tested: 22 Apr 2025, 09:59:10
Project description and instructions
This egg contains the input files for replicating the reaction discovery and enhanced sampling OPES simulations for alpha-amylase enzyme with a sugar substrate using graph CV, Deep TDA CVs, and path CV. The graph CVs accelerate the exploration of the enzymatic reaction space in QM/MM discovery MD simulations with the explore version of OPES. The path CV used in OPES simulations enhances the sampling (in the Deep TDA CVs’ space) of different substrate-binding modes within the enzyme’s active site. For more information about Deep TDA, we refer to plumID:21.028 and graph-CV to plumID:22.004. The CVs were trained with Pytorch version 1.8 and the simulations were run with GROMACS 2021.5, CP2K 9.1, and PLUMED 2.9.
Click here to open manual pages for actions used in this project.
Submission history
[v1] 10 May 2023: original submission
Badge
Click on the image below and get the code to add the badge to your website!
