Protein structure prediction by global optimization of a potential energy function

被引:155
作者
Liwo, A
Lee, J
Ripoll, DR
Pillardy, J
Scheraga, HA [1 ]
机构
[1] Cornell Univ, Baker Lab Chem & Chem Biol, Ithaca, NY 14853 USA
[2] Univ Gdansk, Fac Chem, PL-80952 Gdansk, Poland
[3] Cornell Theory Ctr, Ithaca, NY 14853 USA
关键词
D O I
10.1073/pnas.96.10.5482
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
An approach based exclusively on finding the global minimum of an appropriate potential energy function has been used to predict the unknown structures of five globular proteins with sizes rang;ng from 89 to 140 amino acid residues. Comparison of the computed lowest-energy structures of two of them (HDEA and MarA) with the crystal structures, released by the Protein Data Bank after the predictions were made, shows that large fragments (61 residues) of both proteins were predicted with rms deviations of 4.2 and 6.0 Angstrom for the Ca atoms, for HDEA and MarA, respectively. This represents 80% and 53% of the observed structures of HDEA and MarA respectively. Similar rms deviations were obtained for similar to 60-residue fragments of the other three proteins. These results constitute an important step toward the prediction of protein structure based solely on global optimization of a potential energy function for a given amino acid sequence.
引用
收藏
页码:5482 / 5485
页数:4
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