# 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](/source/structural_comparison) and [structural alignment](/source/structural_alignment).
==Structural comparison and alignment==
{| class="sortable wikitable" border="0" align="center" style="border: 1px solid #999; background-color:#FFFFFF"
|-align="left" bgcolor="#CCCCCC"
! NAME
! Description || Class || Type || Flexible || Link || Author || Year
|-
|Reseek[{{Cite journal |last=Edgar |first=Robert C |date=2024-11-01 |editor-last=Elofsson |editor-first=Arne |title=Protein structure alignment by Reseek improves sensitivity to remote homologs |journal=Bioinformatics |language=en |volume=40 |issue=11 |article-number=btae687 |doi=10.1093/bioinformatics/btae687 |issn=1367-4811 |pmc=11601161 |pmid=39546374}}]
|Fast and accurate protein structure alignment, search and visualization
|Cα
|Pair
|Yes
|[https://github.com/rcedgar/reseek download]
[https://reseek.online server]
|Edgar R.C.
|2024
|-
|MUSCLE-3D[{{cite bioRxiv|last1=Edgar |first1=Robert C. |title=Muscle-3D: scalable multiple protein structure alignment |date=2024-10-28 |language=en |biorxiv=10.1101/2024.10.26.620413 |last2=Tolstoy |first2=Igor}}]
|Fast and accurate multiple protein structure alignment and visualization
|Cα
|Multi
|Yes
|[https://github.com/rcedgar/muscle/ download]
|Edgar R.C. & Tolstoy I
|2024
|-
| ARTEMIS[{{Cite journal |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 }}][{{cite journal |author= Sordyl D.; Cielesz J.; Bohdan D.R.; Baulin E.F.; Bujnicki J.M. |year=2026 |title=ARTEM server: an online tool for nucleic acid 3D motif searches, 3D structure superposition and structure-based alignment |journal=Nucleic Acids Research |doi=10.1093/nar/gkag428|doi-access=free}}]
| Topology-independent superposition of RNA/DNA 3D structures and structure-based sequence alignment || AllA || Pair || No ||[https://artemserver.genesilico.pl/ server]
[https://github.com/david-bogdan-r/ARTEMIS download]
|| Bohdan D.R.; Bujnicki J.M.; Baulin E.F. || 2024
|--bgcolor="#EFEFEF"
|-
| ARTEM[{{cite journal |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 }}][{{cite journal |author= Baulin E.F.; Bohdan D.R.; Kowalski D.; Serwatka M.; Świerczyńska J.; Żyra Z.; Bujnicki J.M. |year=2025 |title=ARTEM: a method for RNA tertiary motif identification with backbone permutations |journal=Genome Biology |volume=26 |issue=1 |page=226 |doi=10.1186/s13059-025-03696-2|doi-access=free |pmid=40721818 |pmc=12306022 }}][{{cite journal |author= Sordyl D.; Cielesz J.; Bohdan D.R.; Baulin E.F.; Bujnicki J.M. |year=2026 |title=ARTEM server: an online tool for nucleic acid 3D motif searches, 3D structure superposition and structure-based alignment |journal=Nucleic Acids Research |doi=10.1093/nar/gkag428|doi-access=free}}]
| Superposition of two arbitrary RNA/DNA 3D structure fragments & 3D motif identification || AllA || Pair || No ||[https://artemserver.genesilico.pl/ server]
[https://github.com/david-bogdan-r/ARTEM download]
|| Bohdan D.R.; Voronina V.V.; Bujnicki J.M.; Baulin E.F. || 2023
|--bgcolor="#EFEFEF"
|-
| foldseek[{{cite journal |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 || Seq || Pair || Yes ||[https://search.foldseek.com/ server] [https://foldseek.com/ download] || M. van Kempen & S. Kim & C. Tumescheit & M. Mirdita & J. Lee & C. Gilchrist & J. Söding & M. Steinegger || 2023
|--bgcolor="#EFEFEF"
|-
| 3decision
