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

NAME Description Class Type Flexible Link Author Year
Reseek[1] Fast and accurate protein structure alignment, search and visualization Cα Pair Yes download

server

Edgar R.C. 2024
MUSCLE-3D[2] Fast and accurate multiple protein structure alignment and visualization Cα Multi Yes download Edgar R.C. & Tolstoy I 2024
ARTEMIS[3] 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[4][5] 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[6] 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 Cα Pair No server download CEM Strauss & AR Ortiz 2002
CE Combinatorial Extension Cα Pair No server I. Shindyalov 2000
CE-MC Combinatorial Extension-Monte Carlo Cα 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 Cα Pair nil server and download Y. Zhang & J. Skolnick 2005
mTM-align Multiple protein structure alignment based on TM-align Cα 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 Cα 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[7] 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 Cα 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 Cα 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 Cα Multi No server D. Lupyan 2005
Protein3Dfit NA C-Map Pair nil server D. Schomburg 1994
PRIDE PRobability of IDEntity Cα Pair nil server S. Pongor 2002
FAST FAST Alignment and Search Tool Cα 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 Cα Multi nil server ACR. Martin 1996
TOPOFIT Alignment as a superimposition of common volumes at a topomax point Cα 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 Cα 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 Cα Multi nil server C. Gille 2006
LOVOALIGN Low Order Value Optimization methods for Structural Alignment Cα 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[8] 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 Cα Multi nil site C. Notredame et al. 2007
CAALIGN Cα Align Cα Multi nil site T.J. Oldfield 2007
YAKUSA Internal Coordinates and BLAST type algorithm Cα Pair nil site M. Carpentier et al. 2005
BLOMAPS Conformation-based alphabet alignments Cα Multi nil server W-M. Zheng & S. Wang 2008
CLEPAPS Conformation-based alphabet alignments Cα Pair nil server W-M. Zheng & S. Wang 2008
TALI F Torsion Angle ALIgnment Cα 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 Cα 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 Cα Multi Yes server download M. Menke 2008
TopMatch[9] Protein structure alignment and visualization of structural similarities; alignment of multiprotein complexes Cα 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 Cα 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 Cα 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 Cα Pair nil site W-C. Lo et al. 2007
Fr-TM-align Fragment-TM-score based protein structure alignment Cα 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 Cα 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 Cα Pair Yes server F. Teichert et al. 2007
STON NA Cα 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 Cα Pair No site A. Poleksic 2009
THESEUS Maximum likelihood superpositioning Cα 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[10] Tableau-based protein substructure search using quadratic programming SSE Pair No download 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 Cα 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 Cα Pair No server download Gerstein & Levitt 2005
ProBiS[11] 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 Cα 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[12] Fast and accurate protein substructure searching with simulated annealing and GPUs SSE Pair No download A.Stivala et al. 2010
RCSB PDB Protein Comparison Tool Provides CE, FATCAT, CE variation for Circular Permutations, Sequence Alignments Cα 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 Cα Pair No server download Y. Yang et al. 2012
Kpax[13] Fast Pairwise or Multiple Alignments using Gaussian Overlap Other Pair Yes website D.W. Ritchie 2016
DeepAlign[14] 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[15] extension of DeepAlign Cα Multi No download server S. Wang and J. Xu 2012
TS-AMIR[16] A topology string alignment method for intensive rapid protein structure comparison SSE & Cα Pair No NA J. Razmara et al. 2012
MICAN[17] MICAN can handle Multiple-chains, Inverse alignments, C α only models, Alternative alignments, and Non-sequential alignments Cα Pair No download S.Minami et al. 2013
SPalignNS[18] Structure Pairwise alignment Non-Sequential Cα Pair No server download P. Brown et al. 2015
Fit3D[19] 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[20] Bayesian statistical inference of alignments based on information theory and compression. Cα Pair Yes server download J. Collier et al. 2017
RCSB PDB strucmotif-search[21] 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:
  • 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
  • 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.

References

  1. ^ Edgar, Robert C (2024-11-01). Elofsson, Arne (ed.). "Protein structure alignment by Reseek improves sensitivity to remote homologs". Bioinformatics. 40 (11) btae687. doi:10.1093/bioinformatics/btae687. ISSN 1367-4811. PMC 11601161. PMID 39546374.
  2. ^ Edgar, Robert C.; Tolstoy, Igor (2024-10-28). "Muscle-3D: scalable multiple protein structure alignment". bioRxiv 10.1101/2024.10.26.620413.
  3. ^ 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. 52 (18): 10850–10861. doi:10.1093/nar/gkae758. PMC 11472068. PMID 39258540.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  4. ^ 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)
  5. ^ Baulin E.F.; Bohdan D.R.; Kowalski D.; Serwatka M.; Świerczyńska J.; Żyra Z.; Bujnicki J.M. (2025). "ARTEM: a method for RNA tertiary motif identification with backbone permutations". Genome Biology. 26 (1): 226. doi:10.1186/s13059-025-03696-2. PMC 12306022. PMID 40721818.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  6. ^ 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. PMID 37156916.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  7. ^ 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.
  8. ^ 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.
  9. ^ 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.
  10. ^ Stivala, Alex; Wirth, Anthony; Stuckey, Peter J (2009). "Tableau-based protein substructure search using quadratic programming". BMC Bioinformatics. 10 (1): 153. doi:10.1186/1471-2105-10-153. ISSN 1471-2105. PMC 2705363. PMID 19450287.
  11. ^ 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.
  12. ^ Stivala, Alex D; Stuckey, Peter J; Wirth, Anthony I (2010). "Fast and accurate protein substructure searching with simulated annealing and GPUs". BMC Bioinformatics. 11 (1): 446. doi:10.1186/1471-2105-11-446. ISSN 1471-2105. PMC 2944279. PMID 20813068.
  13. ^ 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.
  14. ^ Wang, Sheng; Jianzhu Ma; Jian Peng; Jinbo Xu (March 2013). "Protein structure alignment beyond spatial proximity". Scientific Reports. 3 1448. Bibcode:2013NatSR...3.1448W. doi:10.1038/srep01448. PMC 3596798. PMID 23486213.
  15. ^ 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.
  16. ^ 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.
  17. ^ 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.
  18. ^ 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.
  19. ^ 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.
  20. ^ 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.
  21. ^ 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)
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