# Structural alignment software

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 | Description | Class | Type | Flexible | Link | Author | Year |
| ARTEMIS | 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 | 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 | 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 |
| 3decision | Protein structure repository with visualisation and structural analytics tools | Seq | Multi | Yes | site | P. Schmidtke | 2015 |
| MAMMOTH | MAtching Molecular Models Obtained from Theory | Cα | Pair | No | server download | CEM Strauss & AR Ortiz | 2002 |
| CE | Combinatorial Extension | Cα | Pair | No | server | I. Shindyalov | 2000 |
| CE-MC | Combinatorial Extension-Monte Carlo | Cα | Multi | No | server | C. Guda | 2004 |
| DaliLite | Distance Matrix Alignment | C-Map | Pair | No | server and download | L. Holm | 1993 |
| TM-align | TM-score based protein structure alignment | Cα | Pair | nil | server and download | Y. Zhang & J. Skolnick | 2005 |
| mTM-align | Multiple protein structure alignment based on TM-align | Cα | Multi | No | server and download | R. Dong, Z. Peng, Y. Zhang & J. Yang | 2018 |
| 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 |
| MOE | Molecular Operating Environment. Extensive platform for protein and protein-ligand structure modelling. | Cα, AllA, Seq | Multi | No | site | Chemical Computing Group | 2000 |
| SSAP | Sequential Structure Alignment Program | SSE | Multi | No | server | C. Orengo & W. Taylor | 1989 |
| SARF2 | Spatial ARrangements of Backbone Fragments | SSE | Pair | nil | server | N. Alexandrov | 1996 |
| KENOBI/K2 | NA | SSE | Pair | nil | server | Z. Weng | 2000 |
| STAMP | STructural Alignment of Multiple Proteins | Cα | Multi | No | download server | R. Russell & G. Barton | 1992 |
| MASS | Multiple Alignment by Secondary Structure | SSE | Multi | No | server | O. Dror & H. Wolfson | 2003 |
| SCALI | Structural Core ALIgnment of proteins | Seq/C-Map | Pair | nil | server download | X. Yuan & C. Bystroff | 2004 |
| DEJAVU | NA | SSE | Pair | nil | server | GJ. Kleywegt | 1997 |
| SSM | Secondary Structure Matching | SSE | Multi | nil | server | E. Krissinel | 2003 |
| SHEBA | Structural Homology by Environment-Based Alignment | Seq | Pair | nil | server | J Jung & B Lee | 2000 |
| LGA | Local-Global Alignment, and Global Distance Test (GDT-TS) structure similarity measure | Cα, AllA, any atom | Pair | nil | server and download | A. Zemla | 2003 |
| POSA | Partial Order Structure Alignment | Cα | Multi | Yes | server | Y. Ye & A. Godzik | 2005 |
| PyMOL | "super" command does sequence-independent 3D alignment | Protein | Hybrid | No | site | W. L. DeLano | 2007 |
| FATCAT | Flexible Structure AlignmenT by Chaining Aligned Fragment Pairs Allowing Twists | Cα | Pair | Yes | server | Y. Ye & A. Godzik | 2003 |
| deconSTRUCT | Database search on substructural level and pairwise alignment. | SSE | Multi | No | server | ZH. Zhang et al. | 2010 |
| Matras | MArkovian TRAnsition of protein Structure | Cα & SSE | Pair | nil | server | K. Nishikawa | 2000 |
| MAMMOTH-mult | MAMMOTH-based multiple structure alignment | Cα | Multi | No | server | D. Lupyan | 2005 |
| Protein3Dfit | NA | C-Map | Pair | nil | server | D. Schomburg | 1994 |
| PRIDE | PRobability of IDEntity | Cα | Pair | nil | server | S. Pongor | 2002 |
| FAST | FAST Alignment and Search Tool | Cα | 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 | Cα | Multi | nil | server | ACR. Martin | 1996 |
| TOPOFIT | Alignment as a superimposition of common volumes at a topomax point | Cα | Pair | nil | server | VA. Ilyin | 2004 |
| MUSTANG | MUltiple STructural AligNment AlGorithm | Cα & C-Map | Multi | nil | download | A.S. Konagurthu et al. | 2006 |
| URMS | Unit-vector RMSD | Cα | Pair | nil | server | K. Kedem | 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 | Cα | Multi | nil | server | C. Gille | 2006 |
