Weighting of experimental evidence in macromolecular structure determination

被引:63
作者
Habeck, M [1 ]
Rieping, W [1 ]
Nilges, M [1 ]
机构
[1] Inst Pasteur, CNRS, Unite Bioinformat Struct, Unite Rech Assoc 2185, F-75724 Paris 15, France
关键词
Bayesian probability theory; Markov chain Monte Carlo;
D O I
10.1073/pnas.0506412103
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
The determination of macromolecular structures requires weighting of experimental evidence relative to prior physical information. Although it can critically affect the quality of the calculated structures, experimental data are routinely weighted on an empirical basis. At present, cross-validation is the most rigorous method to determine the best weight. We describe a general method to adaptively weight experimental data in the course of structure calculation. It is further shown that the necessity to define weights for the data can be completely alleviated. We demonstrate the method on a structure calculation from NMR data and find that the resulting structures are optimal in terms of accuracy and structural quality. Our method is devoid of the bias imposed by an empirical choice of the weight and has some advantages over estimating the weight by cross-validation.
引用
收藏
页码:1756 / 1761
页数:6
相关论文
共 26 条
[1]   Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement [J].
Adams, PD ;
Pannu, NS ;
Read, RJ ;
Brunger, AT .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1997, 94 (10) :5018-5023
[2]  
[Anonymous], 2012, Probability Theory: The Logic Of Science
[3]  
Berger EW, 1900, MEM BIOL LAB J HOPKI, V4, P1
[4]   FREE R-VALUE - A NOVEL STATISTICAL QUANTITY FOR ASSESSING THE ACCURACY OF CRYSTAL-STRUCTURES [J].
BRUNGER, AT .
NATURE, 1992, 355 (6359) :472-475
[5]   ASSESSING THE QUALITY OF SOLUTION NUCLEAR-MAGNETIC-RESONANCE STRUCTURES BY COMPLETE CROSS-VALIDATION [J].
BRUNGER, AT ;
CLORE, GM ;
GRONENBORN, AM ;
SAFFRICH, R ;
NILGES, M .
SCIENCE, 1993, 261 (5119) :328-331
[6]   COMPUTATIONAL CHALLENGES FOR MACROMOLECULAR STRUCTURE DETERMINATION BY X-RAY CRYSTALLOGRAPHY AND SOLUTION NMR-SPECTROSCOPY [J].
BRUNGER, AT ;
NILGES, M .
QUARTERLY REVIEWS OF BIOPHYSICS, 1993, 26 (01) :49-125
[7]  
Brunger AT, 1998, ACTA CRYSTALLOGR D, V54, P905, DOI 10.1107/s0907444998003254
[8]  
CHEN MH, 2002, MONTE CARLO METHODS
[9]   New methods of structure refinement for macromolecular structure determination by NMR [J].
Clore, GM ;
Gronenborn, AM .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1998, 95 (11) :5891-5898
[10]   Validation of protein structure from anisotropic carbonyl chemical shifts in a dilute liquid crystalline phase [J].
Cornilescu, G ;
Marquardt, JL ;
Ottiger, M ;
Bax, A .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1998, 120 (27) :6836-6837