Structural biology computing: Lessons for the biomedical research sciences

被引:8
作者
Morin, Andrew [1 ]
Sliz, Piotr [1 ]
机构
[1] Harvard Univ, Sch Med, Dept Biol Chem & Mol Pharmacol, Boston, MA 02115 USA
基金
美国国家科学基金会;
关键词
structural biology; computing; software; macromolecular crystallography; DENSITY; MODEL; REFINEMENT; INTERFACE; SOFTWARE; PROGRAM;
D O I
10.1002/bip.22343
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
The field of structural biology, whose aim is to elucidate the molecular and atomic structures of biological macromolecules, has long been at the forefront of biomedical sciences in adopting and developing computational research methods. Operating at the intersection between biophysics, biochemistry, and molecular biology, structural biology's growth into a foundational framework on which many concepts and findings of molecular biology are interpreted1 has depended largely on parallel advancements in computational tools and techniques. Without these computing advances, modern structural biology would likely have remained an exclusive pursuit practiced by few, and not become the widely practiced, foundational field it is today. As other areas of biomedical research increasingly embrace research computing techniques, the successes, failures and lessons of structural biology computing can serve as a useful guide to progress in other biomedically related research fields. (c) 2013 Wiley Periodicals, Inc. Biopolymers 99: 809-816, 2013.
引用
收藏
页码:809 / 816
页数:8
相关论文
共 53 条
[1]   Methods used in the structure determination of bovine mitochondrial F-1 ATPase [J].
Abrahams, JP ;
Leslie, AGW .
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 1996, 52 :30-42
[2]   PHENIX: a comprehensive Python']Python-based system for macromolecular structure solution [J].
Adams, Paul D. ;
Afonine, Pavel V. ;
Bunkoczi, Gabor ;
Chen, Vincent B. ;
Davis, Ian W. ;
Echols, Nathaniel ;
Headd, Jeffrey J. ;
Hung, Li-Wei ;
Kapral, Gary J. ;
Grosse-Kunstleve, Ralf W. ;
McCoy, Airlie J. ;
Moriarty, Nigel W. ;
Oeffner, Robert ;
Read, Randy J. ;
Richardson, David C. ;
Richardson, Jane S. ;
Terwilliger, Thomas C. ;
Zwart, Peter H. .
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2010, 66 :213-221
[3]   Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles [J].
Bai, Xiao-chen ;
Fernandez, Israel S. ;
McMullan, Greg ;
Scheres, Sjors H. W. .
ELIFE, 2013, 2
[4]   iMOSFLM: a new graphical interface for diffraction-image processing with MOSFLM [J].
Battye, T. Geoff G. ;
Kontogiannis, Luke ;
Johnson, Owen ;
Powell, Harold R. ;
Leslie, Andrew G. W. .
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2011, 67 :271-281
[5]   Announcing the worldwide Protein Data Bank [J].
Berman, H ;
Henrick, K ;
Nakamura, H .
NATURE STRUCTURAL BIOLOGY, 2003, 10 (12) :980-980
[6]   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
[7]   The march of structural biology [J].
Campbell, ID .
NATURE REVIEWS MOLECULAR CELL BIOLOGY, 2002, 3 (05) :377-381
[8]   MolProbity: all-atom structure validation for macromolecular crystallography [J].
Chen, Vincent B. ;
Arendall, W. Bryan, III ;
Headd, Jeffrey J. ;
Keedy, Daniel A. ;
Immormino, Robert M. ;
Kapral, Gary J. ;
Murray, Laura W. ;
Richardson, Jane S. ;
Richardson, David C. .
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2010, 66 :12-21
[9]   Phase combination and cross validation in iterated density-modification calculations [J].
Cowtan, KD ;
Main, P .
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 1996, 52 :43-48
[10]   The Buccaneer software for automated model building.: 1.: Tracing protein chains [J].
Cowtan, Kevin .
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 2006, 62 :1002-1011