| Protein structure repository with visualisation and structural analytics tools || Seq || Multi || Yes ||[https://3decision.discngine.com/ site] || P. Schmidtke|| 2015
|--bgcolor="#EFEFEF"
|-
| [MAMMOTH](/source/Structural_alignment)
| '''MA'''tching '''M'''olecular '''M'''odels '''O'''btained from '''T'''heory || Cα || Pair || No ||[http://ub.cbm.uam.es/software/online/mamothmult.php server] [http://ub.cbm.uam.es/software/mammoth.php download] ||CEM Strauss & AR Ortiz|| 2002
|--bgcolor="#EFEFEF"
| [CE](/source/Structural_alignment)
| '''C'''ombinatorial '''E'''xtension || Cα || Pair || No || [http://source.rcsb.org/jfatcatserver/ceHome.jsp server] || I. Shindyalov || 2000
|--bgcolor="#EFEFEF"
| [CE-MC](/source/Structural_alignment)
| '''C'''ombinatorial '''E'''xtension-'''M'''onte '''C'''arlo || Cα || Multi || No || [http://schubert.bio.uniroma1.it/CEMC/ server] || C. Guda || 2004
|-
| [DaliLite](/source/Structural_alignment)
| '''D'''istance Matrix '''Ali'''gnment || C-Map || Pair || No || [http://ekhidna.biocenter.helsinki.fi/dali server and download] || L. Holm || 1993
|--bgcolor="#EFEFEF"
| TM-align
| '''TM-'''score based protein structure '''align'''ment || [Cα](/source/C%CE%B1) || Pair || nil ||[http://zhanglab.ccmb.med.umich.edu/TM-align server and download] || Y. Zhang & J. Skolnick || 2005
|-
|mTM-align
|Multiple protein structure alignment based on TM-align
|Cα
|Multi
|No
|[http://yanglab.nankai.edu.cn/mTM-align/ server and download]
|R. Dong, Z. Peng, Y. Zhang & J. Yang
|2018
|-
| VAST
| '''V'''ector '''A'''lignment '''S'''earch '''T'''ool || SSE || Pair || nil || [https://www.ncbi.nlm.nih.gov/Structure/VAST/vast.shtml server] || S. Bryant || 1996
|--bgcolor="#EFEFEF"
| PrISM
| '''Pr'''otein '''I'''nformatics '''S'''ystems for '''M'''odeling || SSE || Multi || nil || [http://honiglab.cpmc.columbia.edu server] || B. Honig || 2000
|-
| [MOE](/source/Molecular_Operating_Environment)
| '''M'''olecular '''O'''perating '''E'''nvironment. Extensive platform for protein and protein-ligand structure modelling. || Cα, AllA, Seq || Multi || No ||[http://www.chemcomp.com/MOE-Molecular_Operating_Environment.htm site] || Chemical Computing Group || 2000
|-
| [SSAP](/source/Structural_alignment)
| '''S'''equential '''S'''tructure '''A'''lignment '''P'''rogram || SSE || Multi || No ||[http://www.cathdb.info/cgi-bin/SsapServer.pl server] || C. Orengo & W. Taylor || 1989
|--bgcolor="#EFEFEF"
| SARF2
| '''S'''patial '''AR'''rangements of Backbone '''F'''ragments || SSE || Pair || nil ||[http://123d.ncifcrf.gov/sarf2.html server] || N. Alexandrov || 1996
|-
| KENOBI/K2
|NA || SSE || Pair || nil || [http://zlab.bu.edu/k2/ server] || Z. Weng || 2000
|--bgcolor="#EFEFEF"
| STAMP
|'''ST'''ructural '''A'''lignment of '''M'''ultiple '''P'''roteins || Cα || Multi || No || [http://www.compbio.dundee.ac.uk/downloads/stamp/ download] [http://www.russell.embl.de/cgi-bin/pdc/stamp.pl server] || R. Russell & G. Barton|| 1992
|-
| MASS
| '''M'''ultiple '''A'''lignment by '''S'''econdary '''S'''tructure || SSE || Multi || No || [http://bioinfo3d.cs.tau.ac.il/MASS server] || O. Dror & H. Wolfson || 2003
|--bgcolor="#EFEFEF"
| SCALI
| '''S'''tructural '''C'''ore '''ALI'''gnment of proteins|| Seq/C-Map || Pair || nil || [http://www.bioinfo.rpi.edu/bystrc/SCALI server] [http://www.bioinfo.rpi.edu/bystrc/pub/scali.tgz download]|| X. Yuan & C. Bystroff || 2004
|-
| DEJAVU
| NA || SSE || Pair || nil || [http://portray.bmc.uu.se/cgi-bin/dejavu/scripts/dejavu.pl server] || GJ. Kleywegt || 1997
