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Comparison of the covariance and cross\u2010correlation matrices shows that the relative motions have many similar features in the different simulations. Many regions of the protein, especially regions of secondary structure, move in a correlated manner. Anharmonic effects, which are included in the molecular dynamics simulations but not in the normal analysis, are of some importance in determining the larger scale collective motions, but not the more local fluctuations. Comparisons of molecular dynamics simulations in the present and absence of solvent indicate that the environment is of significance for the long\u2010range motions.<\/jats:p>","DOI":"10.1002\/prot.340110305","type":"journal-article","created":{"date-parts":[[2005,5,29]],"date-time":"2005-05-29T01:12:22Z","timestamp":1117329142000},"page":"205-217","source":"Crossref","is-referenced-by-count":947,"title":["Collective motions in proteins: A covariance analysis of atomic fluctuations in molecular dynamics and normal mode simulations"],"prefix":"10.1002","volume":"11","author":[{"given":"Toshiko","family":"Ichiye","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Martin","family":"Karplus","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2004,2,3]]},"reference":[{"key":"e_1_2_1_2_2","doi-asserted-by":"publisher","DOI":"10.1002\/9780470141205"},{"key":"e_1_2_1_3_2","doi-asserted-by":"publisher","DOI":"10.1017\/CBO9781139167864"},{"key":"e_1_2_1_4_2","doi-asserted-by":"publisher","DOI":"10.1016\/0076-6879(86)31050-4"},{"key":"e_1_2_1_5_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev.bb.13.060184.001555"},{"key":"e_1_2_1_6_2","doi-asserted-by":"publisher","DOI":"10.1021\/bi00264a019"},{"key":"e_1_2_1_7_2","unstructured":"Ichiye T. 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