http://www.cnr.it/ontology/cnr/individuo/prodotto/ID177079

PDB-REDO: Automated re-refinement of X-ray structure models in the PDB (Articolo in rivista)

Type

Label

PDB-REDO: Automated re-refinement of X-ray structure models in the PDB (Articolo in rivista) (literal)

Anno

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#doi

Alternative label

Gisel, Andreas (6); Stockinger, Heinz (3); Breton, Vincent (2); Mattila, Kimmo (8); Bongcam-Rudloff, Erik (4); Pagni, Marco (3); Joosten, Robbie P. (1); Vriend, Gert (10); Salzemann, Jean (2); Bloch, Vincent (2); Da Costa, Ana L. (2); Diarena, Matteo (2); Fettahi, Géraldine (2); Reichstadt, Matthieu (2); Fabbretti, Roberto (3); Flegel, Volker (3); Berglund, Ann Charlott (4); Blanchet, Christophe (5); Combet, Christophe (5); Deleage, Gilbert (5); Kasam, Vinod (7); Kervinen, Timo (8); Korpelainen, Eija (8); Tickle, Ian J. (9) (2009)
PDB-REDO: Automated re-refinement of X-ray structure models in the PDB
in Journal of applied crystallography (Online)
(literal)

Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#autori

Gisel, Andreas (6); Stockinger, Heinz (3); Breton, Vincent (2); Mattila, Kimmo (8); Bongcam-Rudloff, Erik (4); Pagni, Marco (3); Joosten, Robbie P. (1); Vriend, Gert (10); Salzemann, Jean (2); Bloch, Vincent (2); Da Costa, Ana L. (2); Diarena, Matteo (2); Fettahi, Géraldine (2); Reichstadt, Matthieu (2); Fabbretti, Roberto (3); Flegel, Volker (3); Berglund, Ann Charlott (4); Blanchet, Christophe (5); Combet, Christophe (5); Deleage, Gilbert (5); Kasam, Vinod (7); Kervinen, Timo (8); Korpelainen, Eija (8); Tickle, Ian J. (9) (literal)

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Note

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(1) Centre for Molecular and Biomolecular Informatics - NCMLS; (2) CNRS/IN2P3 - Laboratoire de Physique Corpusculaire; (3) Swiss Institute of Bioinformatics - Vital-IT Group; (4) Uppmax, SLV - Uppsala University; (5) IBCP, CNRS - Université de Lyon1; (6) Institute for Biomedical Technologies Bari - CNR; (7) Fraunhofer-Institute for Algorithms and Scientific Computing - ; (8) CSC - the Finnish IT Center for Science - ; (9) Astex Therapeutics Ltd - ; (10) CMBI 260, NCMLS - Radboud University (literal)

Titolo

PDB-REDO: Automated re-refinement of X-ray structure models in the PDB (literal)

Abstract

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. (literal)

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