Hybrid approaches: applying computational methods in cryo-electron microscopy

被引:28
作者
Lindert, Steffen [1 ,3 ]
Stewart, Phoebe L. [2 ,3 ]
Meiler, Jens [1 ,3 ]
机构
[1] Vanderbilt Univ, Dept Chem, Nashville, TN 37212 USA
[2] Vanderbilt Univ, Med Ctr, Dept Mol Physiol & Biophys, Nashville, TN 37232 USA
[3] Vanderbilt Univ, Struct Biol Ctr, Nashville, TN 37232 USA
基金
美国国家科学基金会;
关键词
STRUCTURAL-INFORMATICS APPROACH; HIGH-RESOLUTION STRUCTURE; CRYO-EM; ELECTRON CRYOMICROSCOPY; STRUCTURE PREDICTION; PROTEIN SECONDARY; ATOMIC STRUCTURES; BETA-SHEETS; REFINEMENT; MAPS;
D O I
10.1016/j.sbi.2009.02.010
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
Recent advances in cryo-electron microscopy have led to an increasing number of high (3-5 angstrom) to medium (5-10 angstrom) resolution cryoEM density maps. These density maps contain valuable information about the protein structure but frequently require computational algorithms to aid their structural interpretation. It is these hybrid approaches between cryoEM and computational protein structure prediction algorithms that will shape protein structure elucidation from density maps.
引用
收藏
页码:218 / 225
页数:8
相关论文
共 51 条
[1]   Ab initio modeling of the herpesvirus VP26 core domain assessed by CryoEM density [J].
Baker, Matthew L. ;
Jiang, Wen ;
Wedemeyer, William J. ;
Rixon, Frazer J. ;
Baker, David ;
Chiu, Wah .
PLOS COMPUTATIONAL BIOLOGY, 2006, 2 (10) :1313-1324
[2]   Identification of secondary structure elements in intermediate-resolution density maps [J].
Baker, Matthew L. ;
Ju, Tao ;
Chiu, Wah .
STRUCTURE, 2007, 15 (01) :7-19
[3]   De novo prediction of three-dimensional structures for major protein families [J].
Bonneau, R ;
Strauss, CEM ;
Rohl, CA ;
Chivian, D ;
Bradley, P ;
Malmström, L ;
Robertson, T ;
Baker, D .
JOURNAL OF MOLECULAR BIOLOGY, 2002, 322 (01) :65-78
[4]   Toward high-resolution de novo structure prediction for small proteins [J].
Bradley, P ;
Misura, KMS ;
Baker, D .
SCIENCE, 2005, 309 (5742) :1868-1871
[5]   A graph-theory algorithm for rapid protein side-chain prediction [J].
Canutescu, AA ;
Shelenkov, AA ;
Dunbrack, RL .
PROTEIN SCIENCE, 2003, 12 (09) :2001-2014
[6]  
Chandonia JM, 1999, PROTEINS, V35, P293
[7]   Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection [J].
Chivian, Dylan ;
Baker, David .
NUCLEIC ACIDS RESEARCH, 2006, 34 (17)
[8]  
Dal Palo A, 2006, Comput Syst Bioinformatics Conf, P89
[9]   EMatch:: an efficient method for aligning atomic resolution subunits into intermediate-resolution cryo-EM maps of large macromolecular assemblies [J].
Dror, Oranit ;
Lasker, Keren ;
Nussinov, Ruth ;
Wolfson, Haim .
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2007, 63 :42-49
[10]   An automatic method for predicting transmembrane protein structures using cryo-EM and evolutionary data [J].
Fleishman, SJ ;
Harrington, S ;
Friesner, RA ;
Honig, B ;
Ben-Tal, N .
BIOPHYSICAL JOURNAL, 2004, 87 (05) :3448-3459