{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,11]],"date-time":"2026-01-11T01:37:27Z","timestamp":1768095447281,"version":"3.49.0"},"reference-count":10,"publisher":"Oxford University Press (OUP)","issue":"15","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Accurate alignment of protein sequences and\/or structures is crucial for many biological analyses, including functional annotation of proteins, classifying protein sequences into families, and comparative protein structure modeling. Described here is a web interface to SALIGN, the versatile protein multiple sequence\/structure alignment module of MODELLER. The web server automatically determines the best alignment procedure based on the inputs, while allowing the user to override default parameter values. Multiple alignments are guided by a dendrogram computed from a matrix of all pairwise alignment scores. When aligning sequences to structures, SALIGN uses structural environment information to place gaps optimally. If two multiple sequence alignments of related proteins are input to the server, a profile\u2013profile alignment is performed. All features of the server have been previously optimized for accuracy, especially in the contexts of comparative modeling and identification of interacting protein partners.<\/jats:p>\n               <jats:p>Availability: The SALIGN web server is freely accessible to the academic community at http:\/\/salilab.org\/salign. SALIGN is a module of the MODELLER software, also freely available to academic users (http:\/\/salilab.org\/modeller).<\/jats:p>\n               <jats:p>Contact: \u00a0sali@salilab.org; madhusudhan@bii.a-star.edu.sg<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts302","type":"journal-article","created":{"date-parts":[[2012,5,23]],"date-time":"2012-05-23T00:13:16Z","timestamp":1337731996000},"page":"2072-2073","source":"Crossref","is-referenced-by-count":74,"title":["SALIGN: a web server for alignment of multiple protein sequences and structures"],"prefix":"10.1093","volume":"28","author":[{"given":"Hannes","family":"Braberg","sequence":"first","affiliation":[{"name":"1 Department of Cellular and Molecular Pharmacology, 2Department of Bioengineering and Therapeutic Sciences, 3Department of Pharmaceutical Chemistry, and California Institute of Quantitative Biosciences (QB3), University of California, San Francisco, CA 94158, USA, 4Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, 138671 Singapore, 5Department of Biological Sciences, National University of Singapore, Singapore and 6School of Biological Sciences, Nanyang Technological University, Singapore"},{"name":"1 Department of Cellular and Molecular Pharmacology, 2Department of Bioengineering and Therapeutic Sciences, 3Department of Pharmaceutical Chemistry, and California Institute of Quantitative Biosciences (QB3), University of California, San Francisco, CA 94158, USA, 4Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, 138671 Singapore, 5Department of Biological Sciences, National University of Singapore, Singapore and 6School of Biological Sciences, Nanyang Technological University, Singapore"},{"name":"1 Department of Cellular and Molecular Pharmacology, 2Department of Bioengineering and Therapeutic Sciences, 3Department of Pharmaceutical Chemistry, and California Institute of Quantitative Biosciences (QB3), University of California, San Francisco, CA 94158, USA, 4Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, 138671 Singapore, 5Department of Biological Sciences, National University of Singapore, Singapore and 6School of Biological Sciences, Nanyang Technological University, Singapore"}]},{"given":"Benjamin M.","family":"Webb","sequence":"additional","affiliation":[{"name":"1 Department of Cellular and Molecular Pharmacology, 2Department of Bioengineering and Therapeutic Sciences, 3Department of Pharmaceutical Chemistry, and California Institute of Quantitative Biosciences (QB3), University of California, San Francisco, CA 94158, USA, 4Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, 138671 Singapore, 5Department of Biological Sciences, National University of Singapore, Singapore and 6School of Biological Sciences, Nanyang Technological University, Singapore"},{"name":"1 Department of Cellular and Molecular Pharmacology, 2Department of Bioengineering and Therapeutic Sciences, 3Department of Pharmaceutical Chemistry, and California Institute of Quantitative Biosciences (QB3), University of California, San Francisco, CA 94158, USA, 4Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, 138671 Singapore, 5Department of Biological Sciences, National University of Singapore, Singapore and 6School of Biological Sciences, Nanyang Technological University, Singapore"}]},{"given":"Elina","family":"Tjioe","sequence":"additional","affiliation":[{"name":"1 Department of Cellular and Molecular Pharmacology, 2Department of Bioengineering and Therapeutic Sciences, 3Department of Pharmaceutical Chemistry, and California Institute of Quantitative Biosciences (QB3), University of California, San Francisco, CA 94158, USA, 4Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, 