Pairwise structure alignment software tools | Protein data analysis
It is well known that conservation of proteins at the structure level can be much higher than at the sequence level. Recognizing similarities in protein structures and classifying them into folds, families, etc. is therefore an important task in biology, and is often used as a basis for designing experiments for gaining further knowledge.
Allows comparison of protein structures in 3D. DALI is a web server performing three types of structure comparisons: (1) Protein Data Bank (PDB) search, (2) pairwise comparison and (3) all against all structure comparison. The software is based on distance matrix comparison. It provides tools to navigate, integrate and organize some data pushed out by genomics and structural genomics.
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.
A program for pairwise structure comparison and for structure database searching. It is a standalone version of the search engine of the popular Dali server. A web interface is provided to view the results, multiple alignments and 3D superimpositions of structures.
Allows calculation of pairwise and multiple protein structure superpositions. SuperPose is a web server that performs a wide range of sophisticated structural superpositions. The software combines sequence alignment and difference distance matrix calculations to constrain its quaternion eigenvalue superposition calculations. It provides a wide range of interactive viewing options. SuperPose generates several textual and visual outputs allowing users to explore and compare complex protein structures.
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.
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.