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FATCAT / Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists

An algorithm which automatically identifies hinges and internal rearrangements in two protein structures. In FATCAT, the structure alignment is formulated as the aligned fragment pairs chaining process allowing at most t twists, and the flexible structure alignment is transformed into a rigid structure alignment when t is forced to be 0. FATCAT server can report the conformational changes of the query structure as compared to other proteins in the structure database.

Dali server

A network service for comparing protein structures in 3D. Dali server provides enhanced analytics for the study of sequence and structure conservation. The server performs three types of structure comparisons: (i) Protein Data Bank (PDB) search compares one query structure against those in the PDB and returns a list of similar structures; (ii) pairwise comparison compares one query structure against a list of structures specified by the user; and (iii) all against all structure comparison returns a structural similarity matrix, a dendrogram and a multidimensional scaling projection of a set of structures specified by the user.

SMS / STING Millennium Suite

Provides a variety of algorithms and validated data, wrapped-up in a user friendly web interface. STING Millennium Suite (SMS) is a new web-based suite of programs and databases providing visualization and a complex analysis of molecular sequence and structure for the data deposited at the Protein Data Bank (PDB). It is described in terms of a solution that brings together a number of protein analysis tools at a single web server. SMS is a very powerful tool which enables a quick estimate of the level of engagement for each amino acid within its own protein chain and functionally more importantly, in the mechanism of binding to substrate and/or inhibitor.

EFICAz / Enzyme Function Inference by a Combined Approach

Allows users to study the proteomic scale inference of enzyme function. EFICAz can identify functionally discriminating residue (FDR) as residues that discriminate the members of a homo-functional family from a hetero-functional family. It combines the prediction from four independent methods, namely: (1) CHIEFc family-based (FDR) identification, (2) multiple PFAM-based FDR recognition, (3) CHIEFc SIT evaluation and (4) high-specificity multiple PROSITE patterns.


A fast protein structure alignment and database search program. Kpax uses Gaussian functions to score very rapidly the local and spatial environment of each amino acid residue in a protein, and it uses dynamic programming to find the optimal global alignment and superpositions of two proteins according to their Gaussian similarity scores. This approach allows very fast searches of structural databases, and it allows three-dimensional superpositions of proteins to be calculated rapidly. Kpax can perform flexible structure alignments, multiple structure alignments, and multiple flexible structure alignments. It can also score alignments calculated by other programs.


Provides a metric for measuring the structural similarity of two protein models. Template modeling score (TM-Score) is designed to solve two major problems in the traditional metrics such as root-mean-square deviation (RMSD): (1) TM-score measures the global fold similarity and is less sensitive to the local structural variations; (2) magnitude of TM-score for random structure pairs is length-independent. TM-score has the value in (0,1], where 1 indicates a perfect match between two structures. Following strict statistics of structures in the protein data bank (PDB), scores below 0.17 corresponds to randomly chosen unrelated proteins whereas with a score higher than 0.5 assume generally the same fold in SCOP/CATH. TM-Score is available online or can be downloaded in Fortran or Java version for local use.


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Aligns the 3D structures of any pair of biomolecules, independent of topology. CLICK is an algorithm that provides 3D structures by matching cliques of points. It consists of four sequential steps: (i) extracting features, (ii) forming cliques, (iii) clique matching and (iv) alignment. This application performs structural superposition on pairs of structures based on similarity of local structural packing, and thus is capable of aligning structures with dissimilar topologies, conformations or even molecular types.


Consists in an algorithm serving for non-sequential structural alignment of proteins and similarity search in databases. GANGSTA+ is able to notice structural similarities between two proteins, although their sequences might be reshuffled during evolution. It can spot non-sequential structural analogs for proteins stated to possess novel folds. Its online interface provides several functions: (1) comparing structures of a pair and performing a score; (2) searching the database; and (3) browsing the database.


Provides answers to simple questions such as these for the domain of protein folds. PartsList is a web application where properties for a protein fold include: (i) amino acid composition, (ii) alignment information, (iii) fold occurrences in various genomes, (iv) statistics related to motions, (v) absolute expression levels of yeast in different experiments, (vi) relative expression ratios for yeast, worm and Escherichia coli in various conditions, (vii) information on protein–protein interactions (based on whole-genome yeast interaction data and databank surveys) and (Viii) sensitivity of the genes associated with the fold to inserted transposons.

ProCKSI / Protein (Structure) Comparison, Knowledge, Similarity and Information

Allows protein structure comparison. ProCKSI is a decision support system that facilitates protein structural comparison by allowing the user to compare multiple protein structures seamlessly using multiple similarity methods through a unique interface. ProCKSI's workflow consists of three main stages: (i) Dataset Management, (ii) Calculation Management and (iii) Results Management. The web server also aims to give an overall picture of the protein universe by providing, for each protein in the dataset, as much information and knowledge as possible.

