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<title>Structural alignment software</title>

</head>

Structural alignment software

</h1>

</header>

<div id="mw-content-text" class="mw-body-content mw-content-ltr" lang="en" dir="ltr"><div class="mw-content-ltr mw-parser-output" lang="en" dir="ltr">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 <a href="Structural_alignment" title="Structural alignment">structural alignment</a>.

<div class="mw-heading mw-heading2"><h2 id="Structural_comparison_and_alignment">Structural comparison and alignment</h2></div>

<th>NAME

</th>

<th>Description</th>

<th>Class</th>

<th>Flexible</th>

<th>Author</th>

<th>Year

</th></tr>

<tr>

<td>ARTEMIS<a href="#cite_note-Bohdan2024-1">[1]</a>

</td>

<td>Topology-independent superposition of RNA/DNA 3D structures and structure-based sequence alignment</td>

<td><a rel="nofollow" class="external text" href="https://github.com/david-bogdan-r/ARTEMIS">download</a></td>

<td>Bohdan D.R.; Bujnicki J.M.; Baulin E.F.</td>

<td>2024

</td></tr>

<tr>

<td>ARTEM<a href="#cite_note-Bohdan2023-2">[2]</a><a href="#cite_note-Baulin2024-3">[3]</a>

</td>

<td>Superposition of two arbitrary RNA/DNA 3D structure fragments & 3D motif identification</td>

<td><a rel="nofollow" class="external text" href="https://github.com/david-bogdan-r/ARTEM">download</a></td>

<td>Bohdan D.R.; Voronina V.V.; Bujnicki J.M.; Baulin E.F.</td>

<td>2023

</td></tr>

<tr>

<td>foldseek<a href="#cite_note-Kempen2023-4">[4]</a>

</td>

<td>Fast and accurate protein structure alignment and visualisation</td>

<td><a rel="nofollow" class="external text" href="https://search.foldseek.com/">server</a> <a rel="nofollow" class="external text" href="https://foldseek.com/">download</a></td>

<td>M. van Kempen & S. Kim & C. Tumescheit & M. Mirdita & J. Lee & C. Gilchrist & J. Söding & M. Steinegger</td>

<td>2023

</td></tr>

<tr>

<td>3decision

</td>

<td>Protein structure repository with visualisation and structural analytics tools</td>

<td>Multi</td>

<td>P. Schmidtke</td>

<td>2015

</td></tr>

<tr>

<td><a href="Structural_alignment#Mammoth" title="Structural alignment">MAMMOTH</a>

</td>

<td>MAtching Molecular Models Obtained from Theory</td>

<td><a rel="nofollow" class="external text" href="http://ub.cbm.uam.es/software/online/mamothmult.php">server</a> <a rel="nofollow" class="external text" href="http://ub.cbm.uam.es/software/mammoth.php">download</a></td>

<td>CEM Strauss & AR Ortiz</td>

<td>2002

</td></tr>

</td>

<td>Combinatorial Extension</td>

<td><a rel="nofollow" class="external text" href="http://source.rcsb.org/jfatcatserver/ceHome.jsp">server</a></td>

<td>I. Shindyalov</td>

<td>2000

</td></tr>

</td>

<td>Combinatorial Extension-Monte Carlo</td>

<td>Multi</td>

<td><a rel="nofollow" class="external text" href="http://schubert.bio.uniroma1.it/CEMC/">server</a></td>

<td>2004

</td></tr>

<tr>

<td><a href="Structural_alignment#DALI" title="Structural alignment">DaliLite</a>

</td>

<td>Distance Matrix Alignment</td>

<td><a rel="nofollow" class="external text" href="http://ekhidna.biocenter.helsinki.fi/dali">server and download</a></td>

<td>1993

</td></tr>

<td>TM-align

</td>

<td>TM-score based protein structure alignment</td>

<td><a rel="nofollow" class="external text" href="http://zhanglab.ccmb.med.umich.edu/TM-align">server and download</a></td>

<td>Y. Zhang & J. Skolnick</td>

<td>2005

</td></tr>

<tr>

<td>mTM-align

</td>

<td>Multiple protein structure alignment based on TM-align

</td>

<td>Cα

</td>

<td>Multi

</td>

<td>No

</td>

<td><a rel="nofollow" class="external text" href="http://yanglab.nankai.edu.cn/mTM-align/">server and download</a>

