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 tested on v2.9 tested on master
QM-MM_MD/8atomsCV/plumed.dat tested on v2.9 tested on master
classical_biased_MD/plumed.dat tested on v2.9 tested on master
classical_unbiased_MD/unbiasedCVs/plumed.dat tested on v2.9 tested on master

Last tested: 28 Feb 2024, 06:47:19

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.

Submission history
[v1] 10 May 2023: original submission

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plumeDnest:23.017