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Structural alignment software

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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[edit]

NAME Description Class Type Flexible Link Author Year
ARTEMIS[1] Topology-independent superposition of RNA/DNA 3D structures and structure-based sequence alignment AllA Pair No download Bohdan D.R.; Bujnicki J.M.; Baulin E.F. 2024
ARTEM[2][3] Superposition of two arbitrary RNA/DNA 3D structure fragments & 3D motif identification AllA Pair No download Bohdan D.R.; Voronina V.V.; Bujnicki J.M.; Baulin E.F. 2023
foldseek[4] Fast and accurate protein structure alignment and visualisation Seq Pair Yes server download M. van Kempen & S. Kim & C. Tumescheit & M. Mirdita & J. Lee & C. Gilchrist & J. Söding & M. Steinegger 2023
3decision Protein structure repository with visualisation and structural analytics tools Seq Multi Yes site P. Schmidtke 2015
MAMMOTH MAtching Molecular Models Obtained from Theory Pair No server download CEM Strauss & AR Ortiz 2002
CE Combinatorial Extension Pair No server I. Shindyalov 2000
CE-MC Combinatorial Extension-Monte Carlo Multi No server C. Guda 2004
DaliLite Distance Matrix Alignment C-Map Pair No server and download L. Holm 1993
TM-align TM-score based protein structure alignment Pair nil server and download Y. Zhang & J. Skolnick 2005
mTM-align Multiple protein structure alignment based on TM-align Multi No server and download R. Dong, Z. Peng, Y. Zhang & J. Yang 2018
VAST Vector Alignment Search Tool SSE Pair nil server S. Bryant 1996
PrISM Protein Informatics Systems for Modeling SSE Multi nil server B. Honig 2000
MOE Molecular Operating Environment. Extensive platform for protein and protein-ligand structure modelling. Cα, AllA, Seq Multi No site Chemical Computing Group 2000
SSAP Sequential Structure Alignment Program SSE Multi No server C. Orengo & W. Taylor 1989
SARF2 Spatial ARrangements of Backbone Fragments SSE Pair nil server N. Alexandrov 1996
KENOBI/K2 NA SSE Pair nil server Z. Weng 2000
STAMP STructural Alignment of Multiple Proteins Multi No download server R. Russell & G. Barton 1992
MASS Multiple Alignment by Secondary Structure SSE Multi No server O. Dror & H. Wolfson 2003
SCALI Structural Core ALIgnment of proteins Seq/C-Map Pair nil server download X. Yuan & C. Bystroff 2004
DEJAVU NA SSE Pair nil server GJ. Kleywegt 1997
SSM Secondary Structure Matching SSE Multi nil server E. Krissinel 2003
SHEBA Structural Homology by Environment-Based Alignment Seq Pair nil server J Jung & B Lee 2000
LGA[5] Local-Global Alignment, and Global Distance Test (GDT-TS) structure similarity measure Cα, AllA, any atom Pair nil server and download A. Zemla 2003
POSA Partial Order Structure Alignment Multi Yes server Y. Ye & A. Godzik 2005
PyMOL "super" command does sequence-independent 3D alignment Protein Hybrid No site W. L. DeLano 2007
FATCAT Flexible Structure AlignmenT by Chaining Aligned Fragment Pairs Allowing Twists Pair Yes server Y. Ye & A. Godzik 2003
deconSTRUCT Database search on substructural level and pairwise alignment. SSE Multi No server ZH. Zhang et al. 2010
Matras MArkovian TRAnsition of protein Structure Cα & SSE Pair nil server K. Nishikawa 2000
MAMMOTH-mult MAMMOTH-based multiple structure alignment Multi No server D. Lupyan 2005
Protein3Dfit NA C-Map Pair nil server D. Schomburg 1994
PRIDE PRobability of IDEntity Pair nil server S. Pongor 2002
FAST FAST Alignment and Search Tool Pair nil server J. Zhu 2004
C-BOP Coordinate-Based Organization of Proteins N/A Multi nil server E. Sandelin 2005
ProFit Protein least-squares Fitting Multi nil server ACR. Martin 1996
TOPOFIT Alignment as a superimposition of common volumes at a topomax point Pair nil server VA. Ilyin 2004
MUSTANG MUltiple STructural AligNment AlGorithm Cα & C-Map Multi nil download A.S. Konagurthu et al. 2006
URMS Unit-vector RMSD Pair nil server K. Kedem 2003
LOCK Hierarchical protein structure superposition SSE Pair No NA AP. Singh 1997
LOCK 2 Improvements over LOCK SSE Pair No download J. Shapiro 2003
CBA Consistency Based Alignment SSE Multi nil download J. Ebert 2006
TetraDA Tetrahedral Decomposition Alignment SSE Multi Yes NA J. Roach 2005
