Structural alignment software

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title: "Structural alignment software" type: doc version: 1 created: 2026-02-28 author: "Wikipedia contributors" status: active scope: public tags: ["structural-bioinformatics-software"] topic_path: "science/biology" source: "https://en.wikipedia.org/wiki/Structural_alignment_software" license: "CC BY-SA 4.0" wikipedia_page_id: 0 wikipedia_revision_id: 0

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

::data[format=table] | NAME | Description || Class || Type || Flexible || Link || Author || Year | |---|---| | Reseek | Fast and accurate protein structure alignment, search and visualization | | MUSCLE-3D | Fast and accurate multiple protein structure alignment and visualization | | author= Bohdan D.R.; Bujnicki J.M.; Baulin E.F. |year=2024 |title=ARTEMIS: a method for topology-independent superposition of RNA 3D structures and structure-based sequence alignment |journal=Nucleic Acids Research |volume=52 |issue=18 |pages=10850–10861 |doi=10.1093/nar/gkae758|doi-access=free |pmid=39258540 |pmc=11472068 }} | Topology-independent superposition of RNA/DNA 3D structures and structure-based sequence alignment | | author= Bohdan D.R.; Voronina V.V.; Bujnicki J.M.; Baulin E.F. |year=2023 |title=A comprehensive survey of long-range tertiary interactions and motifs in non-coding RNA structures |journal=Nucleic Acids Research |volume=51 |issue=16 |pages=8367–8382 |doi=10.1093/nar/gkad605|doi-access=free |pmid=37471030 |pmc=10484739 }} | Superposition of two arbitrary RNA/DNA 3D structure fragments & 3D motif identification | | author=van Kempen M.; Kim S.; Tumescheit C.; Mirdita M.; Lee J.; Gilchrist C.; Söding J.; Steinegger M. |year=2023 |title=Fast and accurate protein structure search with Foldseek |journal=Nature Biotechnology |volume=42 |issue=2 |pages=243–246 |doi=10.1038/s41587-023-01773-0|pmid=37156916 |url=https://www.nature.com/articles/s41587-023-01773-0.pdf }} | Fast and accurate protein structure alignment and visualisation | | 3decision | Protein structure repository with visualisation and structural analytics tools | | MAMMOTH | MAtching Molecular Models Obtained from Theory | | CE | Combinatorial Extension | | CE-MC | Combinatorial Extension-Monte Carlo | | DaliLite | Distance Matrix Alignment | | TM-align | TM-score based protein structure alignment | | mTM-align | Multiple protein structure alignment based on TM-align | | VAST | Vector Alignment Search Tool | | PrISM | Protein Informatics Systems for Modeling | | MOE | Molecular Operating Environment. Extensive platform for protein and protein-ligand structure modelling. | | SSAP | Sequential Structure Alignment Program | | SARF2 | Spatial ARrangements of Backbone Fragments | | KENOBI/K2 | NA | | STAMP | STructural Alignment of Multiple Proteins | | MASS | Multiple Alignment by Secondary Structure | | SCALI | Structural Core ALIgnment of proteins | | DEJAVU | NA | | SSM | Secondary Structure Matching | | SHEBA | Structural Homology by Environment-Based Alignment | | author=Zemla A |year=2003 |title=LGA: A method for finding 3D similarities in protein structures |journal=Nucleic Acids Research |volume=31 |issue=13 |pages=3370–3374 |pmid=12824330 |pmc=168977 |doi=10.1093/nar/gkg571}} | Local-Global Alignment, and Global Distance Test (GDT-TS) structure similarity measure | | POSA | Partial Order Structure Alignment | | PyMOL | "super" command does sequence-independent 3D alignment | | FATCAT | Flexible Structure AlignmenT by Chaining Aligned Fragment Pairs Allowing Twists | | deconSTRUCT | Database search on substructural level and pairwise alignment. | | Matras | MArkovian TRAnsition of protein Structure | | MAMMOTH-mult | MAMMOTH-based multiple structure alignment | | Protein3Dfit | NA | | PRIDE | PRobability of IDEntity | | FAST | FAST Alignment and Search Tool | | C-BOP | Coordinate-Based Organization of Proteins | | ProFit | Protein least-squares Fitting | | TOPOFIT | Alignment as a superimposition of common volumes at a topomax point | | MUSTANG | MUltiple STructural AligNment AlGorithm | | URMS | Unit-vector RMSD | | LOCK | Hierarchical protein structure superposition | | LOCK 2 | Improvements over LOCK | | CBA | Consistency Based Alignment | | TetraDA | Tetrahedral Decomposition Alignment | | STRAP | STRucture based Alignment Program | | LOVOALIGN | Low Order Value Optimization methods for Structural Alignment | | GANGSTA | Genetic Algorithm for Non-sequential, Gapped protein STructure Alignment | | GANGSTA+ | Combinatorial algorithm for nonsequential and gapped structural alignment | | last=Aung|first=Zeyar|author2=Kian-Lee Tan |title=MatAlign: Precise protein structure comparison by matrix alignment|journal=Journal of Bioinformatics and Computational Biology|date=Dec 2006|volume=4|issue=6|pmid=17245810|pages=1197–216|doi=10.1142/s0219720006002417 |url=http://scholarbank.nus.edu.sg/handle/10635/39862 }} | Protein Structure Comparison by Matrix Alignment | | Vorolign | Fast structure alignment using Voronoi contacts | | EXPRESSO | Fast Multiple Structural Alignment using T-Coffee and Sap | | CAALIGN | Cα Align | | YAKUSA | Internal Coordinates and BLAST type algorithm | | BLOMAPS | Conformation-based alphabet alignments | | CLEPAPS | Conformation-based alphabet alignments | | TALI F | Torsion Angle ALIgnment | | MolCom | NA | | MALECON | NA | | FlexProt | Flexible Alignment of Protein Structures | | MultiProt | Multiple Alignment of Protein Structures | | CTSS | Protein Structure Alignment Using Local Geometrical Features | | CURVE | NA | | Matt | Multiple Alignment with Translations and Twists | | TopMatch | Protein structure alignment and visualization of structural similarities; alignment of multiprotein complexes | | SSGS | Secondary Structure Guided Superimposition | | Matchprot | Comparison of protein structures by growing neighborhood alignments | | UCSF Chimera | see MatchMaker tool and "matchmaker" command | | FLASH | Fast aLignment Algorithm for finding Structural Homology of proteins | | RAPIDO | Rapid Alignment of Protein structures In the presence of