CING: an integrated residue-based structure validation program suite

被引：92

作者：

Doreleijers, Jurgen F.

da Silva, Alan W. Sousa ^{[7
]}

Krieger, Elmar ^{[6
]}

Nabuurs, Sander B.

Spronk, Christian A. E. M. ^{[5
]}

Stevens, Tim J. ^{[4
]}

Vranken, Wim F. ^{[2
,3
]}

Vriend, Gert

Vuister, Geerten W. ^{[1
]}

机构：

[1] Univ Leicester, Dept Biochem, Leicester LE1 9HN, Leics, England

[2] Vrije Univ Brussel, B-1050 Brussels, Belgium

[3] VIB, Dept Biol Struct, B-1050 Brussels, Belgium

[4] Univ Cambridge, Dept Biochem, Cambridge CB2 1GA, England

[5] Spronk NMR Consultancy UAB, LT-01402 Vilnius, Lithuania

[6] YASARA Biosci GmbH, A-1220 Vienna, Austria

[7] UniProt, European Bioinformat Inst, Cambridge CB10 1SD, England

来源：

JOURNAL OF BIOMOLECULAR NMR | 2012年 / 54卷 / 03期

基金：

英国生物技术与生命科学研究理事会;

关键词：

NMR; Structure validation; PDB; Errors; Quality; Protein structure; AUTOMATED STRUCTURE DETERMINATION; PROTEIN STRUCTURES; NA+/CA2+ EXCHANGER; CA2+ REGULATION; NMR STRUCTURES; NUCLEIC-ACIDS; QUALITY; DATABASE; PDB; CONFORMATION;

D O I：

10.1007/s10858-012-9669-7

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

We present a suite of programs, named CING for Common Interface for NMR Structure Generation that provides for a residue-based, integrated validation of the structural NMR ensemble in conjunction with the experimental restraints and other input data. External validation programs and new internal validation routines compare the NMR-derived models with empirical data, measured chemical shifts, distance- and dihedral restraints and the results are visualized in a dynamic Web 2.0 report. A red-orange-green score is used for residues and restraints to direct the user to those critiques that warrant further investigation. Overall green scores below 20 % accompanied by red scores over 50 % are strongly indicative of poorly modelled structures. The publically accessible, secure iCing webserver (https://nmr.le.ac.uk) allows individual users to upload the NMR data and run a CING validation analysis.

引用

页码：267 / 283

页数：17

共 72 条

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