FAST / Fast Alignment and Search Tool

Aligns 3D structures of proteins. FAST is a clustering-based algorithm that employs various techniques to eliminate incompatible residue-pairs and reduce computational complexity. The software detects local backbone geometry and produces biologically meaningful alignments. Its performance was evaluated in two ways: measuring its overall sensitivity and specificity of determining whether two proteins can be aligned using the manual Structural classification of proteins (SCOP) and testing FAST against all curated structural alignments in HOMSTRAD database.


A program for protein structural alignment. Fr-TM-align employs fragment alignment and assembly provides better structural alignments in comparison to TM-align. The structural alignments generated using Fr-TM-align have a higher TM-score (~9%) and coverage (~7%) in comparison to those generated by TM-align. Fr-TMalign performs better in comparison to both TM-align and CE and it achieves this higher accuracy and coverage at the expense of longer computation time: it is ~12 times slower than TM-align.


Optimizes SP-score for structure alignment. SPalign was applied to recognize proteins within the same structure fold and having the same function of DNA or RNA binding. For fold discrimination, SPalign improves sensitivity over TMalign for the chain-level comparison by 12% and over DALI for the domain-level comparison by 13% at the same specificity of 99.6%. SPalign is expected to be useful for function prediction and comparing structures with or without domains defined.

PROSTA / PROtein STructure Alignment tools

Automatically determines and aligns the interaction interfaces between two arbitrary types of complex structures, e.g. protein–protein complexes, protein–DNA complexes and protein–RNA complexes. Our method employs sequentially remote fragments that potentially model remote interactions or structure topologies when searching for the optimal superimposition. Then, the optimal residue matching problem is formulated as the maximum weighted bipartite matching (MWBM) problem to find the optimal sequence order-independent alignment.


An algorithm for structurally aligning multiple-chain protein-protein complexes. MM-align is built on a heuristic iteration of a modified Needleman-Wunsch dynamic programming (DP) algorithm, with the alignment score specified by the inter-complex residue distances. The multiple chains in each complex are first joined, in every possible order, and then simultaneously aligned with cross-chain alignments prevented. The alignments of interface residues are enhanced by an interface-specific weighting factor. An optimal alignment between two complexes, as well as the overall TM-score, will be reported for each comparison.

CAB-Align / Contact Area-Based Alignment

A protein structure alignment method which uses the residue-residue contact area to identify regions of similarity. The main purpose of CAB-align is to identify homologous relationships at the residue level between related protein structures. The CAB-align procedure comprises two main steps: First, a rigid-body alignment method based on local and global 3D structure superposition is employed to generate a sufficient number of initial alignments. Then, iterative dynamic programming is executed to find the optimal alignment.


A package for protein structure comparison scheme. Matchprot is capable of detecting correct alignments even in difficult cases. The program calculates correct alignments for proteins with huge amount of indels and internal repeats. The experimental results show that the current programs show better performance on Fischer and Novotny's benchmark datasets, than state of the art programs, e.g. DALI, CE and SSM, in a number of cases. The proposed algorithms aid in identifying structural similarities that may have been missed out with other approaches.


Uses dynamic programming schemes to simultaneously list the complete space of structures and sequence alignments and compute the optimal solution. PartiFold-Align is an algorithm for simultaneous alignment and folding pairs of unaligned protein sequences. This tool exploits scarcity in the set of super-secondary structure pairings and alignment candidates to attain an effectively cubic running time. It also get better secondary structure prediction where current approaches fail.

ASH / Alignment of Structural Homologs

Provides a structural alignment program. ASH, based on a double dynamic programming algorithm, intends to maximize the number of structurally equivalent residues between two proteins. The application includes functions for query and template PDB files as well as options for processing superposition and rotate structures. Moreover, the software provides tools for perform a faster alignment (RASH) or to align structures with multiple solutions (GASH).


Overlaps two protein conformations by their atomic coordinates using a robust statistics technique: least median of squares (LMS). LMSfit can automatically detect and superimpose the rigid core regions of two conformations with small or large displacements. This algorithm is robust and does not require any prior knowledge of the flexible regions. Furthermore, LMSfit can be extended to multiple level superposition between two conformations with several rigid domains. It can be considered as an alternative and complementary tool for structural superposition.


A protein structure alignment algorithm. MICAN is a structure alignment algorithm that can handle Multiple-chain complexes, Inverse direction of secondary structures, Calpha only models, Alternative alignments, and Non-sequential alignments. The algorithm was designed so as to identify the best structural alignment between protein pairs by disregarding the connectivity between secondary structure elements (SSE). One of the key feature of the algorithm is utilizing the multiple vector representation for each SSE, which enables us to correctly treat bent or twisted nature of long SSE.

MAMMOTH / Matching Molecular Models Obtained from Theory

Allows sequence-independent structural alignment. MAMMOTH is a structural alignment approach that (1) is sequence-independent, (2) focuses on model Cα coordinates, and (3) avoids references to sequence or contact maps. The web application enables comparison between protein structure (experimental protein structure and arbitrary low-resolution protein tertiary model, or two experimental structures). Users can also search for similar structures in a database. The software can be useful for structural genomics applications.