|--bgcolor="#EFEFEF"
| SSM
| '''S'''econdary '''S'''tructure '''M'''atching || SSE || Multi || nil ||[https://www.ebi.ac.uk/msd-srv/ssm/ server] || E. Krissinel || 2003
|-
| SHEBA
| '''S'''tructural '''H'''omology by '''E'''nvironment-'''B'''ased '''A'''lignment|| Seq || Pair || nil || [https://archive.today/20041024193444/http://rex.nci.nih.gov/RESEARCH/basic/lmb/mms/sheba.htm server] || J Jung & B Lee || 2000
|--bgcolor="#EFEFEF"
| LGA[{{cite journal |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}}]
| '''L'''ocal-'''G'''lobal '''A'''lignment, and Global Distance Test (GDT-TS) structure similarity measure || Cα, AllA, any atom || Pair || nil || [http://proteinmodel.org/AS2TS/LGA/lga.html server and download] || A. Zemla || 2003
|-
| POSA
| '''P'''artial '''O'''rder '''S'''tructure '''A'''lignment || Cα || Multi || Yes ||[http://fatcat.burnham.org/POSA server] || Y. Ye & A. Godzik || 2005
|--bgcolor="#EFEFEF"
| [PyMOL](/source/PyMOL)
| "super" command does sequence-independent 3D alignment || Protein || Hybrid || No || [http://www.pymol.org site] || W. L. DeLano || 2007
|-
| FATCAT
| '''F'''lexible Structure '''A'''lignmen'''T''' by '''C'''haining '''A'''ligned Fragment Pairs Allowing '''T'''wists || Cα || Pair || Yes || [http://fatcat.burnham.org server] || Y. Ye & A. Godzik || 2003
|--bgcolor="#EFEFEF"
| deconSTRUCT
| Database search on substructural level and pairwise alignment. || SSE || Multi || No || [http://epsf.bmad.bii.a-star.edu.sg/struct_server.html server] || ZH. Zhang et al.|| 2010
|-
| Matras
| '''MA'''rkovian '''TRA'''nsition of protein '''S'''tructure || Cα & SSE || Pair || nil || [http://strcomp.protein.osaka-u.ac.jp/matras/ server] || K. Nishikawa || 2000
|--bgcolor="#EFEFEF"
| [MAMMOTH-mult](/source/Structural_alignment)
| '''MAMMOTH'''-based multiple structure alignment || Cα || Multi || No || [http://ub.cbm.uam.es/software/online/mamothmult.php server] || D. Lupyan || 2005
|-
| Protein3Dfit
| NA || C-Map || Pair || nil ||[http://biotool.uni-koeln.de:8080/3dalign_neu/cgi-bin/3daligner.py server] || D. Schomburg || 1994
|--bgcolor="#EFEFEF"
| PRIDE
| '''PR'''obability of '''IDE'''ntity || Cα || Pair || nil || [http://pride.szbk.u-szeged.hu server] || S. Pongor || 2002
|-
| FAST
| '''F'''AST '''A'''lignment and '''S'''earch '''T'''ool || Cα || Pair || nil || [http://biowulf.bu.edu/FAST/ server] || J. Zhu || 2004
|--bgcolor="#EFEFEF"
| C-BOP
| '''C'''oordinate-'''B'''ased '''O'''rganization of '''P'''roteins || N/A || Multi || nil ||[http://www.sbc.su.se/~erik/cbop/ server] || E. Sandelin || 2005
|-
| ProFit
| '''Pro'''tein least-squares '''Fit'''ting || Cα || Multi || nil || [http://www.bioinf.org.uk/software/profit/ server] || ACR. Martin || 1996
|--bgcolor="#EFEFEF"
| TOPOFIT
| Alignment as a superimposition of common volumes at a topomax point || Cα || Pair || nil ||[http://topofit.ilyinlab.org/topofit server] || VA. Ilyin || 2004
|-
| MUSTANG
| '''MU'''ltiple '''ST'''ructural '''A'''lig'''N'''ment Al'''G'''orithm || Cα & C-Map|| Multi || nil ||[http://www.csse.monash.edu.au/~karun/Site/mustang.html download] || A.S. Konagurthu ''et al.'' || 2006
|--bgcolor="#EFEFEF"
| URMS
| '''U'''nit-vector '''RMSD'''|| Cα || Pair || nil ||[https://cbsusrv01.tc.cornell.edu/urms/ server] || [K. Kedem](/source/Klara_Kedem) || 2003
|-
| LOCK
| Hierarchical protein structure superposition || SSE || Pair || No || NA || AP. Singh || 1997
