Protein structural homology: a metric approach

Fragment Finder 2.0: a computing server to identify structurally similar fragments

Fragment Finder 2.0is a web-based interactive computing server which can be used to retrieve structurally similar protein fragments from 25 and 90% nonredundant data sets. The computing server identifies structurally similar fragments using the protein backbone Cα angles. In addition, the identified fragments can be superimposed using either of the two structural superposition programs,STAMPandPROFIT, provided in the server. The freely available Java plug-inJmolhas been interfaced with the server for the visualization of the query and superposed fragments. The server is the updated version of a previously developed search engine and employs an in-house-developed fast pattern matching algorithm. This server can be accessed freely over the World Wide Web through the URL http://cluster.physics.iisc.ernet.in/ff/.

ProSTRIP: A method to find similar structural repeats in three-dimensional protein structures

The occurrence of similar structural repeats in a protein structure has evolved through gene duplication. These repeats act as a structural building block and form more than one compact structural and functional unit called a repeat domain. The protein families comprising similar structural repeats are mainly involved in protein-protein interactions as well as binding to other ligand molecules. The identification of internal sequence repeats in the primary structure is not sufficient for the analysis of structural repeats. Thus, a new method called ProSTRIP has been developed using dynamic programming to find the similar structural repeats in a three-dimensional protein structure. The detection of these repeats is made by calculating the protein backbone Calpha angles. An internet computing server is also created by implementing this method and enables graphical visualization of the results. It can be freely accessed at http://cluster.physics.iisc.ernet.in/prostrip/.

Swelfe: a detector of internal repeats in sequences and structures

Intragenic duplications of genetic material have important biological roles because of their protein sequence and structural consequences. We developed Swelfe to find internal repeats at three levels. Swelfe quickly identifies statistically significant internal repeats in DNA and amino acid sequences and in 3D structures using dynamic programming. The associated web server also shows the relationships between repeats at each level and facilitates visualization of the results.

AVAILABILITY

http://bioserv.rpbs.jussieu.fr/swelfe.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Protein structure mining using a structural alphabet

We present a comprehensive evaluation of a new structure mining method called PB-ALIGN. It is based on the encoding of protein structure as 1D sequence of a combination of 16 short structural motifs or protein blocks (PBs). PBs are short motifs capable of representing most of the local structural features of a protein backbone. Using derived PB substitution matrix and simple dynamic programming algorithm, PB sequences are aligned the same way amino acid sequences to yield structure alignment. PBs are short motifs capable of representing most of the local structural features of a protein backbone. Alignment of these local features as sequence of symbols enables fast detection of structural similarities between two proteins. Ability of the method to characterize and align regions beyond regular secondary structures, for example, N and C caps of helix and loops connecting regular structures, puts it a step ahead of existing methods, which strongly rely on secondary structure elements. PB-ALIGN achieved efficiency of 85% in extracting true fold from a large database of 7259 SCOP domains and was successful in 82% cases to identify true super-family members. On comparison to 13 existing structure comparison/mining methods, PB-ALIGN emerged as the best on general ability test dataset and was at par with methods like YAKUSA and CE on nontrivial test dataset. Furthermore, the proposed method performed well when compared to flexible structure alignment method like FATCAT and outperforms in processing speed (less than 45 s per database scan). This work also establishes a reliable cut-off value for the demarcation of similar folds. It finally shows that global alignment scores of unrelated structures using PBs follow an extreme value distribution. PB-ALIGN is freely available on web server called Protein Block Expert (PBE) at http://bioinformatics.univ-reunion.fr/PBE/.

YAKUSA: A fast structural database scanning method

YAKUSA is a program designed for rapid scanning of a structural database with a query protein structure. It searches for the longest common substructures called SHSPs (structural high-scoring pairs) existing between a query structure and every structure in the structural database. It makes use of protein backbone internal coordinates (alpha angles) in order to describe protein structures as sequences of symbols. The structural similarities are established in 5 steps, the first 3 being analogous to those used in BLAST: (1) building up a deterministic finite automaton describing all patterns identical or similar to those in the query structure; (2) searching for all these patterns in every structure in the database; (3) extending the patterns to longer matching substructures (i.e., SHSPs); (4) selecting compatible SHSPs for each query-database structure pair; and (5) ranking the query-database structure pairs using 3 scores based on SHSP similarity, on SHSP probabilities, and on spatial compatibility of SHSPs. Structural fragment probabilities are estimated according to a mixture transition distribution model, which is an approximation of a high-order Markov chain model. With regard to sensitivity and selectivity of the structural matches, YAKUSA compares well to the best related programs, although it is by far faster: A typical database scan takes about 40 s CPU time on a desktop personal computer. It has also been implemented on a Web server for real-time searches.

Automated multiple analysis of protein structures: application to homology modeling of cytochromes P450

A computational strategy for homology modeling, using several protein structures comparison, is described. This strategy implies a formalized definition of structural blocks common to several protein structures, a new program to compare these structures simultaneously, and the use of consensus matrices to improve sequence alignment between the structurally known and target proteins. Applying this method to cytochromes P450 led to the definition of 15 substructures common to P450cam, P450BM3, and P450terp, and to proposing a 3D model of P450eryF.