Project ID: plumID:25.014
Name: Atomic resolution ensembles of intrinsically disordered and multi-domain proteins with Alphafold
Archive: https://github.com/COSBlab/bAIes-IDP/archive/refs/heads/main.zip
Category: bio
Keywords: bAIes, AlphaFold2, random coil, IDPs, Bayesian refinement
PLUMED version: 2.11
Contributor: Vincent Schnapka
Submitted on: 17 Jun 2025
Publication: V. Schnapka, T. I. Morozova, S. Sen, M. Bonomi, Atomic resolution ensembles of intrinsically disordered proteins with Alphafold (2025)

PLUMED input files

File Compatible with
./benchmark/bAIes/Ab40/plumed_Ab40.dat tested on master
./benchmark/bAIes/ACTR/plumed_ACTR.dat tested on master
./benchmark/bAIes/Alb3-A3CT/plumed_Alb3-A3CT.dat tested on master
./benchmark/bAIes/asyn/plumed_asyn.dat tested on master
…s/Colicin_N_T_domain/plumed_Colicin_N_T_domain.dat tested on master
./benchmark/bAIes/drkN/plumed_drkN.dat tested on master
…hmark/bAIes/emerin_67-170/plumed_emerin_67-170.dat tested on master
./benchmark/bAIes/FCP1/plumed_FCP1.dat tested on master
./benchmark/bAIes/GS8/plumed_GS8.dat tested on master
…hmark/bAIes/His-PknG_1-75/plumed_His-PknG_1-75.dat tested on master
./benchmark/bAIes/Hug1/plumed_Hug1.dat tested on master
./benchmark/bAIes/idr_SSRP1/plumed_idr_SSRP1.dat tested on master
./benchmark/bAIes/NHE1/plumed_NHE1.dat tested on master
…benchmark/bAIes/Nsp2_CtlIDR/plumed_Nsp2_CtlIDR.dat tested on master
./benchmark/bAIes/Nt-SOCS5/plumed_Nt-SOCS5.dat tested on master
./benchmark/bAIes/p61_Hck/plumed_p61_Hck.dat tested on master
./benchmark/bAIes/PaaA2/plumed_PaaA2.dat tested on master
./benchmark/bAIes/spm_FrpC/plumed_spm_FrpC.dat tested on master
./benchmark/bAIes/UBact/plumed_UBact.dat tested on master
./benchmark/bAIes/Ubq2/plumed_Ubq2.dat tested on master

Last tested: 25 Jul 2025, 11:32:36

Project description and instructions
This repository contains all the input file to reproduce the benchmark on 21 IDPs using bAIes, bAIes-N, and a random coil model. Calculations were performed with LAMMPS 2 Aug. 2023 and the development version of PLUMED.

Click here to open manual pages for actions used in this project.

Submission history
[v1] 17 Jun 2025: original submission

Badge
Click on the image below and get the code to add the badge to your website!
plumeDnest:25.014