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Implementation of 3D spatial indexing and compression in a large-scale molecular dynamics simulation database for rapid atomic contact detection.
(2011) BMC Bioinformatics 12
PubMed: 21831299 | PubMedCentral: PMC3166946 | DOI: 10.1186/1471-2105-12-334
Table 1 11 representative proteins - number of residues and number of atoms PDB4 Name Residue Range # residues # protein atoms 2adr Domain of Adr1 DBD from S. cerevisiae 102-130 29 496 1nr2 Thymus and... activation-regulated chemokine 8-69 62 1011 1okt Glutathione S-transferase 1-85 85 1412 2tgi Domain of transforming growth factor-beta 2 (TGF- B2) 1-112 112 1750 1d0n Horse plasma gelsolin 27-159 133 2095 1bp5 Domain of serum transferrin 82-246 165 2487 1hgu Human growth hormone 2-190 189 3011 1p88 3-phosphoshikimate 1-carboxyvinyltransferase 25-240 216 3272 1fzw Monomer of glucose-1-phosphate thymidylyltransferase 2-293 292 4560 1qaz Alginate Lyase A1-III 4-354 351 5495 1ehe Cytochrome P450nor 5-403 399 6217 Figure 3 Comparison of heavy-atom contacts query with and without spatial indexing for 11 metafold representatives over 1 ns .
Publication Year: 2011
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