Analysis of the structural quality of the CASD-NMR 2013 entries.

Autor: Ragan TJ; Department of Biochemistry, School of Biological Sciences, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 9HN, UK., Fogh RH; Department of Biochemistry, School of Biological Sciences, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 9HN, UK., Tejero R; Departamento de Química Física, Universidad de Valencia, Avda. Dr. Moliner 50, 46100, Burjassot (Valencia), Spain., Vranken W; Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, Brussels, Belgium.; (IB)2 Interuniversity Institute of Bioinformatics in Brussels, ULB-VUB, Triomflaan, 1050, Brussels, Belgium., Montelione GT; Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA.; Robert Wood Johnson Medical School, Piscataway, NJ, 08854, USA., Rosato A; Magnetic Resonance Center, Department of Chemistry, University of Florence, 50019, Sesto Fiorentino, Italy., Vuister GW; Department of Biochemistry, School of Biological Sciences, University of Leicester, Henry Wellcome Building, Lancaster Road, Leicester, LE1 9HN, UK. gv29@le.ac.uk.
Jazyk: angličtina
Zdroj: Journal of biomolecular NMR [J Biomol NMR] 2015 Aug; Vol. 62 (4), pp. 527-40. Date of Electronic Publication: 2015 Jun 03.
DOI: 10.1007/s10858-015-9949-0
Abstrakt: We performed a comprehensive structure validation of both automated and manually generated structures of the 10 targets of the CASD-NMR-2013 effort. We established that automated structure determination protocols are capable of reliably producing structures of comparable accuracy and quality to those generated by a skilled researcher, at least for small, single domain proteins such as the ten targets tested. The most robust results appear to be obtained when NOESY peak lists are used either as the primary input data or to augment chemical shift data without the need to manually filter such lists. A detailed analysis of the long-range NOE restraints generated by the different programs from the same data showed a surprisingly low degree of overlap. Additionally, we found that there was no significant correlation between the extent of the NOE restraint overlap and the accuracy of the structure. This result was surprising given the importance of NOE data in producing good quality structures. We suggest that this could be explained by the information redundancy present in NOEs between atoms contained within a fixed covalent network.
Databáze: MEDLINE
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