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Structural alignment software

This list of structural comparison and alignment software is a compilation of software tools and web portals used in pairwise or multiple structural comparison and structural alignment.

Structural comparison and alignment

Key map:

  • Cα -- Backbone Atom (Cα) Alignment;
  • AllA -- All Atoms Alignment;
  • SSE -- Secondary Structure Elements Alignment;
  • Seq -- Sequence-based alignment
  • Pair -- Pairwise Alignment (2 structures *only*);
  • Multi -- Multiple Structure Alignment (MStA);
  • C-Map -- Contact Map
  • Surf -- Connolly Molecular Surface Alignment
  • SASA -- Solvent Accessible Surface Area
  • Dihed -- Dihedral Backbone Angles
  • PB -- Protein Blocks
  • No -- Only rigid-body transformations are considered between the structures being compared.
  • Yes -- The method allows for some flexibility within the structures being compared, such as movements around hinge regions.

References

  1. ^ Bohdan D.R.; Bujnicki J.M.; Baulin E.F. (2024). "ARTEMIS: a method for topology-independent superposition of RNA 3D structures and structure-based sequence alignment". Nucleic Acids Research. doi:10.1093/nar/gkae758.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  2. ^ Bohdan D.R.; Voronina V.V.; Bujnicki J.M.; Baulin E.F. (2023). "A comprehensive survey of long-range tertiary interactions and motifs in non-coding RNA structures". Nucleic Acids Research. 51 (16): 8367–8382. doi:10.1093/nar/gkad605. PMC 10484739. PMID 37471030.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  3. ^ Baulin E.F.; Bohdan D.R.; Kowalski D.; Serwatka M.; Świerczyńska J.; Żyra Z.; Bujnicki J.M. (2024). "ARTEM: a method for RNA tertiary motif identification with backbone permutations, and its example application to kink-turn-like motifs". bioRxiv. doi:10.1101/2024.05.31.596898.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  4. ^ van Kempen M.; Kim S.; Tumescheit C.; Mirdita M.; Lee J.; Gilchrist C.; Söding J.; Steinegger M. (2023). "Fast and accurate protein structure search with Foldseek" (PDF). Nature Biotechnology. 42 (2): 243–246. doi:10.1038/s41587-023-01773-0.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  5. ^ Zemla A (2003). "LGA: A method for finding 3D similarities in protein structures". Nucleic Acids Research. 31 (13): 3370–3374. doi:10.1093/nar/gkg571. PMC 168977. PMID 12824330.
  6. ^ Aung, Zeyar; Kian-Lee Tan (Dec 2006). "MatAlign: Precise protein structure comparison by matrix alignment". Journal of Bioinformatics and Computational Biology. 4 (6): 1197–216. doi:10.1142/s0219720006002417. PMID 17245810.
  7. ^ Sippl, M.; Wiederstein, M. (2012). "Detection of spatial correlations in protein structures and molecular complexes". Structure. 20 (4): 718–728. doi:10.1016/j.str.2012.01.024. PMC 3320710. PMID 22483118.
  8. ^ Janez Konc; Dušanka Janežič (2010). "ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment". Bioinformatics. 26 (9): 1160–1168. doi:10.1093/bioinformatics/btq100. PMC 2859123. PMID 20305268.
  9. ^ Ritchie, David W. (September 2016). "Calculating and scoring high quality multiple flexible protein structure alignments". Bioinformatics. 32 (17): 2650–2658. doi:10.1093/bioinformatics/btw300. PMID 27187202.
  10. ^ Wang, Sheng; Jianzhu Ma; Jian Peng; Jinbo Xu (March 2013). "Protein structure alignment beyond spatial proximity". Scientific Reports. 3: 1448. Bibcode:2013NatSR...3E1448W. doi:10.1038/srep01448. PMC 3596798. PMID 23486213.
  11. ^ Wang, Sheng; Jian Peng; Jinbo Xu (Sep 2011). "Alignment of distantly related protein structures: algorithm, bound and implications to homology modeling". Bioinformatics. 27 (18): 2537–45. doi:10.1093/bioinformatics/btr432. PMC 3167051. PMID 21791532.
  12. ^ Razmara, Jafar; Safaai Deris; Sepideh Parvizpour (Feb 2012). "TS-AMIR: a topology string alignment method for intensive rapid protein structure comparison". Algorithms for Molecular Biology. 7 (4): 4. doi:10.1186/1748-7188-7-4. PMC 3298807. PMID 22336468.
  13. ^ Minami, S.; Sawada K.; Chikenji G. (Jan 2013). "MICAN : a protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, C α only models, Alternative alignments, and Non-sequential alignments". BMC Bioinformatics. 14 (24): 24. doi:10.1186/1471-2105-14-24. PMC 3637537. PMID 23331634.
  14. ^ Brown, P.; Pullan W.; Yang Y.; Zhou Y. (Oct 2015). "Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic". Bioinformatics. 32 (3): 370–7. doi:10.1093/bioinformatics/btv580. hdl:10072/101971. PMID 26454279.
  15. ^ Kaiser, F.; Eisold A.; Bittrich S.; Labudde D. (Oct 2015). "Fit3D: a web application for highly accurate screening of spatial resiudue patterns in protein structure data". Bioinformatics. 32 (5): 792–4. doi:10.1093/bioinformatics/btv637. PMID 26519504.
  16. ^ Collier, J.; Allison L.; Lesk A.; Stuckey P.; Garcia de la Banda M.; Konagurthu A. (Apr 2017). "Statistical inference of protein structural alignments using information and compression". Bioinformatics. 33 (7): 1005–13. doi:10.1093/bioinformatics/btw757. PMID 28065899.
  17. ^ Bittrich S, Burley SK, Rose AS (2020). "Real-time structural motif searching in proteins using an inverted index strategy". PLOS Comput Biol. 16 (12): e1008502. Bibcode:2020PLSCB..16E8502B. doi:10.1371/journal.pcbi.1008502. PMC 7746303. PMID 33284792.{{cite journal}}: CS1 maint: multiple names: authors list (link)