| NAME
| Description | Class | Type | Link | Author | Year
|
| MAMMOTH
| MAtching Molecular Models Obtained from Theory | Cα | Pair | server | AR. Ortiz | 2002
|
| CE/CE-MC
| Combinatorial Extension -- Monte Carlo | Cα | 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
| NA | SSE | Pair | server | Z. Weng | 2000
|
| STAMP
| STructural Alignment of Multiple Proteins | Cα | 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 | Cα | Pair | server | A. Zemla | 2003
|
| POSA
| Partial Order Structure Alignment | Cα | 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 | Cα | 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 | Cα | Multi | server | D. Lupyan | 2005
|
| Protein3Dfit
| NA | C-Map | Pair | server | D. Schomburg | 1994
|
| PRIDE
| PRobaility of IDEntity | Cα | Pair | server | S. Pongor | 2002
|
| FAST | FAST Alignment and Search Tool | Cα | Pair | server | J. Zhu | 2004
|
| C-BOP | Coordinate-Based Organization of Proteins | N/A | Multi | server | E. Sandelin | 2005
|
| ProFit | Protein least-squares Fitting | Cα | Multi | server | ACR. Martin | 1996
|
| TOPOFIT | Alignment as a superimposition of common volumes at a topomax point | Cα | 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 | Cα | 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 | Cα | Multi | server | C. Gille | 2006
|
| LOVOALIGN | Low Order Value Optimization methods for Structural Alignment | Cα | Pair | server | Andreani et al. | 2006
|
| GANGSTA | Genetic Algorithm for Nonsequential and Gapped STructural Alignment | SSE/C-Map | Pair |
server
| B Kolbeck, P May, T Schmidt-Gönner, EW Knapp | 2006
|
| TM-align
| TM-score based protein structure alignment | Cα | 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 | Cα | Multi | site | Notredame et al. | 2007
|
| CAALIGN | Cα Align | Cα | Multi | site | T.J. Oldfield | 2007
|
| YAKUSA
| Internal Coordinates and BLAST type algorithm | Cα | Pair | site/download | Carpentier et al. | 2005
|
| CLEMAPS | Conformation-based alphabet alignments | Cα | Multi | NA | W-M. Zheng | 2007
|
| TALI | Torsion Angle ALIgnment | Cα | 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
|
