Structural alignment software

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


[edit] Structural alignment

NAME Description Class Type Flexible Link Author Year
MAMMOTH MAtching Molecular Models Obtained from Theory Cα Pair No server AR. Ortiz 2002
CE/CE-MC Combinatorial Extension -- Monte Carlo Cα Multi No server I. Shindyalov 2000
DaliLite Distance Matrix Alignment C-Map Pair No server L. Holm 1993
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
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 server R. Russell & G. Barton 1992
MASS Multiple Alignment by Secondary Structure SSE Multi nil server O. Dror & H. Wolfson 2003
SCALI Structural Core ALIgnment of proteins Seq Pair nil server 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 B. Lee 2000
LGA Local-Global Alignment Cα Pair nil server 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
Matras MArkovian TRAnsition of protein Structure Cα & SSE Pair nil NA 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 PRobaility 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. 2005
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 Nonsequential and Gapped STructural Alignment SSE/C-Map Pair nil server B. Kolbeck et al. 2006
TM-align TM-score based protein structure alignment Cα Pair nil site Y. Zhang & J. Skolnick 2005
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. 2007
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
CLEMAPS Conformation-based alphabet alignments Cα Multi nil NA W-M. Zheng 2007
TALI 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 Yes 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 download M. Menke 2008
TopMatch Protein structure alignment and visualization of structural similarities Cα Pair No server M. Sippl & M. Wiederstein 2008
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

Key map:

  • Cα -- Backbone Atom (Cα) 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