MATRAS: A program for protein 3D structure comparison

Abstract

The recent accumulation of large amounts of 3D structural data warrants a sensitive and automatic method to compare and classify these structures. We developed a web server for comparing protein 3D structures using the program Matras (http://biunit.aist-nara.ac.jp/matras). An advantage of Matras is its structure similarity score, which is defined as the log-odds of the probabilities, similar to Dayhoff's substitution model of amino acids. This score is designed to detect evolutionarily related (homologous) structural similarities. Our web server has three main services. The first one is a pairwise 3D alignment, which is simply align two structures. A user can assign structures by either inputting PDB codes or by uploading PDB format files in the local machine. The second service is a multiple 3D alignment, which compares several protein structures. This program employs the progressive alignment algorithm, in which pairwise 3D alignments are assembled in the proper order. The third service is a 3D library search, which compares one query structure against a large number of library structures. We hope this server provides useful tools for insights into protein 3D structures.

Figure 1

Screenshots of the multiple 3D alignment service. (A) Title page with forms where a user can assign up to 10 structures. (B) A calculated multiple 3D alignment. (C) A Chime plug-in view of superimposed multiple structures. (D) A dendrogram of structural similarity.

Figure 2

A screenshot and email results of the 3D library search service. (A) A screenshot of the title page. A user can assign one query structure, either by inputting the PDB code or by uploading a PDB format file. (B) A portion of the results sent by email. It contains a list of similar library structures and the corresponding pairwise alignments.