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3-D Structure Comparison
Structural Alignment Databases
The Dali Database is based on exhaustive, all-against-all 3D structure comparison of protein structures in the Protein Data Bank* (PDB).
Protein structure neighbors in Entrez are determined by direct comparison of 3-dimensional protein structures with the VAST algorithm. Each of the more than 87,804 domains in MMDB is compared to every other one.
FSSP (families of structurally similar proteins) is a database of structural alignments of proteins in the Protein Data Bank (PDB).
SURFACE is a database containing the results of a large-scale protein annotation and local structural comparison project. A non-redundant set of protein chains is used to build a database of protein surface patches, defined as putative surface functional sites. Each patch is annotated with sequence and structure-derived information about function or interaction abilities.
HOMSTRAD (HOMologous STRucture Alignment Database) is a curated database of structure-based alignments for homologous protein families. All known protein structure are clustered into homologous families (i.e., common ancestry), and the sequences of representative members of each family are aligned on the basis of their 3D structures using the programs MNYFIT, STAMP and COMPARER.
This database provides structure based sequence alignments for homologous proteins of known 3-D structure.
Database Search & Structure Retrieval
The Dali server is a network service for comparing protein structures in 3D. You submit the coordinates of a query protein structure and Dali compares them against those in the Protein Data Bank (PDB).
PDBeFold (also known as SSM) is an interactive service for comparing protein structures in 3D.
deconSTRUCT is a general purpose protein database search on the substructure level for protein structure comparison.
Protein structure neighbors in Entrez are determined by direct comparison of 3-dimensional protein structures with the VAST algorithm. Each of the more than 87,804 domains in MMDB is compared to every other one.
FATCAT (Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists) is an approach for flexible protein structure comparison.
iSARST: an integrated SARST web server for rapid protein structural similarity searches.
SALAMI aligns your structure to every chain in the pdb90 library and returns a list of the most similar chains, their coordinates superimposed onto the query structure, and detailed alignments of your structure and the best matches.
Integrated search and alignment of protein structures using Voronoi contacts.
Integrated Structure Analysis Platforms
Cn3D is NCBI's 3D structure viewer. As a helper application for your Web browser, it allows you to interactively view 3D structures, sequences, and sequence alignments. Cn3D simultaneously displays structure, sequence, and alignment, with annotation and alignment editing features, for use with 3-D structures from NCBI's Entrez; available for Windows, Macintosh, and Unix.
Strap supports the simultaneous analysis of hundreds of proteins and integrates amino acid sequence, secondary structure, 3D-structure and genomic- and mRNA-sequence and residue annotation.
Friend is a bioinformatics application designed for simultaneous analysis and visualization of multiple structures and sequences of proteins and/or DNA/RNA.
ENDscript produces from a single PDB file four PostScript figures containing most required sequence and structure information on a protein of known structure.
SPICE is a browser for protein sequences, structures and their annotations. It can display annotations for PDB, UniProt and Ensembl Peptides. All data is retrieved from different sites on the Internet, that make their annotations available using the DAS protocol. It is possible to add new annotations to SPICE, and to compare them with the already available information.
Sequence-To-Structure Alignment
EXPRESSO aligns protein sequences using structural information.
PROMALS3D constructs alignments for multiple protein sequences and/or structures using information from sequence database searches, secondary structure prediction, available homologs with 3D structures and user-defined constraints.
Pairwise Structure Aligment Servers
Protein (Structure) Comparison, Knowledge, Similarity and Information Server (ProCKSI) is a decision support system for protein structure comparison. It computes structural similarities using a variety of similarity comparison methods in order to produce a similarity consensus.
FeatureMap3D combines protein sequence-based information with structural data from the Protein Data Bank (PDB).
DaliLite is a program for pairwise structure comparison.
The SSAP server allows users to compare the structures of two proteins and view the subsequent structural alignment.
MAMMOTH (Matching Molecular Models Obtained from Theory) is a sequence-independent protein structural alignment method. It allows the comparison of an experimental protein structure with an arbitrary low-resolution protein tertiary model. It also allows the comparison of two experimental structures, or the search for similar structures to a query structure in a database.
FAST is a new algorithm for aligning three-dimensional structures of proteins. FAST employs an elimination heuristic to quickly and reliably detect the global optimum residue-residue alignment.
FATCAT (Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists) is an approach for flexible protein structure comparison. It simultaneously addresses the two major goals of flexible structure alignment; optimizing the alignment and minimizing the number of rigid-body movements (twists) around pivot points (hinges) introduced in the reference structure.
deconSTRUCT is a general purpose protein database search on the substructure level for protein structure comparison.
CE calculates structural alignment for two polypeptide chains using the Combinatorial Extension (CE) Method.
Databases and Tools for 3-D Protein Structure Comparison and Alignment Using the Combinatorial Extension (CE) Method.
K2SA is a protein structure alignment program based on K2 program.
Automated Structural Alignment Server at Uppsala University.
FlexProt detects the optimal flexible structural alignment of a pair of protein structures. The first structure is assumed to be rigid, while in the second structure potential flexible regions are automatically detected.
Protein 3D Structure Comparison using MArkovian TRAnsition of Structure evolution
LovoAlign is a new protein structural alignment package. The methods used for structural alignment are based on Low Order Value Optimization (LOVO) theory. The use of LOVO theory led to the development of fast convergent algorithms that provide very robust optimization of scoring functions.
SHEBA is a new protein structure alignment procedure. The initial alignment is made by comparing a one-dimensional list of primary, secondary and tertiary structural profiles of two proteins, without explicitly considering the geometry of the structures. The alignment is then iteratively refined in the second step, in which new alignments are found by three-dimensional superposition of the structures based on the current alignment.
RAPIDO is an algorithm for the 3D alignment of protein structures.
Translate sequence - structure alignment (AL) into tertiary structure (TS)
Multiple Structure Alignment
Protein (Structure) Comparison, Knowledge, Similarity and Information Server (ProCKSI) is a decision support system for protein structure comparison. It computes structural similarities using a variety of similarity comparison methods in order to produce a similarity consensus.
Mistral implements the energy-based multiple protein structural alignment method.
Multiple flexible structure alignment using partial order graphs.
MultiProt is a fully automated highly efficient technique which detects the multiple structural alignments of protein structures.
MAMMOTH-mult is a multiple alignment version of MAMMOTH. It multiply aligns protein structures, providing a common 3D superimposition, a corresponding structure-based sequence alignment and a dendrogram for the set of structures aligned.
MASS is an efficient method for multiple alignment of protein structures and detection of structural motifs. Exploiting the secondary structure representation aids in filtering out noisy results and in making the method highly efficient and robust. MASS disregards the sequence order of the secondary structure elements. Thus, it can find non-sequential and even non-topological structural motifs.
3dSS is a web-based interactive computing server, primarily designed to aid researchers, to superpose two or several three-dimensional protein structures. In addition, the server can be effectively used to find the invariant and common water molecules present in the superposed homologous protein structures.
MULTIPLE STRUCTURE ALIGNMENT using FATCAT and the CE meethod.
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