</td>

<td>R. Dong, Z. Peng, Y. Zhang & J. Yang

</td>

<td>2018

</td></tr>

<tr>

<td>VAST

</td>

<td>Vector Alignment Search Tool</td>

<td><a rel="nofollow" class="external text" href="https://www.ncbi.nlm.nih.gov/Structure/VAST/vast.shtml">server</a></td>

<td>S. Bryant</td>

<td>1996

</td></tr>

<td>PrISM

</td>

<td>Protein Informatics Systems for Modeling</td>

<td>Multi</td>

<td><a rel="nofollow" class="external text" href="http://honiglab.cpmc.columbia.edu">server</a></td>

<td>B. Honig</td>

<td>2000

</td></tr>

<tr>

</td>

<td>Molecular Operating Environment. Extensive platform for protein and protein-ligand structure modelling.</td>

<td>Multi</td>

<td>Chemical Computing Group</td>

<td>2000

</td></tr>

<tr>

</td>

<td>Sequential Structure Alignment Program</td>

<td>Multi</td>

<td><a rel="nofollow" class="external text" href="http://www.cathdb.info/cgi-bin/SsapServer.pl">server</a></td>

<td>C. Orengo & W. Taylor</td>

<td>1989

</td></tr>

<td>SARF2

</td>

<td>Spatial ARrangements of Backbone Fragments</td>

<td><a rel="nofollow" class="external text" href="http://123d.ncifcrf.gov/sarf2.html">server</a></td>

<td>N. Alexandrov</td>

<td>1996

</td></tr>

<tr>

<td>KENOBI/K2

</td>

<td><a rel="nofollow" class="external text" href="http://zlab.bu.edu/k2/">server</a></td>

<td>2000

</td></tr>

<td>STAMP

</td>

<td>STructural Alignment of Multiple Proteins</td>

<td>Multi</td>

<td><a rel="nofollow" class="external text" href="http://www.compbio.dundee.ac.uk/downloads/stamp/">download</a> <a rel="nofollow" class="external text" href="http://www.russell.embl.de/cgi-bin/pdc/stamp.pl">server</a></td>

<td>R. Russell & G. Barton</td>

<td>1992

</td></tr>

<tr>

<td>MASS

</td>

<td>Multiple Alignment by Secondary Structure</td>

<td>Multi</td>

<td><a rel="nofollow" class="external text" href="http://bioinfo3d.cs.tau.ac.il/MASS">server</a></td>

<td>O. Dror & H. Wolfson</td>

<td>2003

</td></tr>

<td>SCALI

</td>

<td>Structural Core ALIgnment of proteins</td>

<td><a rel="nofollow" class="external text" href="http://www.bioinfo.rpi.edu/bystrc/SCALI">server</a> <a rel="nofollow" class="external text" href="http://www.bioinfo.rpi.edu/bystrc/pub/scali.tgz">download</a></td>

<td>X. Yuan & C. Bystroff</td>

<td>2004

</td></tr>

<tr>

<td>DEJAVU

</td>

<td><a rel="nofollow" class="external text" href="http://portray.bmc.uu.se/cgi-bin/dejavu/scripts/dejavu.pl">server</a></td>

<td>GJ. Kleywegt</td>

<td>1997

</td></tr>

<td>SSM

</td>

<td>Secondary Structure Matching</td>

<td>Multi</td>

<td><a rel="nofollow" class="external text" href="https://www.ebi.ac.uk/msd-srv/ssm/">server</a></td>

<td>E. Krissinel</td>

<td>2003

</td></tr>

<tr>

<td>SHEBA

</td>

<td>Structural Homology by Environment-Based Alignment</td>

<td><a rel="nofollow" class="external text" href="https://archive.today/20041024193444/http://rex.nci.nih.gov/RESEARCH/basic/lmb/mms/sheba.htm">server</a></td>

<td>2000

</td></tr>

</td>

<td>Local-Global Alignment, and Global Distance Test (GDT-TS) structure similarity measure</td>

<td><a rel="nofollow" class="external text" href="http://proteinmodel.org/AS2TS/LGA/lga.html">server and download</a></td>

<td>A. Zemla</td>

<td>2003

</td></tr>

<tr>

<td>POSA

</td>

<td>Partial Order Structure Alignment</td>

<td>Multi</td>

<td><a rel="nofollow" class="external text" href="http://fatcat.burnham.org/POSA">server</a></td>

<td>Y. Ye & A. Godzik</td>

<td>2005

</td></tr>

<td><a href="PyMOL" title="PyMOL">PyMOL</a>

</td>

<td>"super" command does sequence-independent 3D alignment</td>

<td>Protein</td>

<td>Hybrid</td>

<td>W. L. DeLano</td>

<td>2007

</td></tr>

<tr>

<td>FATCAT

</td>

<td>Flexible Structure AlignmenT by Chaining Aligned Fragment Pairs Allowing Twists</td>