|--bgcolor="#EFEFEF"
| LOCK 2
| Improvements over LOCK || SSE || Pair || No || [http://brutlag.stanford.edu/ download] || J. Shapiro || 2003
|-
| CBA
| '''C'''onsistency '''B'''ased '''A'''lignment || SSE || Multi || nil || [http://brutlag.stanford.edu/software/ download] || J. Ebert || 2006
|--bgcolor="#EFEFEF"
| TetraDA
| '''Tetra'''hedral '''D'''ecomposition '''A'''lignment || SSE || Multi || Yes || NA || J. Roach || 2005
|-
| STRAP
| '''STR'''ucture based '''A'''lignment '''P'''rogram || Cα || Multi || nil || [http://3d-alignment.eu/ server] || C. Gille || 2006
|--bgcolor="#EFEFEF"
| LOVOALIGN
| '''L'''ow '''O'''rder '''V'''alue '''O'''ptimization methods for Structural '''Align'''ment || Cα || Pair || nil || [http://www.ime.unicamp.br/~martinez/lovoalign/ server] || Andreani ''et al.'' || 2006
|-
| GANGSTA
| '''G'''enetic '''A'''lgorithm for '''N'''on-sequential, '''G'''apped protein '''ST'''ructure '''A'''lignment || SSE/C-Map || Pair || No || [http://agknapp.chemie.fu-berlin.de/gangsta_old server] || B. Kolbeck || 2006
|--bgcolor="#EFEFEF"
| [GANGSTA+](/source/Structural_alignment)
| Combinatorial algorithm for nonsequential and gapped structural alignment || SSE/C-Map || Pair || No || [http://agknapp.chemie.fu-berlin.de/gplus server] ||A. Guerler & E.W. Knapp || 2008
|--bgcolor="#EFEFEF"
| MatAlign[{{cite journal|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 '''Mat'''rix '''Align'''ment || C-Map || Pair || nil ||[http://www.aungz.com/MatAlign/ site] || Z. Aung & K.L. Tan || 2006
|-
| Vorolign
| Fast structure alignment using Voronoi contacts || C-Map || Multi || Yes ||[http://www2.bio.ifi.lmu.de/Vorolign/ server] || F. Birzele ''et al.'' || 2006
|--bgcolor="#EFEFEF"
| EXPRESSO
| Fast Multiple Structural Alignment using T-Coffee and Sap|| Cα || Multi || nil ||[http://www.tcoffee.org site] || C. Notredame ''et al.'' || 2007
|-
| CAALIGN
| Cα Align || Cα || Multi || nil || [http://www.accelrys.com site] || T.J. Oldfield || 2007
|--bgcolor="#EFEFEF"
| YAKUSA
| Internal Coordinates and BLAST type algorithm|| Cα || Pair || nil || [http://bioserv.rpbs.jussieu.fr/Yakusa/index.html site] || M. Carpentier ''et al.'' || 2005
|-
| BLOMAPS
| Conformation-based alphabet alignments || Cα || Multi || nil || [http://www.weblab.org.cn/program.inputForm.do?program=BLoMAPS server] || W-M. Zheng & S. Wang || 2008
|--bgcolor="#EFEFEF"
| CLEPAPS
| Conformation-based alphabet alignments || Cα || Pair || nil || [http://www.weblab.org.cn/program.inputForm.do?program=CLePAPS server] || W-M. Zheng & S. Wang || 2008
|-
| TALI F
| '''T'''orsion Angle '''ALI'''gnment || Cα || Pair || No || NA || X. Mioa || 2006
|--bgcolor="#EFEFEF"
| MolCom
| NA || Geometry || Multi || nil || NA || S.D. O'Hearn || 2003
|-
| MALECON
| NA || Geometry ||Multi || nil || NA || S. Wodak || 2004
|--bgcolor="#EFEFEF"
| FlexProt
| '''Flex'''ible Alignment of '''Prot'''ein Structures || Cα || Pair || Yes || [http://bioinfo3d.cs.tau.ac.il/FlexProt/ server] || M. Shatsky & H. Wolfson|| 2002
|-
| MultiProt
| '''Multi'''ple Alignment of '''Prot'''ein Structures || Geometry || Multi || No || [http://bioinfo3d.cs.tau.ac.il/MultiProt server] || M. Shatsky & H. Wolfson|| 2004
|--bgcolor="#EFEFEF"
| CTSS
| Protein Structure Alignment Using Local Geometrical Features || Geometry || Pair || nil || [http://www.ceng.metu.edu.tr/~tcan/CTSS/ site] || T. Can || 2004
|-
| CURVE
