期刊
JOURNAL OF APPLIED CRYSTALLOGRAPHY
卷 42, 期 -, 页码 376-384出版社
INT UNION CRYSTALLOGRAPHY
DOI: 10.1107/S0021889809008784
关键词
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资金
- EU [2004-512092]
- Netherlands Bioinformatics Centre (NBIC)
- BSIK grant through the Netherlands Genomics Initiative (NGI)
Structural biology, homology modelling and rational drug design require accurate three-dimensional macromolecular coordinates. However, the coordinates in the Protein Data Bank (PDB) have not all been obtained using the latest experimental and computational methods. In this study a method is presented for automated re-refinement of existing structure models in the PDB. A large-scale benchmark with 16 807 PDB entries showed that they can be improved in terms of fit to the deposited experimental X-ray data as well as in terms of geometric quality. The re-refinement protocol uses TLS models to describe concerted atom movement. The resulting structure models are made available through the PDB_REDO databank (http://www.cmbi.ru.nl/pdb_redo/). Grid computing techniques were used to overcome the computational requirements of this endeavour.
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