<td><a rel="nofollow" class="external text" href="http://fatcat.burnham.org">server</a></td>

<td>Y. Ye & A. Godzik</td>

<td>2003

</td></tr>

<td>deconSTRUCT

</td>

<td>Database search on substructural level and pairwise alignment.</td>

<td>Multi</td>

<td><a rel="nofollow" class="external text" href="http://epsf.bmad.bii.a-star.edu.sg/struct_server.html">server</a></td>

<td>ZH. Zhang et al.</td>

<td>2010

</td></tr>

<tr>

<td>Matras

</td>

<td>MArkovian TRAnsition of protein Structure</td>

<td><a rel="nofollow" class="external text" href="http://strcomp.protein.osaka-u.ac.jp/matras/">server</a></td>

<td>K. Nishikawa</td>

<td>2000

</td></tr>

<td><a href="Structural_alignment#MAMMOTH" title="Structural alignment">MAMMOTH-mult</a>

</td>

<td>MAMMOTH-based multiple structure alignment</td>

<td>Multi</td>

<td><a rel="nofollow" class="external text" href="http://ub.cbm.uam.es/software/online/mamothmult.php">server</a></td>

<td>D. Lupyan</td>

<td>2005

</td></tr>

<tr>

<td>Protein3Dfit

</td>

<td><a rel="nofollow" class="external text" href="http://biotool.uni-koeln.de:8080/3dalign_neu/cgi-bin/3daligner.py">server</a></td>

<td>D. Schomburg</td>

<td>1994

</td></tr>

<td>PRIDE

</td>

<td>PRobability of IDEntity</td>

<td><a rel="nofollow" class="external text" href="http://pride.szbk.u-szeged.hu">server</a></td>

<td>S. Pongor</td>

<td>2002

</td></tr>

<tr>

<td>FAST

</td>

<td>FAST Alignment and Search Tool</td>

<td><a rel="nofollow" class="external text" href="http://biowulf.bu.edu/FAST/">server</a></td>

<td>2004

</td></tr>

<td>C-BOP

</td>

<td>Coordinate-Based Organization of Proteins</td>

<td>Multi</td>

<td><a rel="nofollow" class="external text" href="http://www.sbc.su.se/~erik/cbop/">server</a></td>

<td>E. Sandelin</td>

<td>2005

</td></tr>

<tr>

<td>ProFit

</td>

<td>Protein least-squares Fitting</td>

<td>Multi</td>

<td><a rel="nofollow" class="external text" href="http://www.bioinf.org.uk/software/profit/">server</a></td>

<td>ACR. Martin</td>

<td>1996

</td></tr>

<td>TOPOFIT

</td>

<td>Alignment as a superimposition of common volumes at a topomax point</td>

<td><a rel="nofollow" class="external text" href="http://topofit.ilyinlab.org/topofit">server</a></td>

<td>VA. Ilyin</td>

<td>2004

</td></tr>

<tr>

<td>MUSTANG

</td>

<td>MUltiple STructural AligNment AlGorithm</td>

<td>Multi</td>

<td><a rel="nofollow" class="external text" href="http://www.csse.monash.edu.au/~karun/Site/mustang.html">download</a></td>

<td>A.S. Konagurthu et al.</td>

<td>2006

</td></tr>

<td>URMS

</td>

<td>Unit-vector RMSD</td>

<td><a rel="nofollow" class="external text" href="http://cbsusrv01.tc.cornell.edu/urms/">server</a></td>

<td><a href="Klara_Kedem" title="Klara Kedem">K. Kedem</a></td>

<td>2003

</td></tr>

<tr>

<td>LOCK

</td>

<td>Hierarchical protein structure superposition</td>

<td>AP. Singh</td>

<td>1997

</td></tr>

<td>LOCK 2

</td>

<td>Improvements over LOCK</td>

<td><a rel="nofollow" class="external text" href="http://brutlag.stanford.edu/">download</a></td>

<td>J. Shapiro</td>

<td>2003

</td></tr>

<tr>

<td>CBA

</td>

<td>Consistency Based Alignment</td>

<td>Multi</td>

<td><a rel="nofollow" class="external text" href="http://brutlag.stanford.edu/software/">download</a></td>

