Structural alignment software explained

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

NAMEDescription Class Type Flexible Link Author Year
ARTEMIS[1] 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[2] [3] 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[4] 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
3decisionProtein structure repository with visualisation and structural analytics tools Seq Multi Yes site P. Schmidtke2015
MAMMOTHMAtching Molecular Models Obtained from Theory Pair No server download CEM Strauss & AR Ortiz2002
CECombinatorial Extension Pair No server I. Shindyalov 2000
CE-MCCombinatorial Extension-Monte Carlo Multi No server C. Guda 2004
DaliLiteDistance Matrix Alignment C-Map Pair No server and download L. Holm 1993
TM-align TM-score based protein structure alignment Pair nil server and download Y. Zhang & J. Skolnick 2005
mTM-alignMultiple protein structure alignment based on TM-alignMultiNoserver and downloadR. Dong, Z. Peng, Y. Zhang & J. Yang2018
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
MOEMolecular Operating Environment. Extensive platform for protein and protein-ligand structure modelling. Cα, AllA, Seq Multi No site Chemical Computing Group 2000
SSAPSequential Structure Alignment Program SSE Multi No server C. Orengo & W. Taylor 1989
SARF2Spatial ARrangements of Backbone Fragments SSE Pair nil server N. Alexandrov 1996
KENOBI/K2NA SSE Pair nil server Z. Weng 2000
STAMPSTructural Alignment of Multiple Proteins Multi No download server R. Russell & G. Barton1992
MASSMultiple Alignment by Secondary Structure SSE Multi No server O. Dror & H. Wolfson 2003
SCALI Structural Core ALIgnment of proteinsSeq/C-Map Pair nil server downloadX. Yuan & C. Bystroff 2004
DEJAVUNA SSE Pair nil server GJ. Kleywegt 1997
SSMSecondary Structure Matching SSE Multi nil server E. Krissinel 2003
SHEBAStructural Homology by Environment-Based AlignmentSeq Pair nil server J Jung & B Lee 2000
LGA[5] Local-Global Alignment, and Global Distance Test (GDT-TS) structure similarity measure Cα, AllA, any atom Pair nil server and download A. Zemla 2003
POSAPartial Order Structure Alignment Multi Yes server Y. Ye & A. Godzik 2005
PyMOL"super" command does sequence-independent 3D alignment Protein Hybrid No site W. L. DeLano 2007
FATCATFlexible Structure AlignmenT by Chaining Aligned Fragment Pairs Allowing Twists Pair Yes server Y. Ye & A. Godzik 2003
deconSTRUCTDatabase search on substructural level and pairwise alignment. SSE Multi No server ZH. Zhang et al.2010
MatrasMArkovian TRAnsition of protein Structure Cα & SSE Pair nil server K. Nishikawa 2000
MAMMOTH-multMAMMOTH-based multiple structure alignment Multi No server D. Lupyan 2005
Protein3DfitNA C-Map Pair nil server D. Schomburg 1994
PRIDEPRobability of IDEntity Pair nil server S. Pongor 2002
FAST FAST Alignment and Search Tool 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 Multi nil server ACR. Martin 1996
TOPOFIT Alignment as a superimposition of common volumes at a topomax point Pair nil server VA. Ilyin 2004
MUSTANG MUltiple STructural AligNment AlGorithm Cα & C-MapMulti nil download A.S. Konagurthu et al. 2006
URMS Unit-vector RMSDPair nil server 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 Multi nil server C. Gille 2006
LOVOALIGN Low Order Value Optimization methods for Structural Alignment Pair nil server Andreani et al. 2006
GANGSTAGenetic 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[6] Protein Structure Comparison by Matrix Alignment C-Map Pair nil site Z. Aung & K.L. Tan 2006
VorolignFast structure alignment using Voronoi contacts C-Map Multi Yes server F. Birzele et al. 2006
EXPRESSOFast Multiple Structural Alignment using T-Coffee and SapMulti nil site C. Notredame et al. 2007
CAALIGN Cα Align Multi nil site T.J. Oldfield 2007
YAKUSAInternal Coordinates and BLAST type algorithmPair nil site M. Carpentier et al. 2005
BLOMAPS Conformation-based alphabet alignments Multi nil server W-M. Zheng & S. Wang 2008
CLEPAPS Conformation-based alphabet alignments Pair nil server W-M. Zheng & S. Wang 2008
TALI FTorsion Angle ALIgnment 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
FlexProtFlexible Alignment of Protein Structures Pair Yes server M. Shatsky & H. Wolfson2002
MultiProtMultiple Alignment of Protein Structures Geometry Multi No server M. Shatsky & H. Wolfson2004
CTSS Protein Structure Alignment Using Local Geometrical Features Geometry Pair nil site T. Can 2004
CURVE NA Geometry Multi No site D. Zhi 2006
MattMultiple Alignment with Translations and Twists Multi Yes server download M. Menke 2008
TopMatch[7] Protein structure alignment and visualization of structural similarities; alignment of multiprotein complexes Pair No server downloadM. Sippl & M. Wiederstein 2012
SSGSSecondary Structure Guided Superimposition Ca Pair Nosite G. Wainreb et al. 2006
Matchprot Comparison of protein structures by growing neighborhood alignments Pair No server S. Bhattacharya et al. 2007
