HASEGAWA, Hitomi; HOLM, Liisa. Advances and pitfalls of protein structural alignment. Current Opinion in Structural Biology. 2009-06, roč. 19, čís. 3, s. 341–348. Dostupné online [cit. 2020-01-28]. ISSN0959-440X. DOI10.1016/j.sbi.2009.04.003.
CSABA, G.; BIRZELE, F.; ZIMMER, R. Protein structure alignment considering phenotypic plasticity. Bioinformatics. 2008-08-09, roč. 24, čís. 16, s. i98–i104. Dostupné online [cit. 2020-01-28]. ISSN1367-4803. DOI10.1093/bioinformatics/btn271.
GUERLER, Aysam; KNAPP, Ernst-Walter. Novel protein folds and their nonsequential structural analogs. Protein Science. 2008-08, roč. 17, čís. 8, s. 1374–1382. Dostupné online [cit. 2020-01-28]. ISSN0961-8368. DOI10.1110/ps.035469.108.
MARTÍNEZ, Leandro; ANDREANI, Roberto; MARTÍNEZ, José Mario. Convergent algorithms for protein structural alignment. BMC Bioinformatics. 2007-08-22, roč. 8, čís. 1. Dostupné online [cit. 2020-01-28]. ISSN1471-2105. DOI10.1186/1471-2105-8-306.
MENKE, Matthew; BERGER, Bonnie; COWEN, Lenore. Matt: Local Flexibility Aids Protein Multiple Structure Alignment. PLoS Computational Biology. 2008, roč. 4, čís. 1, s. e10. Dostupné online [cit. 2020-01-28]. ISSN1553-734X. DOI10.1371/journal.pcbi.0040010.
MOSCA, R.; SCHNEIDER, T. R. RAPIDO: a web server for the alignment of protein structures in the presence of conformational changes. Nucleic Acids Research. 2008-05-19, roč. 36, čís. Web Server, s. W42–W46. Dostupné online [cit. 2020-01-28]. ISSN0305-1048. DOI10.1093/nar/gkn197.
BIRZELE, F.; GEWEHR, J. E.; CSABA, G. Vorolign--fast structural alignment using Voronoi contacts. Bioinformatics. 2007-01-15, roč. 23, čís. 2, s. e205–e211. Dostupné online [cit. 2020-01-28]. ISSN1367-4803. DOI10.1093/bioinformatics/btl294.
LESLIN, C. M.; ABYZOV, A.; ILYIN, V. A. TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method. Nucleic Acids Research. 2007-01-03, roč. 35, čís. Database, s. D317–D321. Dostupné online [cit. 2020-01-28]. ISSN0305-1048. DOI10.1093/nar/gkl809.
SACAN, A.; TOROSLU, I. H.; FERHATOSMANOGLU, H. Integrated search and alignment of protein structures. Bioinformatics. 2008-10-22, roč. 24, čís. 24, s. 2872–2879. Dostupné online [cit. 2020-01-28]. ISSN1367-4803. DOI10.1093/bioinformatics/btn545.
LIU, Xin; ZHAO, Ya-Pu; ZHENG, Wei-Mou. CLEMAPS: Multiple alignment of protein structures based on conformational letters. Proteins: Structure, Function, and Bioinformatics. 2008-05-01, roč. 71, čís. 2, s. 728–736. Dostupné online [cit. 2020-01-28]. ISSN0887-3585. DOI10.1002/prot.21739.
SIERK, M. L. Sensitivity and selectivity in protein structure comparison. Protein Science. 2004-02-06, roč. 13, čís. 3, s. 773–785. Dostupné online [cit. 2020-01-28]. ISSN0961-8368. DOI10.1110/ps.03328504.
CHU, Chia-Han; TANG, Chuan Yi; TANG, Cheng-Yin. Angle-distance image matching techniques for protein structure comparison. Journal of Molecular Recognition. 2008-11, roč. 21, čís. 6, s. 442–452. Dostupné online [cit. 2020-01-28]. ISSN0952-3499. DOI10.1002/jmr.914.
KONAGURTHU, Arun S.; STUCKEY, Peter J.; LESK, Arthur M. Structural search and retrieval using a tableau representation of protein folding patterns. Bioinformatics. 2008-01-05, roč. 24, čís. 5, s. 645–651. Dostupné online [cit. 2020-01-28]. ISSN1460-2059. DOI10.1093/bioinformatics/btm641.
SHINDYALOV, I. N.; BOURNE, P. E. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Engineering Design and Selection. 1998-09-01, roč. 11, čís. 9, s. 739–747. Dostupné online [cit. 2020-01-28]. ISSN1741-0126. DOI10.1093/protein/11.9.739.
SHATSKY, Maxim; NUSSINOV, Ruth; WOLFSON, Haim J. Algorithms for Multiple Protein Structure Alignment and Structure-Derived Multiple Sequence Alignment. New Jersey: Humana Press Dostupné online. ISBN1-59745-574-1. S. 125–146.