Domain mOvements | | ComSubstruct | Structural Alignment based on Differential Geometrical Encoding | | ProCKSI | Protein (Structure) Comparison, Knowledge, Similarity and Information | | SARST | Structure similarity search Aided by Ramachandran Sequential Transformation | | Fr-TM-align | Fragment-TM-score based protein structure alignment | | TOPS+ COMPARISON | Comparing topological models of protein structures enhanced with ligand information | | TOPS++FATCAT | Flexible Structure AlignmenT by Chaining Aligned Fragment Pairs Allowing Twists derived from TOPS+ String Model | | MolLoc | Molecular Local Surface Alignment | | FASE | Flexible Alignment of Secondary Structure Elements | | SABERTOOTH | Protein Structural Alignment based on a vectorial Structure Representation | | STON | NA | | SALIGN | Sequence-Structure Hybrid Method | | MAX-PAIRS | NA | | THESEUS | Maximum likelihood superpositioning | | TABLEAUSearch | Structural Search and Retrieval using a Tableau Representation of Protein Folding Patterns | | QP Tableau Search | Tableau-based protein substructure search using quadratic programming | | ProSMoS | Protein Structure Motif Search | | MISTRAL | Energy-based multiple structural alignment of proteins | | MSVNS for MaxCMO | A simple and fast heuristic for protein structure comparison | | Structal | Least Squares Root Mean Square deviation minimization by dynamic programming | | ProBiS | Detection of Structurally Similar Protein Binding Sites by Local Structural Alignment | | ALADYN | Dynamics-based Alignment: superposing proteins by matching their collective movements | | 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. | | SA Tableau Search | Fast and accurate protein substructure searching with simulated annealing and GPUs | | RCSB PDB Protein Comparison Tool | Provides CE, FATCAT, CE variation for Circular Permutations, Sequence Alignments | | CSR | Maximal common 3D motif; non-parametric; outputs pairwise correspondence; works also on small molecules | | EpitopeMatch | discontinuous structure matching; induced fit consideration; flexible geometrical and physicochemical specificity definition; transplantation of similar spatial arrangements of amino acid residues | | CLICK | Topology-independent 3D structure comparison | | Smolign | Spatial motifs based protein structural alignment | | 3D-Blast | Comparing three-dimensional shape-density | | DEDAL | DEscriptor Defined ALignment | | msTALI | multiple sTructure ALIgnment | | mulPBA | multiple PB sequence alignment | | SAS-Pro | Similtaneous Alignment and Superimposition of PROteins | | MIRAGE-align | Match Index based structural alignment method | | SPalign | Structure Pairwise alignment | | last=Ritchie|first=David W.|title=Calculating and scoring high quality multiple flexible protein structure alignments|journal=Bioinformatics|date=September 2016|doi=10.1093/bioinformatics/btw300|pmid=27187202|volume=32|issue=17 |pages= 2650–2658|doi-access=free}} | Fast Pairwise or Multiple Alignments using Gaussian Overlap | | last=Wang|first=Sheng |author2=Jianzhu Ma |author3=Jian Peng |author4=Jinbo Xu|title=Protein structure alignment beyond spatial proximity|journal=Scientific Reports|date=March 2013|doi=10.1038/srep01448|pmid=23486213|volume=3|article-number=1448 |pmc=3596798|bibcode=2013NatSR...3.1448W }} | Protein structure alignment beyond spatial proximity (evolutionary information and hydrogen-bonding are taken into consideration) | | last=Wang|first=Sheng |author2=Jian Peng |author3=Jinbo Xu|title=Alignment of distantly related protein structures: algorithm, bound and implications to homology modeling|journal=Bioinformatics|date=Sep 2011|volume=27|issue=18|pages=2537–45|doi=10.1093/bioinformatics/btr432|pmid=21791532|pmc=3167051}} | extension of DeepAlign | | last=Razmara|first=Jafar |author2=Safaai Deris |author3=Sepideh Parvizpour|title=TS-AMIR: a topology string alignment method for intensive rapid protein structure comparison|journal=Algorithms for Molecular Biology|date=Feb 2012|volume=7|issue=4|pmid=22336468|doi=10.1186/1748-7188-7-4|page=4|pmc=3298807 |doi-access=free }} | A topology string alignment method for intensive rapid protein structure comparison | | last=Minami|first=S.|author2=Sawada K. |author3=Chikenji G. |title=MICAN: a protein structure alignment algorithm that can handle Multiple-chains, Inverse alignments, C α only models, Alternative alignments, and Non-sequential alignments|journal=BMC Bioinformatics|date=Jan 2013|volume=14|issue=24|page=24|pmid=23331634 |doi=10.1186/1471-2105-14-24 |pmc=3637537 |doi-access=free }} | MICAN can handle Multiple-chains, Inverse alignments, C α only models, Alternative alignments, and Non-sequential alignments | | last=Brown|first=P.|author2=Pullan W. |author3=Yang Y. |author4=Zhou Y. |title=Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic|journal=Bioinformatics|date=Oct 2015|pmid=26454279 |doi=10.1093/bioinformatics/btv580 |volume=32 |issue=3|pages=370–7|doi-access=free|hdl=10072/101971|hdl-access=free}} | Structure Pairwise alignment Non-Sequential | | last=Kaiser|first=F.|author2=Eisold A. |author3=Bittrich S. |author4=Labudde D. |title=Fit3D: a web application for highly accurate screening of spatial resiudue patterns in protein structure data|journal=Bioinformatics|date=Oct 2015|pmid=26519504 |doi=10.1093/bioinformatics/btv637 |volume=32 |issue=5|pages=792–4|doi-access=free}} | 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 | | last=Collier|first=J.|author2=Allison L. |author3=Lesk A. |author4=Stuckey P. |author5=Garcia de la Banda M.|author5-link=María García de la Banda |author6=Konagurthu A. |title=Statistical inference of protein structural alignments using information and compression|journal=Bioinformatics|date=Apr 2017|pmid=28065899 |doi=10.1093/bioinformatics/btw757 |volume=33 |issue=7 |pages=1005–13|doi-access=free }} | Bayesian statistical inference of alignments based on information theory and compression. | | RCSB PDB strucmotif-search | Small structural motifs search that takes seconds to run on 180k or more structures, with nucleic acid & bioassembly support | ::