| LOVOALIGN | Low Order Value Optimization methods for Structural Alignment | Cα | Pair | nil | server | Andreani et al. | 2006 |
| GANGSTA | Genetic 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 | Protein Structure Comparison by Matrix Alignment | C-Map | Pair | nil | site | Z. Aung & K.L. Tan | 2006 |
| Vorolign | Fast structure alignment using Voronoi contacts | C-Map | Multi | Yes | server | F. Birzele et al. | 2006 |
| EXPRESSO | Fast Multiple Structural Alignment using T-Coffee and Sap | Cα | Multi | nil | site | C. Notredame et al. | 2007 |
| CAALIGN | Cα Align | Cα | Multi | nil | site | T.J. Oldfield | 2007 |
| YAKUSA | Internal Coordinates and BLAST type algorithm | Cα | Pair | nil | site | M. Carpentier et al. | 2005 |
| BLOMAPS | Conformation-based alphabet alignments | Cα | Multi | nil | server | W-M. Zheng & S. Wang | 2008 |
| CLEPAPS | Conformation-based alphabet alignments | Cα | Pair | nil | server | W-M. Zheng & S. Wang | 2008 |
| TALI F | Torsion Angle ALIgnment | Cα | 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 |
| FlexProt | Flexible Alignment of Protein Structures | Cα | Pair | Yes | server | M. Shatsky & H. Wolfson | 2002 |
| MultiProt | Multiple Alignment of Protein Structures | Geometry | Multi | No | server | M. Shatsky & H. Wolfson | 2004 |
| CTSS | Protein Structure Alignment Using Local Geometrical Features | Geometry | Pair | nil | site | T. Can | 2004 |
| CURVE | NA | Geometry | Multi | No | site | D. Zhi | 2006 |
| Matt | Multiple Alignment with Translations and Twists | Cα | Multi | Yes | server download | M. Menke | 2008 |
| TopMatch | Protein structure alignment and visualization of structural similarities; alignment of multiprotein complexes | Cα | Pair | No | server download | M. Sippl & M. Wiederstein | 2012 |
| SSGS | Secondary Structure Guided Superimposition | Ca | Pair | No | site | G. Wainreb et al. | 2006 |
| Matchprot | Comparison of protein structures by growing neighborhood alignments | Cα | Pair | No | server | S. Bhattacharya et al. | 2007 |
| UCSF Chimera | see MatchMaker tool and "matchmaker" command | Seq & SSE | Multi | No | site | E. Meng et al. | 2006 |
| FLASH | Fast aLignment Algorithm for finding Structural Homology of proteins | SSE | Pair | No | NA | E.S.C. Shih & M-J Hwang | 2003 |
| RAPIDO | Rapid Alignment of Protein structures In the presence of Domain mOvements | Cα | 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 |
| SARST | Structure similarity search Aided by Ramachandran Sequential Transformation | Cα | Pair | nil | site | W-C. Lo et al. | 2007 |
| Fr-TM-align | Fragment-TM-score based protein structure alignment | Cα | Pair | no | site | S.B. Pandit & J. Skolnick | 2008 |
| TOPS+ COMPARISON | Comparing topological models of protein structures enhanced with ligand information | Topology | Pair | Yes | server | M. Veeramalai & D. Gilbert | 2008 |
| TOPS++FATCAT | Flexible Structure AlignmenT by Chaining Aligned Fragment Pairs Allowing Twists derived from TOPS+ String Model | Cα | Pair | Yes | server | M. Veeramalai et al. | 2008 |
| MolLoc | Molecular Local Surface Alignment | Surf | Pair | No | server | M.E. Bock et al. | 2007 |
| FASE | Flexible Alignment of Secondary Structure Elements | SSE | Pair | Yes | NA | J. Vesterstrom & W. R. Taylor | 2006 |
| SABERTOOTH | Protein Structural Alignment based on a vectorial Structure Representation | Cα | Pair | Yes | server | F. Teichert et al. | 2007 |
| STON | NA | Cα | Pair | No | site | C. Eslahchi et al. | 2009 |
| SALIGN | Sequence-Structure Hybrid Method | Seq | Multi | No | site | M.S. Madhusudhan et al. | 2007 |
| MAX-PAIRS | NA | Cα | Pair | No | site | A. Poleksic | 2009 |
| THESEUS | Maximum likelihood superpositioning | Cα | Multi | No | site | D.L. Theobald & D.S. Wuttke | 2006 |