<td>J. Ebert</td>

<td>2006

</td></tr>

<td>TetraDA

</td>

<td>Tetrahedral Decomposition Alignment</td>

<td>Multi</td>

<td>J. Roach</td>

<td>2005

</td></tr>

<tr>

<td>STRAP

</td>

<td>STRucture based Alignment Program</td>

<td>Multi</td>

<td><a rel="nofollow" class="external text" href="http://3d-alignment.eu/">server</a></td>

<td>C. Gille</td>

<td>2006

</td></tr>

<td>LOVOALIGN

</td>

<td>Low Order Value Optimization methods for Structural Alignment</td>

<td><a rel="nofollow" class="external text" href="http://www.ime.unicamp.br/~martinez/lovoalign/">server</a></td>

<td>Andreani et al.</td>

<td>2006

</td></tr>

<tr>

<td>GANGSTA

</td>

<td>Genetic Algorithm for Non-sequential, Gapped protein STructure Alignment</td>

<td><a rel="nofollow" class="external text" href="http://agknapp.chemie.fu-berlin.de/gangsta_old">server</a></td>

<td>B. Kolbeck</td>

<td>2006

</td></tr>

<td><a href="Structural_alignment#GANGSTA+" title="Structural alignment">GANGSTA+</a>

</td>

<td>Combinatorial algorithm for nonsequential and gapped structural alignment</td>

<td><a rel="nofollow" class="external text" href="http://agknapp.chemie.fu-berlin.de/gplus">server</a></td>

<td>A. Guerler & E.W. Knapp</td>

<td>2008

</td></tr>

<td>MatAlign<a href="#cite_note-MatAlign-6">[6]</a>

</td>

<td>Protein Structure Comparison by Matrix Alignment</td>

<td>2006

</td></tr>

<tr>

<td>Vorolign

</td>

<td>Fast structure alignment using Voronoi contacts</td>

<td>Multi</td>

<td><a rel="nofollow" class="external text" href="http://www2.bio.ifi.lmu.de/Vorolign/">server</a></td>

<td>F. Birzele et al.</td>

<td>2006

</td></tr>

<td>EXPRESSO

</td>

<td>Fast Multiple Structural Alignment using T-Coffee and Sap</td>

<td>Multi</td>

<td>C. Notredame et al.</td>

<td>2007

</td></tr>

<tr>

<td>CAALIGN

</td>

<td>Cα Align</td>

<td>Multi</td>

<td>T.J. Oldfield</td>

<td>2007

</td></tr>

<td>YAKUSA

</td>

<td>Internal Coordinates and BLAST type algorithm</td>

<td>M. Carpentier et al.</td>

<td>2005

</td></tr>

<tr>

<td>BLOMAPS

</td>

<td>Conformation-based alphabet alignments</td>

<td>Multi</td>

<td><a rel="nofollow" class="external text" href="http://www.weblab.org.cn/program.inputForm.do?program=BLoMAPS">server</a></td>

<td>W-M. Zheng & S. Wang</td>

<td>2008

</td></tr>

<td>CLEPAPS

</td>

<td>Conformation-based alphabet alignments</td>

<td><a rel="nofollow" class="external text" href="http://www.weblab.org.cn/program.inputForm.do?program=CLePAPS">server</a></td>

<td>W-M. Zheng & S. Wang</td>

<td>2008

</td></tr>

<tr>

<td>TALI F

</td>

<td>Torsion Angle ALIgnment</td>

<td>2006

</td></tr>

<td>MolCom

</td>

<td>Geometry</td>

<td>Multi</td>

<td>S.D. O'Hearn</td>

<td>2003

</td></tr>

<tr>

<td>MALECON

</td>

<td>Geometry</td>

<td>Multi</td>

<td>S. Wodak</td>

<td>2004

</td></tr>

<td>FlexProt

</td>

<td>Flexible Alignment of Protein Structures</td>

<td><a rel="nofollow" class="external text" href="http://bioinfo3d.cs.tau.ac.il/FlexProt/">server</a></td>

<td>M. Shatsky & H. Wolfson</td>

<td>2002

</td></tr>

<tr>

<td>MultiProt

</td>

<td>Multiple Alignment of Protein Structures</td>

<td>Geometry</td>

<td>Multi</td>

<td><a rel="nofollow" class="external text" href="http://bioinfo3d.cs.tau.ac.il/MultiProt">server</a></td>

