{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T00:45:03Z","timestamp":1740185103653,"version":"3.37.3"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2021,8,16]],"date-time":"2021-08-16T00:00:00Z","timestamp":1629072000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004821","name":"IMDiK PAN","doi-asserted-by":"crossref","award":["Z-526\/22","PP\/BF-501-D111-01-1110102","POIG.02.03.00-00-003\/09"],"award-info":[{"award-number":["Z-526\/22","PP\/BF-501-D111-01-1110102","POIG.02.03.00-00-003\/09"]}],"id":[{"id":"10.13039\/501100004821","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Biocentrum-Ochota","award":["POIG.02.01.00-14-122\/09"],"award-info":[{"award-number":["POIG.02.01.00-14-122\/09"]}]},{"name":"Physics at the basis of new technologies"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,12,22]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>The well-known fact that protein structures are more conserved than their sequences forms the basis of several areas of computational structural biology. Methods based on the structure analysis provide more complete information on residue conservation in evolutionary processes. This is crucial for the determination of evolutionary relationships between proteins and for the identification of recurrent structural patterns present in biomolecules involved in similar functions. However, algorithmic structural alignment is much more difficult than multiple sequence alignment. This study is devoted to the development and applications of DAMA\u2014a novel effective environment capable to compute and analyze multiple structure alignments.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>DAMA is based on local structural similarities, using local 3D structure descriptors and thus accounts for nearest-neighbor molecular environments of aligned residues. It is constrained neither by protein topology nor by its global structure. DAMA is an extension of our previous study (DEDAL) which demonstrated the applicability of local descriptors to pairwise alignment problems. Since the multiple alignment problem is NP-complete, an effective heuristic approach has been developed without imposing any artificial constraints. The alignment algorithm searches for the largest, consistent ensemble of similar descriptors. The new method is capable to capture most of the biologically significant similarities present in canonical test sets and is discriminatory enough to prevent the emergence of larger, but meaningless, solutions. Tests performed on the test sets, including protein kinases, demonstrate DAMA\u2019s capability of identifying equivalent residues, which should be very useful in discovering the biological nature of proteins similarity. Performance profiles show the advantage of DAMA over other methods, in particular when using a strict similarity measure QC, which is the ratio of correctly aligned columns, and when applying the methods to more difficult cases.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>DAMA is available online at http:\/\/dworkowa.imdik.pan.pl\/EP\/DAMA. Linux binaries of the software are available upon request.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab571","type":"journal-article","created":{"date-parts":[[2021,8,12]],"date-time":"2021-08-12T11:25:54Z","timestamp":1628767554000},"page":"80-85","source":"Crossref","is-referenced-by-count":2,"title":["DAMA: a method for computing multiple alignments of protein structures using local structure descriptors"],"prefix":"10.1093","volume":"38","author":[{"given":"Pawe\u0142","family":"Daniluk","sequence":"first","affiliation":[{"name":"Bioinformatics Laboratory, Mossakowski Medical Research Centre, Polish Academy of Sciences , 02-106 Warsaw, Poland"}]},{"given":"Tymoteusz","family":"Oleniecki","sequence":"additional","affiliation":[{"name":"College of Inter-Faculty Individual Studies in Mathematics and Natural Sciences, University of Warsaw , 02-089 Warsaw, Poland"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5528-902X","authenticated-orcid":false,"given":"Bogdan","family":"Lesyng","sequence":"additional","affiliation":[{"name":"Department of Biophysics, Faculty of Physics, University of Warsaw , 02-093 Warsaw, Poland"}]}],"member":"286","published-online":{"date-parts":[[2021,8,16]]},"reference":[{"key":"2023020108390236700_btab571-B1","doi-asserted-by":"crossref","first-page":"981","DOI":"10.1016\/j.csbj.2020.03.011","article-title":"Caretta \u2013 a multiple protein structure alignment and feature extraction suite","volume":"18","author":"Akdel","year":"2020","journal-title":"Comput. 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