{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,21]],"date-time":"2026-05-21T05:53:58Z","timestamp":1779342838198,"version":"3.51.4"},"reference-count":34,"publisher":"Wiley","issue":"5","license":[{"start":{"date-parts":[[2008,12,31]],"date-time":"2008-12-31T00:00:00Z","timestamp":1230681600000},"content-version":"vor","delay-in-days":4627,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Protein Science"],"published-print":{"date-parts":[[1996,5]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>In protein fold recognition, one assigns a probe amino acid sequence of unknown structure to one of a library of target 3D structures. Correct assignment depends on effective scoring of the probe sequence for its compatibility with each of the target structures. Here we show that, in addition to the amino acid sequence of the probe, sequence\u2010derived properties of the probe sequence (such as the predicted secondary structure) are useful in fold assignment. The additional measure of compatibility between probe and target is the level of agreement between the predicted secondary structure of the probe and the known secondary structure of the target fold. That is, we recommend a sequence\u2010structure compatibility function that combines previously developed compatibility functions (such as the 3D\u20101D scores of Bowie et al. [1991] or sequence\u2010sequence replacement tables) with the predicted secondary structure of the probe sequence.<\/jats:p><jats:p>The effect on fold assignment of adding predicted secondary structure is evaluated here by using a benchmark set of proteins (Fischer et al., 1996a). The 3D structures of the probe sequences of the benchmark are actually known, but are ignored by our method. The results show that the inclusion of the predicted secondary structure improves fold assignment by about 25%. The results also show that, if the true secondary structure of the probe were known, correct fold assignment would increase by an additional 8\u201332%. We conclude that incorporating sequence\u2010derived predictions significantly improves assignment of sequences to known 3D folds.<\/jats:p><jats:p>Finally, we apply the new method to assign folds to sequences in the SWISSPROT database; six fold assignments are given that are not detectable by standard sequence\u2010sequence comparison methods; for two of these, the fold is known from X\u2010ray crystallography and the fold assignment is correct.<\/jats:p>","DOI":"10.1002\/pro.5560050516","type":"journal-article","created":{"date-parts":[[2010,7,12]],"date-time":"2010-07-12T06:30:54Z","timestamp":1278916254000},"page":"947-955","source":"Crossref","is-referenced-by-count":281,"title":["Protein fold recognition using sequence\u2010derived predictions"],"prefix":"10.1002","volume":"5","author":[{"given":"Daniel","family":"Fischer","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Eisenberg","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2008,12,31]]},"reference":[{"key":"e_1_2_1_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(91)90193-A"},{"key":"e_1_2_1_3_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(05)80360-2"},{"key":"e_1_2_1_4_1","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/20.suppl.2019"},{"key":"e_1_2_1_5_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0022-2836(77)80200-3"},{"key":"e_1_2_1_6_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0959-440X(05)80118-6"},{"key":"e_1_2_1_7_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1853201"},{"key":"e_1_2_1_8_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.340160110"},{"key":"e_1_2_1_9_1","first-page":"345","volume-title":"Atlas 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