<td>M. Shatsky & H. Wolfson</td>

<td>2004

</td></tr>

<td>CTSS

</td>

<td>Protein Structure Alignment Using Local Geometrical Features</td>

<td>Geometry</td>

<td>2004

</td></tr>

<tr>

<td>CURVE

</td>

<td>Geometry</td>

<td>Multi</td>

<td>2006

</td></tr>

<td>Matt

</td>

<td>Multiple Alignment with Translations and Twists</td>

<td>Multi</td>

<td><a rel="nofollow" class="external text" href="http://bcb.cs.tufts.edu/mattweb">server</a> <a rel="nofollow" class="external text" href="http://matt.cs.tufts.edu">download</a></td>

<td>M. Menke</td>

<td>2008

</td></tr>

<tr>

<td><a rel="nofollow" class="external text" href="http://topmatch.services.came.sbg.ac.at">TopMatch</a><a href="#cite_note-7">[7]</a>

</td>

<td>Protein structure alignment and visualization of structural similarities; alignment of multiprotein complexes</td>

<td><a rel="nofollow" class="external text" href="http://topmatch.services.came.sbg.ac.at">server</a> <a rel="nofollow" class="external text" href="https://www.came.sbg.ac.at/app_download.php?app=topmatch">download</a></td>

<td>M. Sippl & M. Wiederstein</td>

<td>2012

</td></tr>

<td>SSGS

</td>

<td>Secondary Structure Guided Superimposition</td>

<td>G. Wainreb et al.</td>

<td>2006

</td></tr>

<tr>

<td>Matchprot

</td>

<td>Comparison of protein structures by growing neighborhood alignments</td>

<td><a rel="nofollow" class="external text" href="http://mllab.csa.iisc.ernet.in/mp2/runprog.html">server</a></td>

<td>S. Bhattacharya et al.</td>

<td>2007

</td></tr>

<td><a href="UCSF_Chimera" title="UCSF Chimera">UCSF Chimera</a>

</td>

<td>see MatchMaker tool and "matchmaker" command</td>

<td>Multi</td>

<td>2006

</td></tr>

<tr>

<td>FLASH

</td>

<td>Fast aLignment Algorithm for finding Structural Homology of proteins</td>

<td>E.S.C. Shih & M-J Hwang</td>

<td>2003

</td></tr>

<td>RAPIDO

</td>

<td>Rapid Alignment of Protein structures In the presence of Domain mOvements</td>

<td><a rel="nofollow" class="external text" href="http://webapps.embl-hamburg.de/rapido/">server</a></td>

<td>R. Mosca & T.R. Schneider</td>

<td>2008

</td></tr>

<tr>

<td>ComSubstruct

</td>

<td>Structural Alignment based on Differential Geometrical Encoding</td>

<td>Geometry</td>

<td>N. Morikawa</td>

<td>2008

</td></tr>

<td>ProCKSI

</td>

<td>Protein (Structure) Comparison, Knowledge, Similarity and Information</td>

<td>Other</td>

<td>D. Barthel et al.</td>

<td>2007

</td></tr>

<tr>

<td>SARST

</td>

<td>Structure similarity search Aided by Ramachandran Sequential Transformation

</td>

<td>2007

</td></tr>

<td>Fr-TM-align

</td>

<td>Fragment-TM-score based protein structure alignment</td>

<td>S.B. Pandit & J. Skolnick</td>

<td>2008

</td></tr>

<tr>

<td>TOPS+ COMPARISON

</td>

<td>Comparing topological models of protein structures enhanced with ligand information</td>

<td>Topology</td>

<td><a rel="nofollow" class="external text" href="http://balabio.dcs.gla.ac.uk/mallika/WebTOPS/">server</a></td>

<td>M. Veeramalai & D. Gilbert</td>

<td>2008

</td></tr>

<td>TOPS++FATCAT

</td>

<td>Flexible Structure AlignmenT by Chaining Aligned Fragment Pairs Allowing Twists derived from TOPS+ String Model</td>

<td><a rel="nofollow" class="external text" href="http://fatcat.burnham.org/TOPS">server</a></td>

<td>M. Veeramalai et al.</td>

<td>2008

</td></tr>

<tr>

<td>MolLoc

</td>

<td>Molecular Local Surface Alignment</td>

<td><a rel="nofollow" class="external text" href="http://bcb.dei.unipd.it/MolLoc/">server</a></td>

<td>2007

</td></tr>

<td>FASE

</td>

<td>Flexible Alignment of Secondary Structure Elements</td>

<td>J. Vesterstrom & W. R. Taylor</td>

<td>2006

</td></tr>

<tr>

<td><a href="Structural_alignment#SABERTOOTH" title="Structural alignment">SABERTOOTH</a>

