Structural alignment software
Encyclopedia
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
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Key map:
Structural alignment
Structural alignment attempts to establish homology between two or more polymer structures based on their shape and three-dimensional conformation. This process is usually applied to protein tertiary structures but can also be used for large RNA molecules...
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Structural comparison and alignment
| NAME | Description | Class | Type | Flexible | Link | Author | Year |
|---|---|---|---|---|---|---|---|
| MAMMOTH | MAtching Molecular Models Obtained from Theory | Cα | Pair | No | server download | CEM Strauss & 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 |
| TM-align | TM-score based protein structure alignment | Cα | Pair | nil | server and download | Y. Zhang & J. Skolnick | 2005 |
| 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 | site 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/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 | 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 PyMOL PyMOL is an open-source, user-sponsored, molecular visualization system created by Warren Lyford DeLano and commercialized by DeLano Scientific LLC, which is a private software company dedicated to creating useful tools that become universally accessible to scientific and educational communities... |
"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 | 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 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. | 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 |
| 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 | 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 | server 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 UCSF Chimera UCSF Chimera is an extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality and can be created... |
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 [ftp://iole.swmed.edu/pub/ProSMoS 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 | 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 Data Bank The Protein Data Bank is a repository for the 3-D structural data of large biological molecules, such as proteins and nucleic acids.... Protein Comparison Tool |
Provides CE, FATCAT, CE variation for Circular Permutations Circular permutation in proteins Circular permutation is a process during evolution that changes the order of amino acids in a protein sequence, resulting in a protein structure with different connectivity, but overall similar three dimensional shape. As a consequence of the circular permutation, the N-terminus of one protein... , 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 | Multi | nil | download | H. Sun | 2011 |
| 3D-Blast | Comparing three-dimensional shape-density | Density | Pair | No | server | L. Mavridis et. al. | 2011 |
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
- Flexible:
- Yes indicates that the method allows rotations around hinges or some other means of allowing for the flexibility of structures rather than treating them as rigid bodies.