Fast protein fold estimation from NMR-derived distance restraints

被引：7

作者：

Angyan, Annamaria F. ^{[1
]}

Perczel, Andras ^{[1
,2
]}

Pongor, Sandor ^{[3
,4
]}

Gaspari, Zoltan ^{[1
]}

机构：

[1] Eotvos Lorand Univ, Inst Chem, H-1117 Budapest, Hungary

[2] MHAS ELTE Prot Modelling Grp, H-1117 Budapest, Hungary

[3] Int Ctr Genet Engn & Biotechnol, Prot Struct & Bioinformat Grp, I-34012 Trieste, Italy

[4] Hungarian Acad Sci, Biol Res Ctr, Bioinformat Grp, H-6701 Szeged, Hungary

来源：

BIOINFORMATICS | 2008年 / 24卷 / 02期

基金：

匈牙利科学研究基金会;

关键词：

D O I：

10.1093/bioinformatics/btm564

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

PRIDE-NMR is a fast novel method to relate known protein folds to NMR distance restraints. It can be used to obtain a first guess about a structure being determined, as well as to estimate the completeness or verify the correctness of NOE data.

引用

页码：272 / 275

页数：4

共 15 条

[1] Recognition of protein folds via dipolar couplings [J].

Annila, A ;

Aitio, H ;

Thulin, E ;

Drakenberg, T .

JOURNAL OF BIOMOLECULAR NMR, 1999, 14 (03) :223-230

[2] Crystallography & NMR system:: A new software suite for macromolecular structure determination [J].

Brunger, AT ;

Adams, PD ;

Clore, GM ;

DeLano, WL ;

Gros, P ;

Grosse-Kunstleve, RW ;

Jiang, JS ;

Kuszewski, J ;

Nilges, M ;

Pannu, NS ;

Read, RJ ;

Rice, LM ;

Simonson, T ;

Warren, GL .

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 1998, 54 :905-921

[3] Protein fold similarity estimated by a probabilistic approach based on Cα-Cα distance comparison [J].

Carugo, O ;

Pongor, S .

JOURNAL OF MOLECULAR BIOLOGY, 2002, 315 (04) :887-898

[4] Protein structure determination from NMR chemical shifts [J].

Cavalli, Andrea ;

Salvatella, Xavier ;

Dobson, Christopher M. ;

Vendruscolo, Michele .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2007, 104 (23) :9615-9620

[5] Protein structure determination using molecular fragment replacement and NMR dipolar couplings [J].

Delaglio, F ;

Kontaxis, G ;

Bax, A .

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2000, 122 (09) :2142-2143

[6] Efficient recognition of folds in protein 3D structures by the improved PRIDE algorithm [J].

Gáspári, Z ;

Vlahovicek, K ;

Pongor, S .

BIOINFORMATICS, 2005, 21 (15) :3322-3323

[7] Protein NMR structure determination with automated NOE-identification in the NOESY spectra using the new software ATNOS [J].

Herrmann, T ;

Güntert, P ;

Wüthrich, K .

JOURNAL OF BIOMOLECULAR NMR, 2002, 24 (03) :171-189

[8] Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides [J].

Kaminski, GA ;

Friesner, RA ;

Tirado-Rives, J ;

Jorgensen, WL .

JOURNAL OF PHYSICAL CHEMISTRY B, 2001, 105 (28) :6474-6487

[9] Simultaneous determination of protein structure and dynamics [J].

Lindorff-Larsen, K ;

Best, RB ;

DePristo, MA ;

Dobson, CM ;

Vendruscolo, M .

NATURE, 2005, 433 (7022) :128-132

[10] SCOP - A STRUCTURAL CLASSIFICATION OF PROTEINS DATABASE FOR THE INVESTIGATION OF SEQUENCES AND STRUCTURES [J].

MURZIN, AG ;

BRENNER, SE ;

HUBBARD, T ;

CHOTHIA, C .

JOURNAL OF MOLECULAR BIOLOGY, 1995, 247 (04) :536-540

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