</td>

<td>Protein Structural Alignment based on a vectorial Structure Representation</td>

<td><a rel="nofollow" class="external text" href="http://www.fkp.tu-darmstadt.de/sabertooth/">server</a></td>

<td>F. Teichert et al.</td>

<td>2007

</td></tr>

<td>STON

</td>

<td>C. Eslahchi et al.</td>

<td>2009

</td></tr>

<tr>

<td>SALIGN

</td>

<td>Sequence-Structure Hybrid Method</td>

<td>Multi</td>

<td>M.S. Madhusudhan et al.</td>

<td>2007

</td></tr>

<td>MAX-PAIRS

</td>

<td>A. Poleksic</td>

<td>2009

</td></tr>

<tr>

<td>THESEUS

</td>

<td>Maximum likelihood superpositioning</td>

<td>Multi</td>

<td>D.L. Theobald & D.S. Wuttke</td>

<td>2006

</td></tr>

<td>TABLEAUSearch

</td>

<td>Structural Search and Retrieval using a Tableau Representation of Protein Folding Patterns</td>

<td><a rel="nofollow" class="external text" href="http://hollywood.bx.psu.edu/TabSearch">server</a></td>

<td>A.S. Konagurthu et al.</td>

<td>2008

</td></tr>

<tr>

<td>QP Tableau Search<a href="#cite_note-8">[8]</a>

</td>

<td>Tableau-based protein substructure search using quadratic programming</td>

<td><a rel="nofollow" class="external text" href="https://github.com/stivalaa/qptabsearch">download</a></td>

<td>A.Stivala et al.</td>

<td>2009

</td></tr>

<td>ProSMoS

</td>

<td>Protein Structure Motif Search</td>

<td><a rel="nofollow" class="external text" href="http://prodata.swmed.edu/ProSMoS/">server</a> <a rel="nofollow" class="external text" href="ftp://iole.swmed.edu/pub/ProSMoS">download</a></td>

<td>2007

</td></tr>

<tr>

<td>MISTRAL

</td>

<td>Energy-based multiple structural alignment of proteins</td>

<td>Multi</td>

<td><a rel="nofollow" class="external text" href="http://ipht.cea.fr/protein.php">server</a></td>

<td>C. Micheletti & H. Orland</td>

<td>2009

</td></tr>

<td>MSVNS for MaxCMO

</td>

<td>A simple and fast heuristic for protein structure comparison</td>

<td>D. Pelta et al.</td>

<td>2008

</td></tr>

<tr>

<td>Structal

</td>

<td>Least Squares Root Mean Square deviation minimization by dynamic programming</td>

<td><a rel="nofollow" class="external text" href="http://www.molmovdb.org/geometry/3dhmm/">server</a> <a rel="nofollow" class="external text" href="http://csb.stanford.edu/levitt/Structal/">download</a></td>

<td>Gerstein & Levitt</td>

<td>2005

</td></tr>

<td><a href="ProBiS" title="ProBiS">ProBiS</a><a href="#cite_note-9">[9]</a>

</td>

<td>Detection of Structurally Similar Protein Binding Sites by Local Structural Alignment</td>

<td><a rel="nofollow" class="external text" href="http://probis.cmm.ki.si/">server</a> <a rel="nofollow" class="external text" href="http://probis.cmm.ki.si/?what=parallel">download</a></td>

<td>J. Konc & D. Janezic</td>

<td>2010

</td></tr>

<tr>

<td>ALADYN

</td>

<td>Dynamics-based Alignment: superposing proteins by matching their collective movements</td>

<td><a rel="nofollow" class="external text" href="http://aladyn.escience-lab.org/">server</a></td>

<td>Potestio et al.</td>

<td>2010

</td></tr>

<td>SWAPSC

</td>

<td>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.</td>

<td>Multi</td>

<td><a rel="nofollow" class="external text" href="http://www.may.ie/academic/biology/staff/mfmolecevolandbioinf.shtml">Server</a></td>

<td>Mario A. Fares</td>

<td>2004

</td></tr>

<tr>

<td>SA Tableau Search<a href="#cite_note-10">[10]</a>

</td>

<td>Fast and accurate protein substructure searching with simulated annealing and GPUs</td>

<td><a rel="nofollow" class="external text" href="https://github.com/stivalaa/cuda_satabsearch">download</a></td>

<td>A.Stivala et al.</td>

<td>2010

</td></tr>

<td><a href="Protein_Data_Bank" title="Protein Data Bank">RCSB PDB</a> Protein Comparison Tool