| NA || Geometry || Multi || No || [http://pops.burnham.org/curve/ site] || D. Zhi || 2006
|--bgcolor="#EFEFEF"
| Matt
| '''M'''ultiple '''A'''lignment with '''T'''ranslations and '''T'''wists || Cα || Multi || Yes ||[http://bcb.cs.tufts.edu/mattweb server] [http://matt.cs.tufts.edu download] || M. Menke || 2008
|-
| [http://topmatch.services.came.sbg.ac.at TopMatch][{{cite journal|last=Sippl|first=M.|author2=Wiederstein, M. |title=Detection of spatial correlations in protein structures and molecular complexes|journal=Structure|date=2012|volume=20|issue=4|pages=718–728|doi=10.1016/j.str.2012.01.024|pmid=22483118|pmc=3320710}}]
| Protein structure alignment and visualization of structural similarities; alignment of multiprotein complexes || Cα || Pair || No || [http://topmatch.services.came.sbg.ac.at server] [https://www.came.sbg.ac.at/app_download.php?app=topmatch download]|| M. Sippl & M. Wiederstein || 2012
|--bgcolor="#EFEFEF"
| SSGS
| '''S'''econdary '''S'''tructure '''G'''uided '''S'''uperimposition || Ca || Pair || No|| [http://www.tau.ac.il/~wainreb site] || G. Wainreb ''et al.'' || 2006
|-
| Matchprot
| Comparison of protein structures by growing neighborhood alignments || Cα || Pair || No ||[http://mllab.csa.iisc.ernet.in/mp2/runprog.html server] || S. Bhattacharya ''et al.'' || 2007
|--bgcolor="#EFEFEF"
| [UCSF Chimera](/source/UCSF_Chimera)
| see '''MatchMaker''' tool and "matchmaker" command || Seq & SSE || Multi || No|| [http://www.cgl.ucsf.edu/chimera site] || E. Meng ''et al.'' || 2006
|-
| FLASH
| '''F'''ast a'''L'''ignment '''A'''lgorithm for finding '''S'''tructural '''H'''omology of proteins || SSE || Pair || No || NA || E.S.C. Shih & M-J Hwang || 2003
|--bgcolor="#EFEFEF"
| RAPIDO
| '''R'''apid '''A'''lignment of '''P'''rotein structures '''I'''n the presence of '''D'''omain m'''O'''vements || Cα || Pair || Yes || [http://webapps.embl-hamburg.de/rapido/ server] || R. Mosca & T.R. Schneider || 2008
|-
| ComSubstruct
| Structural Alignment based on Differential Geometrical Encoding || Geometry || Pair || Yes || [http://www.genocript.com/ site] || N. Morikawa || 2008
|--bgcolor="#EFEFEF"
| ProCKSI
| '''Pro'''tein (Structure) '''C'''omparison, '''K'''nowledge, '''S'''imilarity and '''I'''nformation || Other || Pair || No || [http://www.procksi.net/ site] || D. Barthel ''et al.'' || 2007
|-
| SARST
| '''S'''tructure similarity search '''A'''ided by '''R'''amachandran '''S'''equential '''T'''ransformation
| Cα || Pair || nil || |[http://sarst.life.nthu.edu.tw/sarst/ site] || W-C. Lo ''et al.'' || 2007
|--bgcolor="#EFEFEF"
| Fr-TM-align
| '''Fr'''agment-'''TM'''-score based protein structure '''align'''ment || Cα || Pair || no ||[http://cssb.biology.gatech.edu/skolnick/files/FrTMalign site] || S.B. Pandit & J. Skolnick || 2008
|-
| TOPS+ COMPARISON
| Comparing topological models of protein structures enhanced with ligand information || Topology || Pair || Yes || [http://balabio.dcs.gla.ac.uk/mallika/WebTOPS/ server] || M. Veeramalai & D. Gilbert || 2008
|--bgcolor="#EFEFEF"
| TOPS++FATCAT
| '''F'''lexible Structure '''A'''lignmen'''T''' by '''C'''haining '''A'''ligned Fragment Pairs Allowing '''T'''wists derived from '''TOPS+''' String Model || Cα || Pair || Yes || [http://fatcat.burnham.org/TOPS server] || M. Veeramalai ''et al.'' || 2008
|-
| MolLoc
| '''Mol'''ecular '''Loc'''al Surface Alignment || Surf || Pair || No|| [http://bcb.dei.unipd.it/MolLoc/ server] || M.E. Bock ''et al.'' || 2007
|--bgcolor="#EFEFEF"
