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The dataset viewer is not available for this split.
Cannot extract the features (columns) for the split 'train' of the config 'default' of the dataset.
Error code: FeaturesError
Exception: UnicodeDecodeError
Message: 'utf-8' codec can't decode bytes in position 15-16: invalid continuation byte
Traceback: Traceback (most recent call last):
File "/src/services/worker/src/worker/job_runners/split/first_rows.py", line 246, in compute_first_rows_from_streaming_response
iterable_dataset = iterable_dataset._resolve_features()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 4196, in _resolve_features
features = _infer_features_from_batch(self.with_format(None)._head())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 2533, in _head
return next(iter(self.iter(batch_size=n)))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 2711, in iter
for key, pa_table in ex_iterable.iter_arrow():
^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 2249, in _iter_arrow
yield from self.ex_iterable._iter_arrow()
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 494, in _iter_arrow
for key, pa_table in iterator:
^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/iterable_dataset.py", line 384, in _iter_arrow
for key, pa_table in self.generate_tables_fn(**gen_kwags):
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/packaged_modules/csv/csv.py", line 196, in _generate_tables
csv_file_reader = pd.read_csv(file, iterator=True, dtype=dtype, **self.config.pd_read_csv_kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/streaming.py", line 73, in wrapper
return function(*args, download_config=download_config, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/datasets/utils/file_utils.py", line 1250, in xpandas_read_csv
return pd.read_csv(xopen(filepath_or_buffer, "rb", download_config=download_config), **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/pandas/io/parsers/readers.py", line 1026, in read_csv
return _read(filepath_or_buffer, kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/pandas/io/parsers/readers.py", line 620, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/pandas/io/parsers/readers.py", line 1620, in __init__
self._engine = self._make_engine(f, self.engine)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/pandas/io/parsers/readers.py", line 1898, in _make_engine
return mapping[engine](f, **self.options)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/local/lib/python3.12/site-packages/pandas/io/parsers/c_parser_wrapper.py", line 93, in __init__
self._reader = parsers.TextReader(src, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "pandas/_libs/parsers.pyx", line 574, in pandas._libs.parsers.TextReader.__cinit__
File "pandas/_libs/parsers.pyx", line 663, in pandas._libs.parsers.TextReader._get_header
File "pandas/_libs/parsers.pyx", line 874, in pandas._libs.parsers.TextReader._tokenize_rows
File "pandas/_libs/parsers.pyx", line 891, in pandas._libs.parsers.TextReader._check_tokenize_status
File "pandas/_libs/parsers.pyx", line 2053, in pandas._libs.parsers.raise_parser_error
File "<frozen codecs>", line 322, in decode
UnicodeDecodeError: 'utf-8' codec can't decode bytes in position 15-16: invalid continuation byteNeed help to make the dataset viewer work? Make sure to review how to configure the dataset viewer, and open a discussion for direct support.
A Dataset of Small Protein Conformational Ensembles from All-Atom Molecular Dynamics Simulations
Authors
Zilin Ren, Ying Hu, Xin Yang
Dataset Overview
This dataset, hereafter referred to as DynoDB, consists of 8,385 molecular dynamics (MD) trajectories of small proteins (5–100 amino acids). Each entry contains 1,000 ensemble frames extracted from 100 ns production runs, providing a systematic characterization of small protein conformational landscapes at the atomic scale.
License
This dataset is licensed under the Creative Commons Attribution 4.0 International License (CC BY 4.0). By using this dataset, you agree to cite the original work as specified below.
Citing The Dataset
If you use this dataset in your research, please cite the following paper:
[... (Scientific Data, 2026)]
DOI: https://doi.org/10.57967/HF/7057
Dataset Structure
The data is organized as follows:
static_structures/: Initial PDB conformations.processed_structures/: Preprocessed and repaired models.trajectory_frames/: Extracted frames (1,000 per system).metadata/: Multi-sheet Excel/CSV files providing comprehensive structural, dynamic, and functional annotations.
Dataset Size
| Dataset Metric | Value |
|---|---|
| Number of trajectories | 8,385 |
| Length per trajectory | 100 ns |
| Cumulative simulation time | 838.5 µs (~0.84 s) |
| Total number of atoms | 3,990,516 |
| Average system size (atoms) | ~476 |
| Total number of residues | 491,395 |
| Average system size (residues) | ~59 |
| Storage size | ~611 GB |
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