STRAP STRucture based Alignment Program Multi nil server C. Gille 2006
LOVOALIGN Low Order Value Optimization methods for Structural Alignment Pair nil server Andreani et al. 2006
GANGSTA Genetic Algorithm for Non-sequential, Gapped protein STructure Alignment SSE/C-Map Pair No server B. Kolbeck 2006
GANGSTA+ Combinatorial algorithm for nonsequential and gapped structural alignment SSE/C-Map Pair No server A. Guerler & E.W. Knapp 2008
MatAlign[6] Protein Structure Comparison by Matrix Alignment C-Map Pair nil site Z. Aung & K.L. Tan 2006
Vorolign Fast structure alignment using Voronoi contacts C-Map Multi Yes server F. Birzele et al. 2006
EXPRESSO Fast Multiple Structural Alignment using T-Coffee and Sap Multi nil site C. Notredame et al. 2007
CAALIGN Cα Align Multi nil site T.J. Oldfield 2007
YAKUSA Internal Coordinates and BLAST type algorithm Pair nil site M. Carpentier et al. 2005
BLOMAPS Conformation-based alphabet alignments Multi nil server W-M. Zheng & S. Wang 2008
CLEPAPS Conformation-based alphabet alignments Pair nil server W-M. Zheng & S. Wang 2008
TALI F Torsion Angle ALIgnment Pair No NA X. Mioa 2006
MolCom NA Geometry Multi nil NA S.D. O'Hearn 2003
MALECON NA Geometry Multi nil NA S. Wodak 2004
FlexProt Flexible Alignment of Protein Structures Pair Yes server M. Shatsky & H. Wolfson 2002
MultiProt Multiple Alignment of Protein Structures Geometry Multi No server M. Shatsky & H. Wolfson 2004
CTSS Protein Structure Alignment Using Local Geometrical Features Geometry Pair nil site T. Can 2004
CURVE NA Geometry Multi No site D. Zhi 2006
Matt Multiple Alignment with Translations and Twists Multi Yes server download M. Menke 2008
TopMatch[7] Protein structure alignment and visualization of structural similarities; alignment of multiprotein complexes Pair No server download M. Sippl & M. Wiederstein 2012
SSGS Secondary Structure Guided Superimposition Ca Pair No site G. Wainreb et al. 2006
Matchprot Comparison of protein structures by growing neighborhood alignments Pair No server S. Bhattacharya et al. 2007
UCSF Chimera see MatchMaker tool and "matchmaker" command Seq & SSE Multi No site E. Meng et al. 2006
FLASH Fast aLignment Algorithm for finding Structural Homology of proteins SSE Pair No NA E.S.C. Shih & M-J Hwang 2003
RAPIDO Rapid Alignment of Protein structures In the presence of Domain mOvements Pair Yes server R. Mosca & T.R. Schneider 2008
ComSubstruct Structural Alignment based on Differential Geometrical Encoding Geometry Pair Yes site N. Morikawa 2008
ProCKSI Protein (Structure) Comparison, Knowledge, Similarity and Information Other Pair No site D. Barthel et al. 2007
SARST Structure similarity search Aided by Ramachandran Sequential Transformation Pair nil site W-C. Lo et al. 2007
Fr-TM-align Fragment-TM-score based protein structure alignment Pair no site S.B. Pandit & J. Skolnick 2008
TOPS+ COMPARISON Comparing topological models of protein structures enhanced with ligand information Topology Pair Yes server M. Veeramalai & D. Gilbert 2008
TOPS++FATCAT Flexible Structure AlignmenT by Chaining Aligned Fragment Pairs Allowing Twists derived from TOPS+ String Model Pair Yes server M. Veeramalai et al. 2008
MolLoc Molecular Local Surface Alignment Surf Pair No server M.E. Bock et al. 2007
FASE Flexible Alignment of Secondary Structure Elements SSE Pair Yes NA J. Vesterstrom & W. R. Taylor 2006
SABERTOOTH Protein Structural Alignment based on a vectorial Structure Representation Pair Yes server F. Teichert et al. 2007
STON NA Pair No site C. Eslahchi et al. 2009
SALIGN Sequence-Structure Hybrid Method Seq Multi No site M.S. Madhusudhan et al. 2007
MAX-PAIRS NA Pair No site A. Poleksic 2009
THESEUS Maximum likelihood superpositioning Multi No site D.L. Theobald & D.S. Wuttke 2006
TABLEAUSearch Structural Search and Retrieval using a Tableau Representation of Protein Folding Patterns SSE Pair No server A.S. Konagurthu et al. 2008
QP Tableau Search Tableau-based protein substructure search using quadratic programming SSE Pair No download server A.Stivala et al. 2009
ProSMoS Protein Structure Motif Search SSE Pair No server download S. Shi et al. 2007
