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Obtaining a structure without a hydrophobic core requires a different type of external force field than those generated by a water. The examples are membrane proteins, where the distribution of hydrophobicity is opposite to that of water-soluble proteins. Apart from these two extreme examples, the process of protein folding can be directed by chaperones, resulting in a structure devoid of a hydrophobic core.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>The current work presents such example: DnaJ Hsp40 in complex with alkaline phosphatase PhoA-U (PDB ID\u20146PSI)\u2014the client molecule. The availability of WT form of the folding protein\u2014alkaline phosphatase (PDB ID\u20141EW8) enables a comparative analysis of the structures: at the stage of interaction with the chaperone and the final, folded structure of this biologically active protein. The fuzzy oil drop model in its modified FOD-M version was used in this analysis, taking into account the influence of an external force field, in this case coming from a chaperone.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>The FOD-M model identifies the external force field introduced by chaperon influencing the folding proces. The identified specific external force field can be applied in Ab Initio protein structure prediction as the environmental conditioning the folding proces.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12859-023-05545-0","type":"journal-article","created":{"date-parts":[[2023,11,6]],"date-time":"2023-11-06T22:01:54Z","timestamp":1699308114000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":12,"title":["Ab initio protein structure prediction: the necessary presence of external force field as it is delivered by Hsp40 chaperone"],"prefix":"10.1186","volume":"24","author":[{"given":"Irena","family":"Roterman","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Katarzyna","family":"Stapor","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Leszek","family":"Konieczny","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2023,11,7]]},"reference":[{"issue":"1323","key":"5545_CR1","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1098\/rstb.1995.0051","volume":"348","author":"FU Hartl","year":"1995","unstructured":"Hartl FU. 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