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In comparison with hundred\u2010of\u2010microsecond timescale conventional molecular dynamics (cMD) simulations performed on the Anton supercomputer, aMD captured complete folding of the four proteins in significantly shorter simulation time. The folded protein conformations were found within 0.2\u20132.1 \u00c5 of the native NMR or X\u2010ray crystal structures. Free energy profiles calculated through improved reweighting of the aMD simulations using cumulant expansion to the second\u2010order are in good agreement with those obtained from cMD simulations. This allows us to identify distinct conformational states (e.g., unfolded and intermediate) other than the native structure and the protein folding energy barriers. Detailed analysis of protein secondary structures and local key residue interactions provided important insights into the protein folding pathways. Furthermore, the selections of force fields and aMD simulation parameters are discussed in detail. Our work shows usefulness and accuracy of aMD in studying protein folding, providing basic references in using aMD in future protein\u2010folding studies. \u00a9 2015 Wiley Periodicals, Inc.<\/jats:p>","DOI":"10.1002\/jcc.23964","type":"journal-article","created":{"date-parts":[[2015,6,19]],"date-time":"2015-06-19T18:48:26Z","timestamp":1434739706000},"page":"1536-1549","source":"Crossref","is-referenced-by-count":159,"title":["Accelerated molecular dynamics simulations of protein folding"],"prefix":"10.1002","volume":"36","author":[{"given":"Yinglong","family":"Miao","sequence":"first","affiliation":[{"name":"Howard Hughes Medical Institute University of California at San Diego La Jolla, California"}]},{"given":"Ferran","family":"Feixas","sequence":"additional","affiliation":[{"name":"Department of Chemistry and Biochemistry University of California at San Diego La Jolla California"},{"name":"Department of Pharmacology University of California at San Diego La Jolla California"}]},{"given":"Changsun","family":"Eun","sequence":"additional","affiliation":[{"name":"Howard Hughes Medical Institute University of California at San Diego La Jolla, California"}]},{"given":"J. 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