Project ID: plumID:26.005
Name: Cryptic pocket discovery in Alzheimer disease risk proteins BIN1, PICALM, and CD2AP via well-tempered metadynamics
Archive: https://zenodo.org/records/19649272/files/plumed_nest_cryptad.zip
Category: methods
Keywords: cryptic pockets, Alzheimer disease, BIN1, PICALM, CD2AP, well-tempered metadynamics, endocytosis, clathrin-mediated trafficking, virtual screening
PLUMED version: 2.9
Contributor: Cagrı Ozkurt
Submitted on: 19 Apr 2026
Publication: unpublished
PLUMED input files
| File | Compatible with |
|---|---|
| plumed_S5_CD2AP_SH3-1.dat |   |
| plumed_S4_CD2AP_SH3-2.dat | |
| plumed_S3_PICALM_ANTH.dat | |
| plumed_S2_BIN1_SH3.dat | |
| plumed_S1_BIN1_BAR.dat | |
Last tested: 20 Apr 2026, 09:13:43
Project description and instructions
GROMACS 2023.3 patched with PLUMED 2.9.2 (see singularity/gromacs-plumed.def in the paper repository for a reproducible build). Run with gmx_mpi mdrun -plumed plumed_S*.dat -ntomp 2 -npme 4 -deffnm meta. One .dat file per system; each uses 2 distance CVs and well-tempered MetaD (SIGMA=0.05 nm, HEIGHT=1.2 kJ/mol, BIASFACTOR=15, PACE=500).
Click here to open manual pages for actions used in this project.
Submission history
[v1] 19 Apr 2026: original submission
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