</td>

<td>Provides CE, FATCAT, CE variation for <a href="Circular_permutation_in_proteins" title="Circular permutation in proteins">Circular Permutations</a>, Sequence Alignments</td>

<td><a rel="nofollow" class="external text" href="http://www.rcsb.org/pdb/workbench/workbench.do">server</a> <a rel="nofollow" class="external text" href="http://source.rcsb.org">download</a></td>

<td>A. Prlic et al.</td>

<td>2010

</td></tr>

<tr>

<td>CSR

</td>

<td>Maximal common 3D motif; non-parametric; outputs pairwise correspondence; works also on small molecules</td>

<td><a rel="nofollow" class="external text" href="http://bioserv.rpbs.univ-paris-diderot.fr/Help/wwLigCSRre.html">server</a> <a rel="nofollow" class="external text" href="http://petitjeanmichel.free.fr/itoweb.petitjean.freeware.html">download</a></td>

<td>M. Petitjean</td>

<td>1998

</td></tr>

<td>EpitopeMatch

</td>

<td>discontinuous structure matching; induced fit consideration; flexible geometrical and physicochemical specificity definition; transplantation of similar spatial arrangements of amino acid residues</td>

<td>Multi</td>

<td><a rel="nofollow" class="external text" href="http://www.epitopematch.org">download</a></td>

<td>S. Jakuschev</td>

<td>2011

</td></tr>

<tr>

<td>CLICK

</td>

<td>Topology-independent 3D structure comparison</td>

<td><a rel="nofollow" class="external text" href="http://mspc.bii.a-star.edu.sg/click">server</a></td>

<td>M. Nguyen</td>

<td>2011

</td></tr>

<td>Smolign

</td>

<td>Spatial motifs based protein structural alignment</td>

<td>Multi</td>

<td><a rel="nofollow" class="external text" href="http://bio.cse.ohio-state.edu/Smolign">download</a></td>

<td>2010

</td></tr>

<tr>

<td>3D-Blast

</td>

<td>Comparing three-dimensional shape-density</td>

<td>Density</td>

<td><a rel="nofollow" class="external text" href="http://threedblast.loria.fr">server</a></td>

<td>L. Mavridis et al.</td>

<td>2011

</td></tr>

<td>DEDAL

</td>

<td>DEscriptor Defined ALignment</td>

<td><a rel="nofollow" class="external text" href="https://bioexploratorium.pl/EP/DEDAL">server</a></td>

<td>P. Daniluk & B. Lesyng</td>

<td>2011

</td></tr>

<td>msTALI

</td>

<td>multiple sTructure ALIgnment</td>

<td>Cα & Dihed & SSE & Surf</td>

<td>Multi</td>

<td><a rel="nofollow" class="external text" href="http://ifestos.cse.sc.edu/mstali">server</a></td>

<td>P. Shealy & H. Valafar</td>

<td>2012

</td></tr>

<tr>

<td>mulPBA

</td>

<td>multiple PB sequence alignment</td>

<td>Multi</td>

<td>A.P. Joseph et al.</td>

<td>2012

</td></tr>

<td>SAS-Pro

</td>

<td>Similtaneous Alignment and Superimposition of PROteins</td>

<td><a rel="nofollow" class="external text" href="http://eudoxus.cheme.cmu.edu/saspro/SAS-Pro.html">server</a></td>

<td>Shah & Sahinidis</td>

<td>2012

</td></tr>

<tr>

<td>MIRAGE-align

</td>

<td>Match Index based structural alignment method</td>

<td><a rel="nofollow" class="external text" href="http://homepage.ntu.edu.tw/~d92548009">website</a></td>

<td>2012

</td></tr>

<td><a href="Structural_alignment#SPalign" title="Structural alignment">SPalign</a>

</td>

<td>Structure Pairwise alignment</td>

<td><a rel="nofollow" class="external text" href="http://sparks-lab.org/yueyang/server/SPalign">server</a> <a rel="nofollow" class="external text" href="http://sparks-lab.org/yueyang/download/index.php?Download=SP-simple_all.cc">download</a></td>

<td>2012

</td></tr>

<tr>

</td>

<td>Fast Pairwise or Multiple Alignments using Gaussian Overlap</td>

<td>Other</td>

<td><a rel="nofollow" class="external text" href="http://kpax.loria.fr">website</a></td>

<td>D.W. Ritchie</td>

<td>2016

</td></tr>

<td>DeepAlign<a href="#cite_note-DeepAlign-12">[12]</a>

</td>

<td>Protein structure alignment beyond spatial proximity (evolutionary information and hydrogen-bonding are taken into consideration)</td>