138671 Singapore, 5Department of Biological Sciences, National University of Singapore, Singapore and 6School of Biological Sciences, Nanyang Technological University, Singapore"},{"name":"1 Department of Cellular and Molecular Pharmacology, 2Department of Bioengineering and Therapeutic Sciences, 3Department of Pharmaceutical Chemistry, and California Institute of Quantitative Biosciences (QB3), University of California, San Francisco, CA 94158, USA, 4Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, 138671 Singapore, 5Department of Biological Sciences, National University of Singapore, Singapore and 6School of Biological Sciences, Nanyang Technological University, Singapore"}]},{"given":"Ursula","family":"Pieper","sequence":"additional","affiliation":[{"name":"1 Department of Cellular and Molecular Pharmacology, 2Department of Bioengineering and Therapeutic Sciences, 3Department of Pharmaceutical Chemistry, and California Institute of Quantitative Biosciences (QB3), University of California, San Francisco, CA 94158, USA, 4Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, 138671 Singapore, 5Department of Biological Sciences, National University of Singapore, Singapore and 6School of Biological Sciences, Nanyang Technological University, Singapore"},{"name":"1 Department of Cellular and Molecular Pharmacology, 2Department of Bioengineering and Therapeutic Sciences, 3Department of Pharmaceutical Chemistry, and California Institute of Quantitative Biosciences (QB3), University of California, San Francisco, CA 94158, USA, 4Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, 138671 Singapore, 5Department of Biological Sciences, National University of Singapore, Singapore and 6School of Biological Sciences, Nanyang Technological University, Singapore"}]},{"given":"Andrej","family":"Sali","sequence":"additional","affiliation":[{"name":"1 Department of Cellular and Molecular Pharmacology, 2Department of Bioengineering and Therapeutic Sciences, 3Department of Pharmaceutical Chemistry, and California Institute of Quantitative Biosciences (QB3), University of California, San Francisco, CA 94158, USA, 4Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, 138671 Singapore, 5Department of Biological Sciences, National University of Singapore, Singapore and 6School of Biological Sciences, Nanyang Technological University, Singapore"},{"name":"1 Department of Cellular and Molecular Pharmacology, 2Department of Bioengineering and Therapeutic Sciences, 3Department of Pharmaceutical Chemistry, and California Institute of Quantitative Biosciences (QB3), University of California, San Francisco, CA 94158, USA, 4Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, 138671 Singapore, 5Department of Biological Sciences, National University of Singapore, Singapore and 6School of Biological Sciences, Nanyang Technological University, Singapore"}]},{"given":"M.S.","family":"Madhusudhan","sequence":"additional","affiliation":[{"name":"1 Department of Cellular and Molecular Pharmacology, 2Department of Bioengineering and Therapeutic Sciences, 3Department of Pharmaceutical Chemistry, and California Institute of Quantitative Biosciences (QB3), University of California, San Francisco, CA 94158, USA, 4Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, 138671 Singapore, 5Department of Biological Sciences, National University of Singapore, Singapore and 6School of Biological Sciences, Nanyang Technological University, Singapore"},{"name":"1 Department of Cellular and Molecular Pharmacology, 2Department of Bioengineering and Therapeutic Sciences, 3Department of Pharmaceutical Chemistry, and California Institute of Quantitative Biosciences (QB3), University of California, San Francisco, CA 94158, USA, 4Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, 138671 Singapore, 5Department of Biological Sciences, National University of Singapore, Singapore and 6School of Biological Sciences, Nanyang Technological University, Singapore"},{"name":"1 Department of Cellular and Molecular Pharmacology, 2Department of Bioengineering and Therapeutic Sciences, 3Department of Pharmaceutical Chemistry, and California Institute of Quantitative Biosciences (QB3), University of California, San Francisco, CA 94158, USA, 4Bioinformatics Institute, 30 Biopolis Street, #07-01, Matrix, 138671 Singapore, 5Department of Biological Sciences, National University of Singapore, Singapore and 6School of Biological Sciences, Nanyang Technological University, Singapore"}]}],"member":"286","published-online":{"date-parts":[[2012,5,21]]},"reference":[{"key":"2023012512452695900_B1","doi-asserted-by":"crossref","first-page":"2943","DOI":"10.1093\/nar\/gkl353","article-title":"Protein complex compositions predicted by structural similarity","volume":"34","author":"Davis","year":"2006","journal-title":"Nucleic Acids Res."},{"key":"2023012512452695900_B2","doi-asserted-by":"crossref","first-page":"W13","DOI":"10.1093\/nar\/gkr245","article-title":"T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension","volume":"39","author":"Di 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