peptide
Datasets
All datasets matching “peptide”many-peptides-md
[!IMPORTANT]
Critical Update
The original 8AA TICA models within subsampled_trajectories/*/8AA/*.npz employed a CA-only atom selection. These models are not valid for comparison to results in our paper.
Updated files (uploaded 15/12/2025) now contain corrected models. If you previously downloaded this dataset, please re-download to ensure accurate results.
Note: Codebase references to tica_features_ca must now be replaced with tica_features. This was resolved in our codebase by PR #26.
Note:… See the full description on the dataset page: https://huggingface.co/datasets/transferable-samplers/many-peptides-md.vacuum_peptides
Vacuum Peptide Ensembles
Molecular-dynamics trajectories derived from ManyPeptidesMD. This repository provides vacuum ensembles for a small subset of peptides, initialized from ManyPeptidesMD conformers.
Overview
Path
Model
Use
trajectories/v1/
Amber14, peptide only
Gas-phase sampling
webdatasets/v1/300K/
Streamable samples from the 300 K state
Model training
webdatasets/v1/300-500K/
Streamable samples from all REMD states
Temperature-conditioned… See the full description on the dataset page: https://huggingface.co/datasets/niklastr/vacuum_peptides.microsolvated_peptides
Microsolvated Peptide Ensembles
This repository provides explicit-water microsolvated structures for a subset of peptides initialized from ManyPeptidesMD conformers.
Overview
Path
Model
Use
trajectories/v1/
Amber14 in TIP3P, cropped to the nearest 128 waters
Peptide-solvent sampling
webdatasets/v1/train_300K/
Streamable samples from the 300 K state
Model training
webdatasets/v1/train_300-500K/
Streamable samples from all REMD states… See the full description on the dataset page: https://huggingface.co/datasets/niklastr/microsolvated_peptides.LRGB_Peptides-func
LRGB Peptides-func
Peptides-func (Peptides functional) dataset, part of Long Range Graph Benchmark (LRGB) [1]. It is intended to be used through
scikit-fingerprints library.
The task is to predict functional properties of peptides.
Characteristic
Description
Tasks
10
Task type
classification
Total samples
15535
Recommended split
stratified random
Recommended metric
AUPRC
References
[1]
Dwivedi, Vijay Prakash, et al.
"Long Range Graph Benchmark"… See the full description on the dataset page: https://huggingface.co/datasets/scikit-fingerprints/LRGB_Peptides-func.LRGB_Peptides-struct
LRGB Peptides-struct
Peptides-struct (Peptides structural) dataset, part of Long Range Graph Benchmark (LRGB) [1]. It is intended to be used through
scikit-fingerprints library.
The task is to predict structural properties of peptides. Note that this is raw data, whereas the original paper [1] specifies
that targets should be standardized (mean 0, standard deviation 1) before training and evaluation. scikit-fingerprints does this by
default in the loader function, otherwise this… See the full description on the dataset page: https://huggingface.co/datasets/scikit-fingerprints/LRGB_Peptides-struct.solvated_peptides
Neutral Peptide Ensembles
Molecular-dynamics ensembles combining matched neutral peptide samples from vacuum REMD, ManyPeptidesMD OBC1 implicit-solvent trajectories, and neutral microsolvated peptide frames. The vacuum and microsolvated ensembles are initialized from ManyPeptidesMD conformers.
Overview
Path
Model
Use
webdatasets/v1/joint_neutral/base_temperature/
Amber14 vacuum, Amber14/OBC1, and Amber14/TIP3P microsolvated clusters
300 K training… See the full description on the dataset page: https://huggingface.co/datasets/niklastr/solvated_peptides.