MISTRAL Energy-based multiple structural alignment of proteins Multi No server C. Micheletti & H. Orland 2009
MSVNS for MaxCMO A simple and fast heuristic for protein structure comparison C-Map Pair No site D. Pelta et al. 2008
Structal Least Squares Root Mean Square deviation minimization by dynamic programming Pair No server download Gerstein & Levitt 2005
ProBiS[8] Detection of Structurally Similar Protein Binding Sites by Local Structural Alignment Surf Pair Yes server download J. Konc & D. Janezic 2010
ALADYN Dynamics-based Alignment: superposing proteins by matching their collective movements Pair No server Potestio et al. 2010
SWAPSC Sliding Window Analysis Procedure for detecting Selective Constraints for analysing genetic data structured for a family or phylogenetic tree using constraints in protein-coding sequence alignments. Seq Multi yes Server Mario A. Fares 2004
SA Tableau Search Fast and accurate protein substructure searching with simulated annealing and GPUs SSE Pair No download server A.Stivala et al. 2010
RCSB PDB Protein Comparison Tool Provides CE, FATCAT, CE variation for Circular Permutations, Sequence Alignments Pair yes server download A. Prlic et al. 2010
CSR Maximal common 3D motif; non-parametric; outputs pairwise correspondence; works also on small molecules SSE or Cα Pair No server download M. Petitjean 1998
EpitopeMatch discontinuous structure matching; induced fit consideration; flexible geometrical and physicochemical specificity definition; transplantation of similar spatial arrangements of amino acid residues Cα-AllA Multi Yes download S. Jakuschev 2011
CLICK Topology-independent 3D structure comparison SSE & Cα & SASA Pair Yes server M. Nguyen 2011
Smolign Spatial motifs based protein structural alignment SSE & C-Map Multi Yes download H. Sun 2010
3D-Blast Comparing three-dimensional shape-density Density Pair No server L. Mavridis et al. 2011
DEDAL DEscriptor Defined ALignment SSE & Cα & C-Map Pair Yes server P. Daniluk & B. Lesyng 2011
msTALI multiple sTructure ALIgnment Cα & Dihed & SSE & Surf Multi Yes server P. Shealy & H. Valafar 2012
mulPBA multiple PB sequence alignment PB Multi Yes NA A.P. Joseph et al. 2012
SAS-Pro Similtaneous Alignment and Superimposition of PROteins ??? Pair Yes server Shah & Sahinidis 2012
MIRAGE-align Match Index based structural alignment method SSE & PPE Pair No website K. Hung et al. 2012
SPalign Structure Pairwise alignment Pair No server download Y. Yang et al. 2012
Kpax[9] Fast Pairwise or Multiple Alignments using Gaussian Overlap Other Pair Yes website D.W. Ritchie 2016
DeepAlign[10] Protein structure alignment beyond spatial proximity (evolutionary information and hydrogen-bonding are taken into consideration) Cα + Seq Pair No download server S. Wang and J. Xu 2013
3DCOMB[11] extension of DeepAlign Multi No download server S. Wang and J. Xu 2012
TS-AMIR[12] A topology string alignment method for intensive rapid protein structure comparison SSE & Cα Pair No NA J. Razmara et al. 2012
MICAN[13] MICAN can handle Multiple-chains, Inverse alignments, C α only models, Alternative alignments, and Non-sequential alignments Pair No download S.Minami et al. 2013
SPalignNS[14] Structure Pairwise alignment Non-Sequential Pair No server download P. Brown et al. 2015
Fit3D[15] highly accurate screening for small structural motifs featuring definition of position-specific exchanges, detection of intra- and inter-molecular occurrences, definition of arbitrary atoms used for motif alignment AllA, Cα Multi No server download F. Kaiser et al. 2015
MMLigner[16] Bayesian statistical inference of alignments based on information theory and compression. Pair Yes server download J. Collier et al. 2017
RCSB PDB strucmotif-search[17] Small structural motifs search that takes seconds to run on 180k or more structures, with nucleic acid & bioassembly support AllA Multi No server/documentation download S. Bittrich et al. 2020

Key map:

  • Class:
  • -- 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
  • Flexible:
  • 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.


  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". bioRxiv. doi:10.1101/2024.04.06.588371.{{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)