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 DescriptionClassTypeFlexibleLinkAuthorYear
ARTEM[1] Superposition of two arbitrary RNA 3D structure fragmentsAllAPairNodownloadBohdan D.R.; Voronina V.V.; Bujnicki J.M.; Baulin E.F.2023
foldseek[2] Fast and accurate protein structure alignment and visualisationSeqPairYesserver downloadM. van Kempen & S. Kim & C. Tumescheit & M. Mirdita & J. Lee & C. Gilchrist & J. Söding & M. Steinegger2023
3decision Protein structure repository with visualisation and structural analytics toolsSeqMultiYessiteP. Schmidtke2015
MAMMOTH MAtching Molecular Models Obtained from TheoryPairNoserver downloadCEM Strauss & AR Ortiz2002
CE Combinatorial ExtensionPairNoserverI. Shindyalov2000
CE-MC Combinatorial Extension-Monte CarloMultiNoserverC. Guda2004
DaliLite Distance Matrix AlignmentC-MapPairNoserver and downloadL. Holm1993
TM-align TM-score based protein structure alignmentPairnilserver and downloadY. Zhang & J. Skolnick2005
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 ToolSSEPairnilserverS. Bryant1996
PrISM Protein Informatics Systems for ModelingSSEMultinilserverB. Honig2000
MOE Molecular Operating Environment. Extensive platform for protein and protein-ligand structure modelling.Cα, AllA, SeqMultiNositeChemical Computing Group2000
SSAP Sequential Structure Alignment ProgramSSEMultiNoserverC. Orengo & W. Taylor1989
SARF2 Spatial ARrangements of Backbone FragmentsSSEPairnilserverN. Alexandrov1996
KENOBI/K2 NASSEPairnilserverZ. Weng2000
STAMP STructural Alignment of Multiple ProteinsMultiNodownload serverR. Russell & G. Barton1992
MASS Multiple Alignment by Secondary StructureSSEMultiNoserverO. Dror & H. Wolfson2003
SCALI Structural Core ALIgnment of proteinsSeq/C-MapPairnilserver downloadX. Yuan & C. Bystroff2004
DEJAVU NASSEPairnilserverGJ. Kleywegt1997
SSM Secondary Structure MatchingSSEMultinilserverE. Krissinel2003
SHEBA Structural Homology by Environment-Based AlignmentSeqPairnilserverJ Jung & B Lee2000
LGA[3] Local-Global Alignment, and Global Distance Test (GDT-TS) structure similarity measureCα, AllA, any atomPairnilserver and downloadA. Zemla2003
POSA Partial Order Structure AlignmentMultiYesserverY. Ye & A. Godzik2005
PyMOL "super" command does sequence-independent 3D alignmentProteinHybridNositeW. L. DeLano2007
FATCAT Flexible Structure AlignmenT by Chaining Aligned Fragment Pairs Allowing TwistsPairYesserverY. Ye & A. Godzik2003
deconSTRUCT Database search on substructural level and pairwise alignment.SSEMultiNoserverZH. Zhang et al.2010
Matras MArkovian TRAnsition of protein StructureCα & SSEPairnilserverK. Nishikawa2000
MAMMOTH-mult MAMMOTH-based multiple structure alignmentMultiNoserverD. Lupyan2005
Protein3Dfit NAC-MapPairnilserverD. Schomburg1994
PRIDE PRobability of IDEntityPairnilserverS. Pongor2002
FAST FAST Alignment and Search ToolPairnilserverJ. Zhu2004
C-BOP Coordinate-Based Organization of ProteinsN/AMultinilserverE. Sandelin2005
ProFit Protein least-squares FittingMultinilserverACR. Martin1996
TOPOFIT Alignment as a superimposition of common volumes at a topomax pointPairnilserverVA. Ilyin2004
MUSTANG MUltiple STructural AligNment AlGorithmCα & C-MapMultinildownloadA.S. Konagurthu et al.2006
URMS Unit-vector RMSDPairnilserverK. Kedem2003
LOCK Hierarchical protein structure superpositionSSEPairNoNAAP. Singh1997
LOCK 2 Improvements over LOCKSSEPairNodownloadJ. Shapiro2003
CBA Consistency Based AlignmentSSEMultinildownloadJ. Ebert2006
TetraDA Tetrahedral Decomposition AlignmentSSEMultiYesNAJ. Roach2005
STRAP STRucture based Alignment ProgramMultinilserverC. Gille2006
LOVOALIGN Low Order Value Optimization methods for Structural AlignmentPairnilserverAndreani et al.2006
GANGSTA Genetic Algorithm for Non-sequential, Gapped protein STructure AlignmentSSE/C-MapPairNoserverB. Kolbeck2006
