{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,16]],"date-time":"2026-03-16T12:27:47Z","timestamp":1773664067497,"version":"3.50.1"},"reference-count":38,"publisher":"Wiley","issue":"7","license":[{"start":{"date-parts":[[2008,12,31]],"date-time":"2008-12-31T00:00:00Z","timestamp":1230681600000},"content-version":"vor","delay-in-days":4566,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Protein Science"],"published-print":{"date-parts":[[1996,7]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Structurally similar but sequentially unrelated proteins have been discovered and rediscovered by many researchers, using a variety of structure comparison tools. For several pairs of such proteins, existing structural alignments obtained from the literature, as well as alignments prepared using several different similarity criteria, are compared with each other. It is shown that, in general, they differ from each other, with differences increasing with diminishing sequence similarity. Differences are particularly strong between alignments optimizing global similarity measures, such as RMS deviation between C\u03b1 atoms, and alignments focusing on more local features, such as packing or interaction pattern similarity. Simply speaking, by putting emphasis on different aspects of structure, different structural alignments show the unquestionable similarity in a different way. With differences between various alignments extending to a point where they can differ at all positions, analysis of structural similarities leads to contradictory results reported by groups using different alignment techniques.<\/jats:p><jats:p>The problem of uniqueness and stability of structural alignments is further studied with the help of visualization of the suboptimal alignments. It is shown that alignments are often degenerate and whole families of alignments can be generated with almost the same score as the \u201coptimal alignment.\u201d However, for some similarity criteria, specially those based on side\u2010chain positions, rather than C\u03b1 positions, alignments in some areas of the protein are unique. This opens the question of how and if the structural alignments can be used as \u201cstandards of truth\u201d for protein comparison.<\/jats:p>","DOI":"10.1002\/pro.5560050711","type":"journal-article","created":{"date-parts":[[2009,2,10]],"date-time":"2009-02-10T04:03:50Z","timestamp":1234238630000},"page":"1325-1338","source":"Crossref","is-referenced-by-count":187,"title":["The structural alignment between two proteins: Is there a unique answer?"],"prefix":"10.1002","volume":"5","author":[{"given":"Adam","family":"Godzik","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","published-online":{"date-parts":[[2008,12,31]]},"reference":[{"key":"e_1_2_1_2_1","first-page":"1","volume-title":"Metalloproteins, part I","author":"Adman ET","year":"1985"},{"key":"e_1_2_1_3_1","doi-asserted-by":"publisher","DOI":"10.1002\/pro.5560020602"},{"key":"e_1_2_1_4_1","doi-asserted-by":"publisher","DOI":"10.1126\/science.1853201"},{"key":"e_1_2_1_5_1","volume-title":"Protein structure classification","author":"CATH","year":"1995"},{"key":"e_1_2_1_6_1","doi-asserted-by":"publisher","DOI":"10.1038\/357543a0"},{"key":"e_1_2_1_7_1","doi-asserted-by":"publisher","DOI":"10.1016\/0022-2836(82)90178-4"},{"key":"e_1_2_1_8_1","unstructured":"DALI.1995. 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