3D structure similarity searching software tools | Protein data analysis
3D protein structure similarity searching is one of the important processes performed in structural bioinformatics, since it allows for protein function identification and reconstruction of phylogeny for weakly related organisms. Due to the complexity of 3D protein structures and exponential growth of protein structures in public repositories, like the Protein Data Bank, the process is time-consuming and requires increased computational resources.
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.
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.
A web server for comparing protein 3D structures using the program 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.
Reduces a protein to a series of secondary structure elements (SSEs) and adds information to the SSE descriptors such as relative direction, accessibility, adjacency to the previous SSE, length and length of preceding loop. TOPSCAN is a method for comparing protein structures. It is useful as a preliminary screen to give some idea whether a protein looks like something else. It trades coverage (and to some degree error rate) for great speed. For more accurate comparisons, a method which works at the detailed coordinate level such as SSAP need to be used.
Assists users in standardizing secondary structure assignment. DSSP calculates DSSP entries from PDB entries. It also includes a resource of secondary structure assignments for protein entries in the Protein Data Bank (PDB). This application does not predict secondary structure.
Applies computer visualization techniques to extract the predominant visual patterns encoded in two-dimensional distance matrices generated from the three-dimensional coordinates of protein chains. ProteinDBS is a web server for the life science community to search for similar protein tertiary structures in real time. It applies advanced feature extraction algorithms and scalable indexing techniques to achieve a high-running speed while preserving reasonably high precision of structural comparison.