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However, stereochemical errors in biomolecular structures can have a dramatic impact on the results of simulations.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>Here we illustrate the effects that chirality and peptide bond configuration flips may have on the secondary structure of proteins throughout a simulation. We also analyze the most common sources of stereochemical errors in biomolecular structures and present software tools to identify, correct, and prevent stereochemical errors in molecular dynamics simulations of biomolecules.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>Use of the tools presented here should become a standard step in the preparation of biomolecular simulations and in the generation of predicted structural models for proteins and nucleic acids.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-12-190","type":"journal-article","created":{"date-parts":[[2011,5,24]],"date-time":"2011-05-24T06:41:36Z","timestamp":1306219296000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":53,"title":["Stereochemical errors and their implications for molecular dynamics simulations"],"prefix":"10.1186","volume":"12","author":[{"given":"Eduard","family":"Schreiner","sequence":"first","affiliation":[]},{"given":"Leonardo G","family":"Trabuco","sequence":"additional","affiliation":[]},{"given":"Peter L","family":"Freddolino","sequence":"additional","affiliation":[]},{"given":"Klaus","family":"Schulten","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2011,5,23]]},"reference":[{"key":"4586_CR1","doi-asserted-by":"crossref","first-page":"181","DOI":"10.1128\/MMBR.62.1.181-203.1998","volume":"62","author":"JV H\u00f6ltje","year":"1998","unstructured":"H\u00f6ltje JV: Growth of the Stress-Bearing and Shape-Maintaining Murein Sacculus of Escherichia coli. 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