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

References

  1. Edgar, Robert C. (2024-11-01). "Protein structure alignment by Reseek improves sensitivity to remote homologs". Bioinformatics.
  2. (2024-10-28). "Muscle-3D: scalable multiple protein structure alignment".
  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.
  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.
  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.
  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.
  7. Zemla A. (2003). "LGA: A method for finding 3D similarities in protein structures". Nucleic Acids Research.
  8. Aung, Zeyar. (Dec 2006). "MatAlign: Precise protein structure comparison by matrix alignment". Journal of Bioinformatics and Computational Biology.
  9. Sippl, M.. (2012). "Detection of spatial correlations in protein structures and molecular complexes". Structure.
  10. (2009). "Tableau-based protein substructure search using quadratic programming". BMC Bioinformatics.
  11. (2010). "ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment". Bioinformatics.
  12. (2010). "Fast and accurate protein substructure searching with simulated annealing and GPUs". BMC Bioinformatics.
  13. Ritchie, David W.. (September 2016). "Calculating and scoring high quality multiple flexible protein structure alignments". Bioinformatics.
  14. Wang, Sheng. (March 2013). "Protein structure alignment beyond spatial proximity". Scientific Reports.
  15. Wang, Sheng. (Sep 2011). "Alignment of distantly related protein structures: algorithm, bound and implications to homology modeling". Bioinformatics.
  16. Razmara, Jafar. (Feb 2012). "TS-AMIR: a topology string alignment method for intensive rapid protein structure comparison". Algorithms for Molecular Biology.
  17. Minami, S.. (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.
  18. Brown, P.. (Oct 2015). "Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic". Bioinformatics.
  19. Kaiser, F.. (Oct 2015). "Fit3D: a web application for highly accurate screening of spatial resiudue patterns in protein structure data". Bioinformatics.
  20. Collier, J.. (Apr 2017). "Statistical inference of protein structural alignments using information and compression". Bioinformatics.
  21. Bittrich S, Burley SK, Rose AS. (2020). "Real-time structural motif searching in proteins using an inverted index strategy.". PLOS Comput Biol.

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