TORARINSSON, E. Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure. Genome Research. 2006-07-01, roč. 16, čís. 7, s. 885–889. Dostupné online [cit. 2020-01-28]. ISSN1088-9051. DOI10.1101/gr.5226606.
worldcat.org
HASEGAWA, Hitomi; HOLM, Liisa. Advances and pitfalls of protein structural alignment. Current Opinion in Structural Biology. 2009-06, roč. 19, čís. 3, s. 341–348. Dostupné online [cit. 2020-01-28]. ISSN0959-440X. DOI10.1016/j.sbi.2009.04.003.
CSABA, G.; BIRZELE, F.; ZIMMER, R. Protein structure alignment considering phenotypic plasticity. Bioinformatics. 2008-08-09, roč. 24, čís. 16, s. i98–i104. Dostupné online [cit. 2020-01-28]. ISSN1367-4803. DOI10.1093/bioinformatics/btn271.
GUERLER, Aysam; KNAPP, Ernst-Walter. Novel protein folds and their nonsequential structural analogs. Protein Science. 2008-08, roč. 17, čís. 8, s. 1374–1382. Dostupné online [cit. 2020-01-28]. ISSN0961-8368. DOI10.1110/ps.035469.108.
MARTÍNEZ, Leandro; ANDREANI, Roberto; MARTÍNEZ, José Mario. Convergent algorithms for protein structural alignment. BMC Bioinformatics. 2007-08-22, roč. 8, čís. 1. Dostupné online [cit. 2020-01-28]. ISSN1471-2105. DOI10.1186/1471-2105-8-306.
MENKE, Matthew; BERGER, Bonnie; COWEN, Lenore. Matt: Local Flexibility Aids Protein Multiple Structure Alignment. PLoS Computational Biology. 2008, roč. 4, čís. 1, s. e10. Dostupné online [cit. 2020-01-28]. ISSN1553-734X. DOI10.1371/journal.pcbi.0040010.
MOSCA, R.; SCHNEIDER, T. R. RAPIDO: a web server for the alignment of protein structures in the presence of conformational changes. Nucleic Acids Research. 2008-05-19, roč. 36, čís. Web Server, s. W42–W46. Dostupné online [cit. 2020-01-28]. ISSN0305-1048. DOI10.1093/nar/gkn197.
BIRZELE, F.; GEWEHR, J. E.; CSABA, G. Vorolign--fast structural alignment using Voronoi contacts. Bioinformatics. 2007-01-15, roč. 23, čís. 2, s. e205–e211. Dostupné online [cit. 2020-01-28]. ISSN1367-4803. DOI10.1093/bioinformatics/btl294.
LESLIN, C. M.; ABYZOV, A.; ILYIN, V. A. TOPOFIT-DB, a database of protein structural alignments based on the TOPOFIT method. Nucleic Acids Research. 2007-01-03, roč. 35, čís. Database, s. D317–D321. Dostupné online [cit. 2020-01-28]. ISSN0305-1048. DOI10.1093/nar/gkl809.
SACAN, A.; TOROSLU, I. H.; FERHATOSMANOGLU, H. Integrated search and alignment of protein structures. Bioinformatics. 2008-10-22, roč. 24, čís. 24, s. 2872–2879. Dostupné online [cit. 2020-01-28]. ISSN1367-4803. DOI10.1093/bioinformatics/btn545.
LIU, Xin; ZHAO, Ya-Pu; ZHENG, Wei-Mou. CLEMAPS: Multiple alignment of protein structures based on conformational letters. Proteins: Structure, Function, and Bioinformatics. 2008-05-01, roč. 71, čís. 2, s. 728–736. Dostupné online [cit. 2020-01-28]. ISSN0887-3585. DOI10.1002/prot.21739.
SIERK, M. L. Sensitivity and selectivity in protein structure comparison. Protein Science. 2004-02-06, roč. 13, čís. 3, s. 773–785. Dostupné online [cit. 2020-01-28]. ISSN0961-8368. DOI10.1110/ps.03328504.
CHU, Chia-Han; TANG, Chuan Yi; TANG, Cheng-Yin. Angle-distance image matching techniques for protein structure comparison. Journal of Molecular Recognition. 2008-11, roč. 21, čís. 6, s. 442–452. Dostupné online [cit. 2020-01-28]. ISSN0952-3499. DOI10.1002/jmr.914.
KONAGURTHU, Arun S.; STUCKEY, Peter J.; LESK, Arthur M. Structural search and retrieval using a tableau representation of protein folding patterns. Bioinformatics. 2008-01-05, roč. 24, čís. 5, s. 645–651. Dostupné online [cit. 2020-01-28]. ISSN1460-2059. DOI10.1093/bioinformatics/btm641.
SHINDYALOV, I. N.; BOURNE, P. E. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Engineering Design and Selection. 1998-09-01, roč. 11, čís. 9, s. 739–747. Dostupné online [cit. 2020-01-28]. ISSN1741-0126. DOI10.1093/protein/11.9.739.
TORARINSSON, E. Thousands of corresponding human and mouse genomic regions unalignable in primary sequence contain common RNA structure. Genome Research. 2006-07-01, roč. 16, čís. 7, s. 885–889. Dostupné online [cit. 2020-01-28]. ISSN1088-9051. DOI10.1101/gr.5226606.