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Application of 3D‐Jury, GRDB, and Verify3D in fold recognition
Author(s) -
Grotthuss Marcin von,
Pas Jakub,
Wyrwicz Lucjan,
Ginalski Krzysztof,
Rychlewski Leszek
Publication year - 2003
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.10547
Subject(s) - computer science , casp , artificial intelligence , feature selection , protein structure prediction , fragment (logic) , computational biology , pattern recognition (psychology) , machine learning , data mining , biology , protein structure , algorithm , biochemistry
In CASP5, the BioInfo.PL group has used the structure prediction Meta Server and the associated newly developed flexible meta‐predictor, called 3D‐Jury, as the main structure prediction tools. The most important feature of the meta‐predictor is a high (86%) correlation between the reported confidence score and the quality of the selected model. The Gene Relational Database (GRDB) was used to confirm the fold recognition results by selecting distant homologues and subsequent structure prediction with the Meta Server. A fragment‐splicing procedure was performed as a final processing step with large fragments extracted from selected models using model quality control provided by Verify3D. The comparison of submitted models with the native structure conducted after the CASP meeting showed that the GRDB‐supported structure prediction led to a satisfactory template fold selection, whereas the fragment‐splicing procedure must be improved in the future. Proteins 2003;53:418–423. © 2003 Wiley‐Liss, Inc.