UCSF Chimerasee MatchMaker tool and "matchmaker" command Seq & SSE Multi Nosite E. Meng et al. 2006
FLASHFast aLignment Algorithm for finding Structural Homology of proteins SSE Pair No NA E.S.C. Shih & M-J Hwang 2003
RAPIDORapid Alignment of Protein structures In the presence of Domain mOvements 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
SARSTStructure similarity search Aided by Ramachandran Sequential Transformation Pair nil site W-C. Lo et al. 2007
Fr-TM-alignFragment-TM-score based protein structure alignment Pair no site S.B. Pandit & J. Skolnick 2008
TOPS+ COMPARISONComparing topological models of protein structures enhanced with ligand information Topology Pair Yes server M. Veeramalai & D. Gilbert 2008
TOPS++FATCATFlexible Structure AlignmenT by Chaining Aligned Fragment Pairs Allowing Twists derived from TOPS+ String Model Pair Yes server M. Veeramalai et al. 2008
MolLocMolecular Local Surface Alignment Surf Pair Noserver M.E. Bock et al. 2007
FASEFlexible Alignment of Secondary Structure Elements SSE Pair Yes NA J. Vesterstrom & W. R. Taylor 2006
SABERTOOTHProtein Structural Alignment based on a vectorial Structure Representation Pair Yes server F. Teichert et al. 2007
STONNA Pair No site C. Eslahchi et al. 2009
SALIGNSequence-Structure Hybrid Method Seq Multi No site M.S. Madhusudhan et al. 2007
MAX-PAIRSNA Pair No site A. Poleksic 2009
THESEUSMaximum likelihood superpositioning Multi No site D.L. Theobald & D.S. Wuttke2006
TABLEAUSearchStructural Search and Retrieval using a Tableau Representation of Protein Folding Patterns SSE Pair No server A.S. Konagurthu et al.2008
QP Tableau SearchTableau-based protein substructure search using quadratic programming SSE Pair No download server A.Stivala et al.2009
ProSMoSProtein Structure Motif Search SSE Pair No server [ftp://iole.swmed.edu/pub/ProSMoS download] S. Shi et al.2007
MISTRALEnergy-based multiple structural alignment of proteins Multi No server C. Micheletti & H. Orland2009
MSVNS for MaxCMOA simple and fast heuristic for protein structure comparison C-Map Pair No site D. Pelta et al. 2008
StructalLeast Squares Root Mean Square deviation minimization by dynamic programming Pair No server download Gerstein & Levitt 2005
ProBiS[8] Detection of Structurally Similar Protein Binding Sites by Local Structural Alignment Surf Pair Yesserver download J. Konc & D. Janezic 2010
ALADYNDynamics-based Alignment: superposing proteins by matching their collective movements Pair No server Potestio et al. 2010
SWAPSCSliding 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 SearchFast and accurate protein substructure searching with simulated annealing and GPUs SSE Pair No download server A.Stivala et al.2010
RCSB PDB Protein Comparison ToolProvides CE, FATCAT, CE variation for Circular Permutations, Sequence AlignmentsPair yes server download A. Prlic et al. 2010
CSRMaximal common 3D motif; non-parametric; outputs pairwise correspondence; works also on small molecules SSE or Cα Pair No server download M. Petitjean 1998
EpitopeMatchdiscontinuous 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
CLICKTopology-independent 3D structure comparison SSE & Cα & SASA Pair Yes server M. Nguyen 2011
SmolignSpatial motifs based protein structural alignment SSE & C-Map Multi Yes download H. Sun 2010
3D-BlastComparing three-dimensional shape-density Density Pair No server L. Mavridis et al. 2011
DEDALDEscriptor Defined ALignment SSE & Cα & C-Map Pair Yes server P. Daniluk & B. Lesyng 2011
msTALImultiple sTructure ALIgnment Cα & Dihed & SSE & SurfMulti Yes server P. & H. Valafar 2012
mulPBAmultiple PB sequence alignment PB Multi Yes NA A.P. Joseph et al. 2012
SAS-ProSimiltaneous Alignment and Superimposition of PROteins??? Pair Yes server Shah & Sahinidis 2012
MIRAGE-alignMatch Index based structural alignment method SSE & PPE Pair No website K. Hung et al. 2012
SPalignStructure Pairwise alignment Pair No server download Y. Yang et al. 2012
Kpax[9] Fast Pairwise or Multiple Alignments using Gaussian Overlap Other Pair Yes website D.W. Ritchie2016
DeepAlign[10] 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[11] extension of DeepAlign Multi No download server S. Wang and J. Xu 2012
TS-AMIR[12] A topology string alignment method for intensive rapid protein structure comparison SSE & Cα Pair No NA J. Razmara et al.2012
MICAN[13] MICAN can handle Multiple-chains, Inverse alignments, C α only models, Alternative alignments, and Non-sequential alignments Pair No download S.Minami et al.2013
SPalignNS[14] Structure Pairwise alignment Non-Sequential Pair No server download P. Brown et al. 2015
Fit3D[15] 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[16] Bayesian statistical inference of alignments based on information theory and compression. Pair Yes server download J. Collier et al. 2017
RCSB PDB strucmotif-search[17] 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:

References

  1. 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 . bioRxiv . 10.1101/2024.04.06.588371. free .
