Structure superposition tools: Difference between revisions
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There are two common applications of structural alignment servers: | 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. | # '''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]], and [[#VAST|VAST]]) 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 | # '''Structure neighbors'''. Some servers (notably [[#Dali|Dali]], [[#FATCAT|FATCAT]], and [[#VAST|VAST]]) 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>. | 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>. | ||
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===Multiple chain structural alignment=== | ===Multiple chain structural alignment=== | ||
CE and FATCAT align only one chain at a time. DaliLite appears to align multiple chains, although the output is confusing and not clearly labeled. [[#DeepView = Swiss-PDBViewer|DeepView = Swiss-PDBViewer]] can align multiple chains, including both protein and DNA chains in a single alignment (''Iterative Magic Fit''). | CE and FATCAT align only one chain at a time. DaliLite appears to align multiple chains, although the output is confusing and not clearly labeled. [[#DeepView = Swiss-PDBViewer|DeepView = Swiss-PDBViewer]] can align multiple chains, including both protein and DNA chains in a single alignment (''Iterative Magic Fit''). | ||
[[#Dali|Dali]], [[#FATCAT|FATCAT]], and [[#VAST|VAST]] enable you to upload a 3D model, or specify a [[PDB code]], and obtain a list of the most similar structures in the [[PDB]], called '''structure neighbors'''. | |||
==Structural Alignment Servers== | ==Structural Alignment Servers== | ||
