Non-classical MHC Class I molecule MICA with NKG2D at 2.70Å resolution
Data provenance
Information sections
Complex type
Species
Locus / Allele group
Complex structure of the activating immunoreceptor NKG2D and its MHC class I-like ligand MICA.
To date, non-wear detection algorithms commonly employ a 30, 60, or even 90 mins interval or window in which acceleration values need to be below a threshold value. A major drawback of such intervals is that they need to be long enough to prevent false positives (type I errors), while short enough to prevent false negatives (type II errors), which limits detecting both short and longer episodes of non-wear time. In this paper, we propose a novel non-wear detection algorithm that eliminates the need for an interval. Rather than inspecting acceleration within intervals, we explore acceleration right before and right after an episode of non-wear time. We trained a deep convolutional neural network that was able to infer non-wear time by detecting when the accelerometer was removed and when it was placed back on again. We evaluate our algorithm against several baseline and existing non-wear algorithms, and our algorithm achieves a perfect precision, a recall of 0.9962, and an F1 score of 0.9981, outperforming all evaluated algorithms. Although our algorithm was developed using patterns learned from a hip-worn accelerometer, we propose algorithmic steps that can easily be applied to a wrist-worn accelerometer and a retrained classification model.
Structure deposition and release
Data provenance
Publication data retrieved from PDBe REST API8 and PMCe REST API9
Other structures from this publication
1. MICA
MICA
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10 20 30 40 50 60
MEPHSLRYNLTVLSWDGSVQSGFLTEVHLDGQPFLRCDRQKCRAKPQGQWAEDVLGNKTW 70 80 90 100 110 120 DRETRDLTGNGKDLRMTLAHIKDQKEGLHSLQEIRVCEIHEDNSTRSSQHFYYDGELFLS 130 140 150 160 170 180 QNLETKEWTMPQSSRAQTLAMNVRNFLKEDAMKTKTHYHAMHADCLQELRRYLKSGVVLR 190 200 210 220 230 240 RTVPPMVNVTRSEASEGNITVTCRASGFYPWNITLSWRQDGVSLSHDTQQWGDVLPDGNG 250 260 270 TYQTWVATRICQGEEQRFTCYMEHSGNHSTHPVPS |
2. Natural Killer Cell Receptor NKG2d
Natural Killer Cell Receptor NKG2d
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10 20 30 40 50 60
NSLFNQEVQIPLTESYCGPCPKNWICYKNNCYQFFDESKNWYESQASCMSQNASLLKVYS 70 80 90 100 110 120 KEDQDLLKLVKSYHWMGLVHIPTNGSWQWEDGSILSPNLLTIIEMQKGDCALYASSFKGY 130 IENCSTPNTYICMQRTV |
Data provenance
Sequences are retrieved via the Uniprot method of the RSCB REST API. Sequences are then compared to those derived from the PDB file and matched against sequences retrieved from the IPD-IMGT/HLA database for human sequences, or the IPD-MHC database for other species. Mouse sequences are matched against FASTA files from Uniprot. Sequences for the mature extracellular protein (signal petide and cytoplasmic tail removed) are compared to identical length sequences from the datasources mentioned before using either exact matching or Levenshtein distance based matching.
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Footnotes
- Protein Data Bank Europe - Coordinate Server
- 1HHK - HLA-A*02:01 binding LLFGYPVYV at 2.5Å resolution - PDB entry for 1HHK
- Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. - PyMol CEALIGN Method - Publication
- PyMol - PyMol.org/pymol
- Levenshtein distance - Wikipedia entry
- Protein Data Bank Europe REST API - Molecules endpoint
- 3Dmol.js: molecular visualization with WebGL - 3DMol.js - Publication
- Protein Data Bank Europe REST API - Publication endpoint
- PubMed Central Europe REST API - Articles endpoint
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