| FASE
| '''F'''lexible '''A'''lignment of '''S'''econdary Structure '''E'''lements || SSE || Pair || Yes || NA || J. Vesterstrom & W. R. Taylor || 2006
|-
| [SABERTOOTH](/source/Structural_alignment)
| Protein Structural Alignment based on a vectorial Structure Representation || Cα || Pair || Yes ||[http://www.fkp.tu-darmstadt.de/sabertooth/ server] || F. Teichert ''et al.'' || 2007
|--bgcolor="#EFEFEF"
| STON
| NA || Cα || Pair || No || [http://bioinf.cs.ipm.ac.ir/softwares/ston site] || C. Eslahchi ''et al.'' || 2009
|-
| SALIGN
| Sequence-Structure Hybrid Method || Seq || Multi || No ||[http://salilab.org/salign/ site] || M.S. Madhusudhan ''et al.'' || 2007
|--bgcolor="#EFEFEF"
| MAX-PAIRS
| NA || Cα || Pair || No || [http://bioinformatics.cs.uni.edu/opt_align.html site] || A. Poleksic || 2009
|-
| THESEUS
| Maximum likelihood superpositioning || Cα || Multi || No || [http://www.theseus3d.org/ site] || D.L. Theobald & D.S. Wuttke|| 2006
|--bgcolor="#EFEFEF"
| TABLEAUSearch
| Structural Search and Retrieval using a Tableau Representation of Protein Folding Patterns || SSE || Pair || No || [http://hollywood.bx.psu.edu/TabSearch server] || A.S. Konagurthu ''et al.''|| 2008
|-
| QP Tableau Search[{{Cite journal |last1=Stivala |first1=Alex |last2=Wirth |first2=Anthony |last3=Stuckey |first3=Peter J |date=2009 |title=Tableau-based protein substructure search using quadratic programming |journal=BMC Bioinformatics |language=en |volume=10 |issue=1 |page=153 |doi=10.1186/1471-2105-10-153 |doi-access=free |issn=1471-2105 |pmc=2705363 |pmid=19450287}}]
| Tableau-based protein substructure search using quadratic programming || SSE || Pair || No || [https://github.com/stivalaa/qptabsearch download] || A.Stivala ''et al.''|| 2009
|--bgcolor="#EFEFEF"
| ProSMoS
| '''Pro'''tein '''S'''tructure '''Mo'''tif '''S'''earch || SSE || Pair || No || [http://prodata.swmed.edu/ProSMoS/ server] [ftp://iole.swmed.edu/pub/ProSMoS download]{{dead link|date=May 2025|bot=medic}}{{cbignore|bot=medic}} || S. Shi ''et al.''|| 2007
|-
| MISTRAL
| Energy-based multiple structural alignment of proteins || Cα || Multi || No || [http://ipht.cea.fr/protein.php server] || C. Micheletti & H. Orland|| 2009
|--bgcolor="#EFEFEF"
| MSVNS for MaxCMO
| A simple and fast heuristic for protein structure comparison || C-Map || Pair || No || [http://modo.ugr.es/jrgonzalez/msvns4maxcmo site] || D. Pelta ''et al.'' || 2008
|-
| Structal
| Least Squares Root Mean Square deviation minimization by dynamic programming || Cα || Pair || No || [http://www.molmovdb.org/geometry/3dhmm/ server] [http://csb.stanford.edu/levitt/Structal/ download] || Gerstein & Levitt || 2005
|--bgcolor="#EFEFEF"
| [ProBiS](/source/ProBiS)[{{cite journal |author1=Janez Konc |author2=Dušanka Janežič |title=ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment |journal=Bioinformatics |volume=26 |issue=9 |pages=1160–1168 |year=2010 | url= |doi=10.1093/bioinformatics/btq100 |pmid=20305268 |pmc=2859123}}]
| Detection of Structurally Similar '''Pro'''tein '''Bi'''nding '''S'''ites by Local Structural Alignment || Surf || Pair || Yes|| [http://probis.cmm.ki.si/ server] [http://probis.cmm.ki.si/?what=parallel download] || J. Konc & D. Janezic || 2010
|-
| ALADYN
| '''Dyn'''amics-based '''Al'''ignment: superposing proteins by matching their collective movements || Cα || Pair || No || [http://aladyn.escience-lab.org/ server] || Potestio ''et al.'' || 2010