  2. 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 . 10.1093/nar/gkad605. free . 37471030 . 10484739 .
  3. Baulin E.F.; Bohdan D.R.; Kowalski D.; Serwatka M.; Świerczyńska J.; Żyra Z.; Bujnicki J.M. . 2024 . ARTEM: a method for RNA tertiary motif identification with backbone permutations, and its example application to kink-turn-like motifs . bioRxiv . 10.1101/2024.05.31.596898. free .
  4. 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 . 10.1038/s41587-023-01773-0.
  5. Zemla A . 2003 . LGA: A method for finding 3D similarities in protein structures . Nucleic Acids Research . 31 . 13 . 3370–3374 . 12824330 . 168977 . 10.1093/nar/gkg571.
  6. Aung. Zeyar. Kian-Lee Tan . MatAlign: Precise protein structure comparison by matrix alignment. Journal of Bioinformatics and Computational Biology. Dec 2006. 4. 6. 17245810. 1197–216. 10.1142/s0219720006002417.
  7. Sippl. M.. Wiederstein, M. . Detection of spatial correlations in protein structures and molecular complexes. Structure. 2012. 20. 4. 718–728. 10.1016/j.str.2012.01.024. 22483118. 3320710.
  8. Janez Konc . Dušanka Janežič . ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment . Bioinformatics . 26 . 9 . 1160–1168 . 2010 . 10.1093/bioinformatics/btq100 . 20305268 . 2859123.
  9. Ritchie. David W.. Calculating and scoring high quality multiple flexible protein structure alignments. Bioinformatics. September 2016. 10.1093/bioinformatics/btw300. 27187202. 32. 17 . 2650–2658. free.
  10. Wang. Sheng . Jianzhu Ma . Jian Peng . Jinbo Xu. Protein structure alignment beyond spatial proximity. Scientific Reports. March 2013. 10.1038/srep01448. 23486213. 3. 1448 . 3596798. 2013NatSR...3E1448W .
  11. Wang. Sheng . Jian Peng . Jinbo Xu. Alignment of distantly related protein structures: algorithm, bound and implications to homology modeling. Bioinformatics. Sep 2011. 27. 18. 2537–45. 10.1093/bioinformatics/btr432. 21791532. 3167051.
  12. Razmara. Jafar . Safaai Deris . Sepideh Parvizpour. TS-AMIR: a topology string alignment method for intensive rapid protein structure comparison. Algorithms for Molecular Biology. Feb 2012. 7. 4. 22336468. 10.1186/1748-7188-7-4. 4. 3298807 . free .
  13. Minami. S.. Sawada K. . Chikenji G. . 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. Jan 2013. 14. 24. 24. 23331634 . 10.1186/1471-2105-14-24 . 3637537 . free .
  14. Brown. P.. Pullan W. . Yang Y. . Zhou Y. . Fast and accurate non-sequential protein structure alignment using a new asymmetric linear sum assignment heuristic. Bioinformatics. Oct 2015. 26454279 . 10.1093/bioinformatics/btv580 . 32 . 3. 370–7. free. 10072/101971. free.
  15. Kaiser. F.. Eisold A. . Bittrich S. . Labudde D. . Fit3D: a web application for highly accurate screening of spatial resiudue patterns in protein structure data. Bioinformatics. Oct 2015. 26519504 . 10.1093/bioinformatics/btv637 . 32 . 5. 792–4. free.
  16. Collier. J.. Allison L. . Lesk A. . Stuckey P. . Garcia de la Banda M.. María García de la Banda . Konagurthu A. . Statistical inference of protein structural alignments using information and compression. Bioinformatics. Apr 2017. 28065899 . 10.1093/bioinformatics/btw757 . 33 . 7 . 1005–13. free .
  17. Bittrich S, Burley SK, Rose AS. Real-time structural motif searching in proteins using an inverted index strategy. . PLOS Comput Biol . 2020 . 16 . 12 . e1008502 . 33284792 . 10.1371/journal.pcbi.1008502 . 7746303 . 2020PLSCB..16E8502B . free .