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Table 1 Summary of the data available in the D3PM (update on 11th April 2021)

From: D3PM: a comprehensive database for protein motions ranging from residue to domain

The overall protein motions

Number of protein

Overall RMSD (Å)

Mean

Maximum

apo & apo

3684

5.31

54.72

apo & holo

1643

4.68

39.53

holo & holo (different ligands)

1211

4.78

63.03

holo & holo (the same ligand)

1111

5.06

63.03

The pocket residues motions

Number of protein

Pocket RMSD (Å)

Mean

Maximum

apo & holo

1255

1.91

8.64

holo & holo (different ligands)

793

1.76

8.62

holo & holo (the same ligand)

1465

1.10

9.30

  1. The “apo” referred to as ligand-free protein, and the “holo” referred to as ligand-bound protein. The mean and maximum values were calculated with those representative pairs collected in the D3PM
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BMC Bioinformatics

ISSN: 1471-2105

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