| TABLEAUSearch | Structural Search and Retrieval using a Tableau Representation of Protein Folding Patterns | SSE | Pair | No | server | A.S. Konagurthu et al. | 2008 |
| QP Tableau Search | Tableau-based protein substructure search using quadratic programming | SSE | Pair | No | download server | A.Stivala et al. | 2009 |
| ProSMoS | Protein Structure Motif Search | SSE | Pair | No | server download | S. Shi et al. | 2007 |
| MISTRAL | Energy-based multiple structural alignment of proteins | Cα | Multi | No | server | C. Micheletti & H. Orland | 2009 |
| MSVNS for MaxCMO | A simple and fast heuristic for protein structure comparison | C-Map | Pair | No | site | D. Pelta et al. | 2008 |
| Structal | Least Squares Root Mean Square deviation minimization by dynamic programming | Cα | Pair | No | server download | Gerstein & Levitt | 2005 |
| ProBiS | Detection of Structurally Similar Protein Binding Sites by Local Structural Alignment | Surf | Pair | Yes | server download | J. Konc & D. Janezic | 2010 |
| ALADYN | Dynamics-based Alignment: superposing proteins by matching their collective movements | Cα | Pair | No | server | Potestio 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. | Seq | Multi | yes | Server | Mario A. Fares | 2004 |
| SA Tableau Search | Fast and accurate protein substructure searching with simulated annealing and GPUs | SSE | Pair | No | download server | A.Stivala et al. | 2010 |
| RCSB PDB Protein Comparison Tool | Provides CE, FATCAT, CE variation for Circular Permutations, Sequence Alignments | Cα | Pair | yes | server 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 | server download | M. Petitjean | 1998 |
| 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 | download | S. Jakuschev | 2011 |
| CLICK | Topology-independent 3D structure comparison | SSE & Cα & SASA | Pair | Yes | server | M. Nguyen | 2011 |
| Smolign | Spatial motifs based protein structural alignment | SSE & C-Map | Multi | Yes | download | H. Sun | 2010 |
| 3D-Blast | Comparing three-dimensional shape-density | Density | Pair | No | server | L. Mavridis et al. | 2011 |
| DEDAL | DEscriptor Defined ALignment | SSE & Cα & C-Map | Pair | Yes | server | P. Daniluk & B. Lesyng | 2011 |
| msTALI | multiple sTructure ALIgnment | Cα & Dihed & SSE & Surf | Multi | Yes | server | P. Shealy & H. Valafar | 2012 |
| mulPBA | multiple PB sequence alignment | PB | Multi | Yes | NA | A.P. Joseph et al. | 2012 |
| SAS-Pro | Similtaneous Alignment and Superimposition of PROteins | ??? | Pair | Yes | server | Shah & Sahinidis | 2012 |
| MIRAGE-align | Match Index based structural alignment method | SSE & PPE | Pair | No | website | K. Hung et al. | 2012 |
| SPalign | Structure Pairwise alignment | Cα | Pair | No | server download | Y. Yang et al. | 2012 |
| Kpax | Fast Pairwise or Multiple Alignments using Gaussian Overlap | Other | Pair | Yes | website | D.W. Ritchie | 2016 |
| DeepAlign | 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 | extension of DeepAlign | Cα | Multi | No | download server | S. Wang and J. Xu | 2012 |
| TS-AMIR | A topology string alignment method for intensive rapid protein structure comparison | SSE & Cα | Pair | No | NA | J. Razmara et al. | 2012 |
| MICAN | MICAN can handle Multiple-chains, Inverse alignments, C α only models, Alternative alignments, and Non-sequential alignments | Cα | Pair | No | download | S.Minami et al. | 2013 |
| SPalignNS | Structure Pairwise alignment Non-Sequential | Cα | Pair | No | server download | P. Brown et al. | 2015 |
| Fit3D | 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 | Bayesian statistical inference of alignments based on information theory and compression. | Cα | Pair | Yes | server download | J. Collier et al. | 2017 |
| RCSB PDB strucmotif-search | 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:
* 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.