GANGSTA+ Combinatorial algorithm for nonsequential and gapped structural alignmentSSE/C-MapPairNoserverA. Guerler & E.W. Knapp2008
MatAlign[4] Protein Structure Comparison by Matrix AlignmentC-MapPairnilsiteZ. Aung & K.L. Tan2006
Vorolign Fast structure alignment using Voronoi contactsC-MapMultiYesserverF. Birzele et al.2006
EXPRESSO Fast Multiple Structural Alignment using T-Coffee and SapMultinilsiteC. Notredame et al.2007
CAALIGN Cα AlignMultinilsiteT.J. Oldfield2007
YAKUSA Internal Coordinates and BLAST type algorithmPairnilsiteM. Carpentier et al.2005
BLOMAPS Conformation-based alphabet alignmentsMultinilserverW-M. Zheng & S. Wang2008
CLEPAPS Conformation-based alphabet alignmentsPairnilserverW-M. Zheng & S. Wang2008
TALI F Torsion Angle ALIgnmentPairNoNAX. Mioa2006
MolCom NAGeometryMultinilNAS.D. O'Hearn2003
MALECON NAGeometryMultinilNAS. Wodak2004
FlexProt Flexible Alignment of Protein StructuresPairYesserverM. Shatsky & H. Wolfson2002
MultiProt Multiple Alignment of Protein StructuresGeometryMultiNoserverM. Shatsky & H. Wolfson2004
CTSS Protein Structure Alignment Using Local Geometrical FeaturesGeometryPairnilsiteT. Can2004
CURVE NAGeometryMultiNositeD. Zhi2006
Matt Multiple Alignment with Translations and TwistsMultiYesserver downloadM. Menke2008
TopMatch[5] Protein structure alignment and visualization of structural similarities; alignment of multiprotein complexesPairNoserver downloadM. Sippl & M. Wiederstein2012
SSGS Secondary Structure Guided SuperimpositionCaPairNositeG. Wainreb et al.2006
Matchprot Comparison of protein structures by growing neighborhood alignmentsPairNoserverS. Bhattacharya et al.2007
UCSF Chimera see MatchMaker tool and "matchmaker" commandSeq & SSEMultiNositeE. Meng et al.2006
FLASH Fast aLignment Algorithm for finding Structural Homology of proteinsSSEPairNoNAE.S.C. Shih & M-J Hwang2003
RAPIDO Rapid Alignment of Protein structures In the presence of Domain mOvementsPairYesserverR. Mosca & T.R. Schneider2008
ComSubstruct Structural Alignment based on Differential Geometrical EncodingGeometryPairYessiteN. Morikawa2008
ProCKSI Protein (Structure) Comparison, Knowledge, Similarity and InformationOtherPairNositeD. Barthel et al.2007
SARST Structure similarity search Aided by Ramachandran Sequential Transformation PairnilsiteW-C. Lo et al.2007
Fr-TM-align Fragment-TM-score based protein structure alignmentPairnositeS.B. Pandit & J. Skolnick2008
TOPS+ COMPARISON Comparing topological models of protein structures enhanced with ligand informationTopologyPairYesserverM. Veeramalai & D. Gilbert2008
TOPS++FATCAT Flexible Structure AlignmenT by Chaining Aligned Fragment Pairs Allowing Twists derived from TOPS+ String ModelPairYesserverM. Veeramalai et al.2008
MolLoc Molecular Local Surface AlignmentSurfPairNoserverM.E. Bock et al.2007
FASE Flexible Alignment of Secondary Structure ElementsSSEPairYesNAJ. Vesterstrom & W. R. Taylor2006
SABERTOOTH Protein Structural Alignment based on a vectorial Structure RepresentationPairYesserverF. Teichert et al.2007
STON NAPairNositeC. Eslahchi et al.2009
SALIGN Sequence-Structure Hybrid MethodSeqMultiNositeM.S. Madhusudhan et al.2007
MAX-PAIRS NAPairNositeA. Poleksic2009
THESEUS Maximum likelihood superpositioningMultiNositeD.L. Theobald & D.S. Wuttke2006
TABLEAUSearch Structural Search and Retrieval using a Tableau Representation of Protein Folding PatternsSSEPairNoserverA.S. Konagurthu et al.2008
QP Tableau Search Tableau-based protein substructure search using quadratic programmingSSEPairNodownload serverA.Stivala et al.2009
ProSMoS Protein Structure Motif SearchSSEPairNoserver downloadS. Shi et al.2007
MISTRAL Energy-based multiple structural alignment of proteinsMultiNoserverC. Micheletti & H. Orland2009
MSVNS for MaxCMO A simple and fast heuristic for protein structure comparisonC-MapPairNositeD. Pelta et al.2008