|--bgcolor="#EFEFEF"
| SWAPSC
| '''S'''liding '''W'''indow '''A'''nalysis '''P'''rocedure for detecting '''S'''elective '''C'''onstraints for analysing genetic data structured for a family or phylogenetic tree using constraints in protein-coding sequence alignments. || Seq || Multi || yes || [http://www.may.ie/academic/biology/staff/mfmolecevolandbioinf.shtml Server] || Mario A. Fares || 2004
|-
| SA Tableau Search[{{Cite journal |last1=Stivala |first1=Alex D |last2=Stuckey |first2=Peter J |last3=Wirth |first3=Anthony I |date=2010 |title=Fast and accurate protein substructure searching with simulated annealing and GPUs |journal=BMC Bioinformatics |language=en |volume=11 |issue=1 |page=446 |doi=10.1186/1471-2105-11-446 |doi-access=free |issn=1471-2105 |pmc=2944279 |pmid=20813068}}]
| Fast and accurate protein substructure searching with simulated annealing and GPUs || SSE || Pair || No || [https://github.com/stivalaa/cuda_satabsearch download] || A.Stivala ''et al.''|| 2010
|--bgcolor="#EFEFEF"
| [RCSB PDB](/source/Protein_Data_Bank) Protein Comparison Tool
| Provides CE, FATCAT, CE variation for [Circular Permutations](/source/Circular_permutation_in_proteins), Sequence Alignments|| Cα || Pair || yes || [http://www.rcsb.org/pdb/workbench/workbench.do server] [http://source.rcsb.org 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 || [http://bioserv.rpbs.univ-paris-diderot.fr/Help/wwLigCSRre.html server] [http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html download] || M. Petitjean || 1998
|--bgcolor="#EFEFEF"
| 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 || [http://www.epitopematch.org download] || S. Jakuschev || 2011
|-
| CLICK
| Topology-independent 3D structure comparison || SSE & Cα & SASA || Pair || Yes || [http://mspc.bii.a-star.edu.sg/click server] || M. Nguyen || 2011
|-
|--bgcolor="#EFEFEF"
| Smolign
| '''S'''patial '''mo'''tifs based protein structural a'''lign'''ment || SSE & C-Map || Multi || Yes || [http://bio.cse.ohio-state.edu/Smolign download] || H. Sun || 2010
|-
| 3D-Blast
| Comparing three-dimensional shape-density || Density || Pair || No || [http://threedblast.loria.fr server] || L. Mavridis ''et al.'' || 2011
|-
|--bgcolor="#EFEFEF"
| DEDAL
| '''DE'''scriptor '''D'''efined '''AL'''ignment || SSE & Cα & C-Map || Pair || Yes || [http://bioexploratorium.pl/EP/DEDAL server] || P. Daniluk & B. Lesyng || 2011
|--bgcolor="#EFEFEF"
| msTALI
| '''m'''ultiple '''sT'''ructure '''ALI'''gnment || Cα & Dihed & SSE & Surf|| Multi || Yes || [http://ifestos.cse.sc.edu/mstali server] || P. {{Not a typo|Shealy}} & H. Valafar || 2012
|-
| mulPBA
| '''mul'''tiple '''PB''' sequence alignment || PB || Multi || Yes || NA || A.P. Joseph ''et al.'' || 2012
|--bgcolor="#EFEFEF"
| SAS-Pro
| '''S'''imiltaneous '''A'''lignment and '''S'''uperimposition of '''PRO'''teins|| ??? || Pair || Yes || [http://eudoxus.cheme.cmu.edu/saspro/SAS-Pro.html server] || Shah & Sahinidis || 2012
|-
| MIRAGE-align
| '''M'''atch '''I'''ndex based structural alignment method || SSE & PPE || Pair || No || [http://homepage.ntu.edu.tw/~d92548009 website] || K. Hung ''et al.'' || 2012
|--bgcolor="#EFEFEF"
| [SPalign](/source/Structural_alignment)
| '''S'''tructure '''P'''airwise '''align'''ment || Cα || Pair || No ||[http://sparks-lab.org/yueyang/server/SPalign server] [http://sparks-lab.org/yueyang/download/index.php?Download=SP-simple_all.cc download] || Y. Yang ''et al.'' || 2012
