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However, we are not aware of any research done to evaluate how accurately we can model protein structures with dihedral angles and ideal bond lengths and angles.<\/jats:p><jats:p>Here, we introduce the protein structure idealization problem. We focus on the protein backbone structure idealization. We describe a fast<jats:italic>O<\/jats:italic>(<jats:italic>n<\/jats:italic><jats:italic>m<\/jats:italic>\/<jats:italic>\u03b5<\/jats:italic>) dynamic programming algorithm to find an idealized protein backbone structure that is approximately optimal according to our scoring function. The scoring function evaluates not only the free energy, but also the similarity with the target structure. Thus, the idealized protein structures found by our algorithm are guaranteed to be protein-like and close to the target protein structure.<\/jats:p><jats:p>We have implemented our protein structure idealization algorithm and idealized the high resolution protein structures with low sequence identities of the CULLPDB_PC30_RES1.6_R0.25 data set. We demonstrate that idealized backbone structures always exist with small changes and significantly better free energy. We also applied our algorithm to refine protein pseudo-structures determined in NMR experiments.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1748-7188-8-5","type":"journal-article","created":{"date-parts":[[2013,2,25]],"date-time":"2013-02-25T17:16:20Z","timestamp":1361812580000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Protein Structure Idealization: How accurately is it possible to model protein structures with dihedral angles?"],"prefix":"10.1186","volume":"8","author":[{"given":"Xuefeng","family":"Cui","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuai Cheng","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dongbo","family":"Bu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Babak","family":"Alipanahi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ming","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2013,2,25]]},"reference":[{"key":"180_CR1","doi-asserted-by":"publisher","first-page":"392","DOI":"10.1107\/S0108767391001071","volume":"47","author":"RA Engh","year":"1991","unstructured":"Engh RA, Huber R: Accurate bond and angle parameters for X-ray protein structure refinement. 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