Structal Least Squares Root Mean Square deviation minimization by dynamic programmingPairNoserver downloadGerstein & Levitt2005
ProBiS[6] Detection of Structurally Similar Protein Binding Sites by Local Structural AlignmentSurfPairYesserver downloadJ. Konc & D. Janezic2010
ALADYN Dynamics-based Alignment: superposing proteins by matching their collective movementsPairNoserverPotestio 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.SeqMultiyesServerMario A. Fares2004
SA Tableau Search Fast and accurate protein substructure searching with simulated annealing and GPUsSSEPairNodownload serverA.Stivala et al.2010
RCSB PDB Protein Comparison Tool Provides CE, FATCAT, CE variation for Circular Permutations, Sequence AlignmentsPairyesserver downloadA. Prlic et al.2010
CSR Maximal common 3D motif; non-parametric; outputs pairwise correspondence; works also on small moleculesSSE or CαPairNoserver downloadM. Petitjean1998
EpitopeMatch discontinuous structure matching; induced fit consideration; flexible geometrical and physicochemical specificity definition; transplantation of similar spatial arrangements of amino acid residuesCα-AllAMultiYesdownloadS. Jakuschev2011
CLICK Topology-independent 3D structure comparisonSSE & Cα & SASAPairYesserverM. Nguyen2011
Smolign Spatial motifs based protein structural alignmentSSE & C-MapMultiYesdownloadH. Sun2010
3D-Blast Comparing three-dimensional shape-densityDensityPairNoserverL. Mavridis et al.2011
DEDAL DEscriptor Defined ALignmentSSE & Cα & C-MapPairYesserverP. Daniluk & B. Lesyng2011
msTALI multiple sTructure ALIgnmentCα & Dihed & SSE & SurfMultiYesserverP. Shealy & H. Valafar2012
mulPBA multiple PB sequence alignmentPBMultiYesNAA.P. Joseph et al.2012
SAS-Pro Similtaneous Alignment and Superimposition of PROteins ???PairYesserverShah & Sahinidis2012
MIRAGE-align Match Index based structural alignment methodSSE & PPEPairNowebsiteK. Hung et al.2012
SPalign Structure Pairwise alignmentPairNoserver downloadY. Yang et al.2012
Kpax[7] Fast Pairwise or Multiple Alignments using Gaussian OverlapOtherPairYeswebsiteD.W. Ritchie2016
DeepAlign[8] Protein structure alignment beyond spatial proximity (evolutionary information and hydrogen-bonding are taken into consideration)Cα + SeqPairNodownload serverS. Wang and J. Xu2013
3DCOMB[9] extension of DeepAlignMultiNodownload serverS. Wang and J. Xu2012
TS-AMIR[10] A topology string alignment method for intensive rapid protein structure comparisonSSE & CαPairNoNAJ. Razmara et al.2012
MICAN[11] MICAN can handle Multiple-chains, Inverse alignments, C α only models, Alternative alignments, and Non-sequential alignmentsPairNodownloadS.Minami et al.2013
SPalignNS[12] Structure Pairwise alignment Non-SequentialPairNoserver downloadP. Brown et al.2015
Fit3D[13] 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 alignmentAllA, CαMultiNoserver downloadF. Kaiser et al.2015
MMLigner[14] Bayesian statistical inference of alignments based on information theory and compression.PairYesserver downloadJ. Collier et al.2017
RCSB PDB strucmotif-search[15] Small structural motifs search that takes seconds to run on 180k or more structures, with nucleic acid & bioassembly supportAllAMultiNoserver/documentation downloadS. 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.

References

  1. 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.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  2. 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. doi:10.1038/s41587-023-01773-0.{{cite journal}}: CS1 maint: multiple names: authors list (link)
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. 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.
  15. 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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