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Structural alignment software

This list of structural alignment software is a compilation of software tools and web portals used in pairwise or multiple structural alignment

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Structural alignment

NAME Description Class Type Link Author Year
MAMMOTH MAtching Molecular Models Obtained from Theory Pair server AR. Ortiz 2002
CE/CE-MC Combinatorial Extension -- Monte Carlo Multi server I. Shindyalov 2000
DaliLite Distance Matrix Alignment C-Map Pair server download L. Holm 1993
VAST Vector Alignment Search Tool SSE Pair server S. Bryant 1996
PrISM Protein Informatics Systems for Modeling SSE Multi server B. Honig 2000
SSAP Sequential Structure Alignment Program SSE Multi server C. Orengo and W. Taylor 1989
SARF2 Spatial ARrangements of Backbone Fragments SSE Pair server N. Alexandrov 1996
KENOBI/K2 NASSEPair server Z. Weng 2000
STAMP STructural Alignment of Multiple Proteins Multi server R. Russell and G. Barton 1992
MASS Multiple Alignment by Secondary Structure SSE Multi server O. Dror and H. Wolfson 2003
SCALI Structural Core ALIgnment of proteins Sequence Pair server C. Bystroff 2004
DEJAVU NA SSE Pair server GJ. Kleywegt 1997
SSM Secondary Structure Matching SSE/Cα Multi server E. Krissinel 2003
SHEBA Structural Homology by Environment-Based Alignment Sequence Pair server B. Lee 2000
LGA Local-Global Alignment Pair server A. Zemla 2003
POSA Partial Order Structure Alignment Multi server Y. Ye and A. Godzik 2005
PyMOL "super" command does sequence-independent 3D alignment Protein Hybrid site W. L. DeLano 2007
FATCAT Flexible Structure AlignmenT by Chaining Aligned Fragment Pairs Allowing Twists Pair server Y. Ye and A. Godzik 2004
Matras MArkovian TRAnsition of protein Structure Cα & SSE Pair NA K. Nishikawa 2000
MAMMOTH-mult MAMMOTH-based multiple structure alignment Multi server D. Lupyan 2005
Protein3Dfit NA C-Map Pair server D. Schomburg 1994
PRIDE PRobaility of IDEntity Pair server S. Pongor 2002
FAST FAST Alignment and Search Tool Pair server J. Zhu 2004
C-BOP Coordinate-Based Organization of Proteins N/A Multi server E. Sandelin 2005
ProFit Protein least-squares Fitting Multi server ACR. Martin 1996
TOPOFIT Alignment as a superimposition of common volumes at a topomax point Pair server V. A. Ilyin 2004
MUSTANG MUltiple STructural AligNment AlGorithm Cα & C-Map Multi download A.S. Konagurthu et al. 2005
URMS Unit-vector RMSD Pair server K. Kedem 2003
LOCK Hierarchical protein structure superposition SSE Pair NA AP. Singh 1997
LOCK 2 Improvements over LOCK SSE Pair NA J. Shapiro 2003
CBA Consistency Based Alignment SSE Multi download J. Ebert 2006
TetraDA Tetrahedral Decomposition Alignment SSE Multi NA J. Roach 2005
STRAP STRucture based Alignment Program Multi server C. Gille 2006
LOVOALIGN Low Order Value Optimization methods for Structural Alignment Pair server Andreani et al. 2006
GANGSTA Genetic Algorithm for Nonsequential and Gapped STructural Alignment SSE/C-Map Pair


B Kolbeck, P May, T Schmidt-Gönner, EW Knapp 2006
TM-align TM-score based protein structure alignment Pair server Y. Zhang, J. Skolnick 2005
MatAlign Protein Structure Comparison by Matrix Alignment C-Map Pair site Z. Aung and K.L. Tan 2006
Vorolign Fast structure alignment using Voronoi contacts Voronoi contacts Multi server Birzele F, Gewehr J E, Csaba G, Zimmer R 2007
EXPRESSO Fast Multiple Structural Alignment using T-Coffee and Sap Multi site Notredame et al. 2007
CAALIGN Cα Align Multi site T.J. Oldfield 2007
YAKUSA Internal Coordinates and BLAST type algorithm Pair site/download Carpentier et al. 2005
CLEMAPS Conformation-based alphabet alignments Multi NA W-M. Zheng 2007
TALI Torsion Angle ALIgnment Pair NA X. Mioa 2008
MolCom NA Geometry Multi NA S.D. O'Hearn 2003
MALECON NA Geometry Multi NA S. Wodak 2004
MultiProt Multiple Alignment of Protein Structures Geometry Multi server M. Shatsky and H. Wolfson 2004
CTSS Protein Structure Alignment Using Local Geometrical Features Geometry Pair site T. Can 2004
CURVE NA Geometry Multi NA D. Zhi 2006

Key map:

  • -- Backbone Atom (Cα) Alignment;
  • SSE -- Secondary Structure Elements Alignment;
  • Pair -- Pairwise Alignment (2 structures *only*);
  • Multi -- Multiple Structure Alignment (MStA);
  • C-Map -- Contact Map
This article is licensed under the GNU Free Documentation License. It uses material from the Wikipedia article "Structural_alignment_software". A list of authors is available in Wikipedia.
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