Metadynamic metainference: Enhanced sampling of the metainference ensemble using metadynamics

被引:59
作者
Bonomi, Massimiliano [1 ]
Camilloni, Carlo [1 ,2 ,3 ]
Vendruscolo, Michele [1 ]
机构
[1] Univ Cambridge, Dept Chem, Lensfield Rd, Cambridge CB2 1EW, England
[2] Tech Univ Munich, Dept Chem, Lichtenbergstr 4, D-85747 Garching, Germany
[3] Tech Univ Munich, Inst Adv Study, Lichtenbergstr 4, D-85747 Garching, Germany
关键词
FREE-ENERGY LANDSCAPES; MOLECULAR ARCHITECTURE; CROSS-LINKING; COMPLEX; EFFICIENT; MODEL; OPTIMIZATION; ASSEMBLIES; MECHANISM; DYNAMICS;
D O I
10.1038/srep31232
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
070301 [无机化学]; 070403 [天体物理学]; 070507 [自然资源与国土空间规划学]; 090105 [作物生产系统与生态工程];
摘要
Accurate and precise structural ensembles of proteins and macromolecular complexes can be obtained with metainference, a recently proposed Bayesian inference method that integrates experimental information with prior knowledge and deals with all sources of errors in the data as well as with sample heterogeneity. The study of complex macromolecular systems, however, requires an extensive conformational sampling, which represents a separate challenge. To address such challenge and to exhaustively and efficiently generate structural ensembles we combine metainference with metadynamics and illustrate its application to the calculation of the free energy landscape of the alanine dipeptide.
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页数:11
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