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

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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. & 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
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[20] | 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" (in en). Bioinformatics 40 (11). doi:10.1093/bioinformatics/btae687. ISSN 1367-4811. PMID 39546374. PMC 11601161. https://academic.oup.com/bioinformatics/article/doi/10.1093/bioinformatics/btae687/7901215.
2. ↑ Edgar, Robert C.; Tolstoy, Igor (2024-10-28) (in en), Muscle-3D: scalable multiple protein structure alignment, bioRxiv, doi:10.1101/2024.10.26.620413, https://www.biorxiv.org/content/10.1101/2024.10.26.620413v1, retrieved 2025-10-23
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. PMID 39258540.
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. PMID 37471030.
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. doi:10.1186/s13059-025-03696-2.
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". Nature Biotechnology 42 (2): 243–246. doi:10.1038/s41587-023-01773-0. PMID 37156916. https://www.nature.com/articles/s41587-023-01773-0.pdf.
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. 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. PMID 22483118.
10. ↑ Stivala, Alex; Wirth, Anthony; Stuckey, Peter J (2009). "Tableau-based protein substructure search using quadratic programming" (in en). BMC Bioinformatics 10 (1): 153. doi:10.1186/1471-2105-10-153. ISSN 1471-2105. 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. PMID 20305268.
12. ↑ Stivala, Alex D; Stuckey, Peter J; Wirth, Anthony I (2010). "Fast and accurate protein substructure searching with simulated annealing and GPUs" (in en). BMC Bioinformatics 11 (1): 446. doi:10.1186/1471-2105-11-446. ISSN 1471-2105. 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. doi:10.1038/srep01448. PMID 23486213. Bibcode: 2013NatSR...3.1448W.
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. 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. 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. 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. 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. ↑ Bittrich S, Burley SK, Rose AS (2020). "Real-time structural motif searching in proteins using an inverted index strategy.". PLOS Comput Biol 16 (12). doi:10.1371/journal.pcbi.1008502. PMID 33284792. Bibcode: 2020PLSCB..16E8502B.

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