|-
| Kpax[{{cite journal|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 || Other || Pair || Yes || [http://kpax.loria.fr website] || D.W. Ritchie|| 2016
|--bgcolor="#EFEFEF"
| DeepAlign[{{cite journal|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) || Cα + Seq || Pair || No || [http://ttic.uchicago.edu/~jinbo/DeepAlign/StructureAlign.zip download] [http://raptorx.uchicago.edu/DeepAlign/submit/ server] || S. Wang and J. Xu || 2013
|-
| 3DCOMB[{{cite journal|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 || Cα || Multi || No || [http://ttic.uchicago.edu/~jinbo/DeepAlign/StructureAlign.zip download] [http://raptorx.uchicago.edu/DeepAlign/submit/ server] || S. Wang and J. Xu || 2012
|--bgcolor="#EFEFEF"
| TS-AMIR[{{cite journal|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 || SSE & Cα || Pair || No || NA || J. Razmara ''et al.''|| 2012
|-
| MICAN[{{cite journal|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 '''M'''ultiple-chains, '''I'''nverse alignments, '''C''' α only models, '''A'''lternative alignments, and '''N'''on-sequential alignments || Cα || Pair || No || [http://landscape.tbp.cse.nagoya-u.ac.jp/MICAN/Download.html download] || S.Minami ''et al.''|| 2013
|-
|--bgcolor="#EFEFEF"
| SPalignNS[{{cite journal|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}}]
| '''S'''tructure '''P'''airwise '''align'''ment '''N'''on-'''S'''equential || Cα || Pair || No ||[http://sparks-lab.org/server/SPalignNS server] [http://sparks-lab.org/peter/downloads/SPalignNS.tar.gz download] || P. Brown ''et al.'' || 2015
|-
|--bgcolor="#EFEFEF"
| Fit3D[{{cite journal|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 || AllA, Cα || Multi || No ||[https://biosciences.hs-mittweida.de/fit3d server] [https://bitbucket.org/fkaiser/fit3d/downloads/Fit3D_v005.zip download] || F. Kaiser ''et al.'' || 2015
|-
|MMLigner[{{cite journal|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. || Cα || Pair || Yes ||[http://lcb.infotech.monash.edu.au/mmligner/mmlignerweb.html server] [http://lcb.infotech.monash.edu.au/mmligner/ download] || J. Collier ''et al.'' || 2017
|-
|--bgcolor="#EFEFEF"
| [RCSB PDB](/source/Protein_Data_Bank) strucmotif-search[{{cite journal| author=Bittrich S, Burley SK, Rose AS| title=Real-time structural motif searching in proteins using an inverted index strategy. | journal=PLOS Comput Biol | year= 2020 | volume= 16 | issue= 12 | article-number= e1008502 | pmid=33284792 | doi=10.1371/journal.pcbi.1008502 | pmc=7746303 | bibcode=2020PLSCB..16E8502B | doi-access=free }}]
| Small structural motifs search that takes seconds to run on 180k or more structures, with nucleic acid & [bioassembly](/source/bioassembly) support || AllA || Multi || No ||[https://www.rcsb.org/docs/search-and-browse/advanced-search/structure-motif-search server/documentation] [https://github.com/rcsb/strucmotif-search 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==
{{DEFAULTSORT:Structural Alignment Software}}
Category:Structural bioinformatics software
---
Adapted from the Wikipedia article [Structural alignment software](https://en.wikipedia.org/wiki/Structural_alignment_software) by Wikipedia contributors ([contributor history](https://en.wikipedia.org/wiki/Structural_alignment_software?action=history)). Available under [Creative Commons Attribution-ShareAlike 4.0 International](https://creativecommons.org/licenses/by-sa/4.0/). Changes may have been made.