3-D Structure Comparison
This is collection of web tools for superimposing structures and for creating structure based sequence alignments. We included here tools that perform pairwise or multiple alignment for individual structures or against structural databases. In addition, we include here databases of aligned protein structures and specialized tools that designed to visualize and annotate the resulted alignment.
Simple structural superposition, where at least some equivalent residues of the two structures are known, can be preformed easily in most of the visualization software. Some of these software also include more robust alignment tools (such as the “super” command in PyMol).
| open in new windowCn3D | Cn3D is an open-source code visualization tool for biomolecular structures, sequences, and sequence alignments. Cn3D is typically run from a web browser as a helper application for NCBI's Entrez system. Cn3D is the primary visualization tool for open in new windowVAST alignments. |
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| open in new windowSTRAP | STRAP is a work bench for multiple sequence alignments of proteins. It is used to visualize three-dimensional structures, and to align several proteins using the sequences or the structure. |
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| open in new windowAuStrAlis | |
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| open in new windowCE | |
| open in new windowDaliLite | |
| open in new windowdeconSTRUCT | |
| open in new windowFAST | |
| open in new windowFATCAT | Flexible structure comparison |
| open in new windowFlexProt | Flexible structure comparison |
| open in new windowGANGSTA | |
| open in new windowGANGASTA+ | |
| open in new windowK2SA | |
| open in new windowLGA | |
| open in new windowLovoAlign | |
| open in new windowProCKSI | Meta-server for structure comparison and similarity consensus calculations |
| open in new windowProtDeform | Flexible structure comparison |
| open in new windowRapido | Flexible structure comparison |
| open in new windowSCALI | |
| open in new windowSSAP | |
| open in new windowSSM | |
| open in new windowTopMatch | |
| open in new windowURMS | |
| open in new windowVorolign | |
| open in new windowCE-MC | |
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| open in new windowComparer | |
| open in new windowMAMMOTH-mult | |
| open in new windowMASS | |
| open in new windowMATRAS | |
| open in new windowMISTRAL | |
| open in new windowMultiProt | Flexible structure comparison |
| open in new windowPOSA | Flexible structure comparison |
| open in new windowProCKSI | Meta-server for structure comparison and similarity consensus calculations |
| open in new windowSSM | |
| open in new windowSTRALCP | |
| open in new windowVorolign | |
| open in new windowDali Database | The Dali Database is based on exhaustive, all-against-all 3D structure comparison of protein structures in the PDB using the open in new windowDali search engine. (University of Helsinki) |
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| open in new windowDMAPS | DMAPS database contains pre-computed multiple structure alignments for protein chains in the PDB. Automated structure alignments have been generated for classified protein families using CE-MC algorithm. |
| open in new windowDBAli | |
| open in new windowFSSP | FSSP is a database of structural alignments of proteins in PDB. Each data set contains structural alignments of one search structure with all other structurally significantly similar proteins in the representative set of remote and medium homologs proteins (below 70% sequence identity). (EBI-EMBL) |
| open in new windowHOMSTRAD | Collection of manually examined structure-based alignments organized at the level of homologous families. (Cambridge) |
| open in new windowPALI | PALI database provides structural alignments for homologous proteins of known 3-D structure generated by MUSTANG. The database also provides dendrograms depicting phylogentic relationships based on sequence and structural similarities. (IISC) |
| open in new windowVAST | VAST is a database of structural alignments of proteins in MMDB. Structural neighbor information is based on a direct comparison of 3-D structure of domain substructures within the PDB using VAST algorithm. The alignment can be accessed from the open in new windowMMDB Structure summary pages. (NCBI) |
| open in new windowAline | Interactive perl/tk application for editing and annotating multiple sequence alignments. | |
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| open in new windowESPript | A web or standalone utility for structural annotation of multiple sequence alignments. |
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| open in new windowJOY | JOY is a program to annotate protein sequence alignments with 3-D structural features. | |