Structure superposition tools: Difference between revisions

''Structural alignment'' refers to the alignment, in three dimensions, between two or more molecular models. In the case of proteins, this is usually performed without reference to the sequences of the proteins. When the models align well, it suggests evolutionary and functional relationships that may not be discernable from sequence comparisions<ref>PMID: 10686110</ref>.  

The purpose of this article is to help in choosing a server or software package for performing structural alignment. Characteristics of structural alignment servers and software packages are listed, along with results of testing with a few examples.

There are two common applications of structural alignment servers:

# '''Pairwise alignment'''. All servers listed below enable you to upload two 3D models (or specify them from the [[PDB]]) and generate a structural alignment.

# '''Structure neighbors'''. Some servers (notably [[#Dali|Dali]],  [[#FATCAT|FATCAT]], [[#VAST|VAST]] and [[#TopSearch|TopSearch]]) enable you to upload one 3D model (or specify one in the [[PDB]]) and generate a list of the closest structures in the [[PDB]], based on pairwise structural alignments between your query structure versus each structure in the [[PDB]].

Wikipedia offers a [http://en.wikipedia.org/wiki/Structural_alignment_software list of structural alignment software packages] and an overview of [http://en.wikipedia.org/wiki/Structural_alignment structural alignment]. Hasegawa and Holm reviewed structural alignment methods in 2009<ref>PMID: 19481444</ref>.