<td><a rel="nofollow" class="external text" href="http://ttic.uchicago.edu/~jinbo/DeepAlign/StructureAlign.zip">download</a> <a rel="nofollow" class="external text" href="http://raptorx.uchicago.edu/DeepAlign/submit/">server</a></td>

<td>2013

</td></tr>

<tr>

<td>3DCOMB<a href="#cite_note-3DCOMB-13">[13]</a>

</td>

<td>extension of DeepAlign</td>

<td>Multi</td>

<td>2012

</td></tr>

</td>

<td>A topology string alignment method for intensive rapid protein structure comparison</td>

<td>J. Razmara et al.</td>

<td>2012

</td></tr>

<tr>

<td>MICAN<a href="#cite_note-MICAN-15">[15]</a>

</td>

<td>MICAN can handle Multiple-chains, Inverse alignments, C α only models, Alternative alignments, and Non-sequential alignments</td>

<td><a rel="nofollow" class="external text" href="http://landscape.tbp.cse.nagoya-u.ac.jp/MICAN/Download.html">download</a></td>

<td>S.Minami et al.</td>

<td>2013

</td></tr>

<td>SPalignNS<a href="#cite_note-SPalignNS-16">[16]</a>

</td>

<td>Structure Pairwise alignment Non-Sequential</td>

<td><a rel="nofollow" class="external text" href="http://sparks-lab.org/server/SPalignNS">server</a> <a rel="nofollow" class="external text" href="http://sparks-lab.org/peter/downloads/SPalignNS.tar.gz">download</a></td>

<td>P. Brown et al.</td>

<td>2015

</td></tr>

</td>

<td>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</td>

<td>Multi</td>

<td><a rel="nofollow" class="external text" href="https://biosciences.hs-mittweida.de/fit3d">server</a> <a rel="nofollow" class="external text" href="https://bitbucket.org/fkaiser/fit3d/downloads/Fit3D_v005.zip">download</a></td>

<td>F. Kaiser et al.</td>

<td>2015

</td></tr>

<tr>

<td>MMLigner<a href="#cite_note-MMLigner-18">[18]</a>

</td>

<td>Bayesian statistical inference of alignments based on information theory and compression.</td>

<td><a rel="nofollow" class="external text" href="http://lcb.infotech.monash.edu.au/mmligner/mmlignerweb.html">server</a> <a rel="nofollow" class="external text" href="http://lcb.infotech.monash.edu.au/mmligner/">download</a></td>

<td>J. Collier et al.</td>

<td>2017

</td></tr>

<td><a href="Protein_Data_Bank" title="Protein Data Bank">RCSB PDB</a> strucmotif-search<a href="#cite_note-strucmotif-19">[19]</a>

</td>

<td>Small structural motifs search that takes seconds to run on 180k or more structures, with nucleic acid & <a href="Bioassembly" class="mw-redirect" title="Bioassembly">bioassembly</a> support</td>

<td>Multi</td>

<td><a rel="nofollow" class="external text" href="https://www.rcsb.org/docs/search-and-browse/advanced-search/structure-motif-search">server/documentation</a> <a rel="nofollow" class="external text" href="https://github.com/rcsb/strucmotif-search">download</a></td>

<td>S. Bittrich et al.</td>

<td>2020

</td></tr></tbody></table>

Key map:

<ul><li>Class:</li></ul>

<dl><dd><ul><li>Cα -- Backbone Atom (Cα) Alignment;</li>

<li>AllA -- All Atoms Alignment;</li>

<li>SSE -- Secondary Structure Elements Alignment;</li>

<li>Seq -- Sequence-based alignment</li>

<li>Pair -- Pairwise Alignment (2 structures *only*);</li>

<li>Multi -- Multiple Structure Alignment (MStA);</li>

<li>C-Map -- Contact Map</li>

<li>Surf -- Connolly Molecular Surface Alignment</li>

<li>SASA -- Solvent Accessible Surface Area</li>

<li>Dihed -- Dihedral Backbone Angles</li>

<li>PB -- Protein Blocks</li></ul></dd></dl>

<ul><li>Flexible:</li></ul>

<dl><dd><ul><li>No -- Only rigid-body transformations are considered between the structures being compared.</li>

<li>Yes -- The method allows for some flexibility within the structures being compared, such as movements around hinge regions.</li></ul></dd></dl>

<div class="mw-heading mw-heading2"><h2 id="References">References</h2></div>

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