| Revision as of 07:18, 14 March 2004 editSmack (talk | contribs)Extended confirmed users6,969 edits factual accuracy dispute message← Previous edit | Revision as of 17:07, 27 March 2004 edit undo80.4.6.55 (talk) this is a minor changeNext edit → | ||
| Line 1: | Line 1: | ||
| {{msg:disputed}} | {{msg:disputed}} | ||
| So we should fix it (please do)! | |||
| ⚫ | |||
| ⚫ | Protein structural alignment (also known as structure superposition) is a powerful form of ]. | ||
| Two ] structures (]) can be aligned by superposing their 3D ], with the aim of minimizing the ] deviation (RMSD) of the ] (which is not quite the same as ]). | Two ] structures (]) can be aligned by superposing their 3D ], with the aim of minimizing the ] deviation (RMSD) of the ] (which is not quite the same as ]). | ||
| Line 34: | Line 38: | ||
| ... And many many more! | ... And many many more! | ||
| For example see... | |||
| o ProSup The ProSup - structure comparison server. | |||
Revision as of 17:07, 27 March 2004
 | This article's factual accuracy is disputed. Relevant discussion may be found on the talk page. Please help to ensure that disputed statements are reliably sourced. (Learn how and when to remove this message) |
So we should fix it (please do)!
Protein structural alignment (also known as structure superposition) is a powerful form of alignment.
Two protein domain structures (structural domains) can be aligned by superposing their 3D coordinates, with the aim of minimizing the root mean square deviation (RMSD) of the structural superposition (which is not quite the same as quantum superposition).
Many algorithms have been developed to optimize this complex task.
The task is complex because of the large number of degrees of freedom between two datasets of points in 3D (each protein molecule has six degrees of freedom, three translational and three rotational). This is just the simple case of 'rigid body' superposition.
Algorithms
Some approaches use quaternerions to reduce the dimensionality of the space without removing any information (isomorphic translation).
A major class of approaches is based on reducing the representation of the complex protein molecules into its secondary structure. Secondary structucture elements can be approximatly represented as vectors and aligned in pairs.
Dynamic programming can be used to find local regions of similarity which are then expanded.
The Dali algorithm (named after Salvador Dali) uses network isomorphism between the contact networks of two proteins to perform alignment.
Sequence similarity between proteins can be used to optimize structural alignmens.
Geometric hashing is a good technique!
Packages
Many tools exist to perform structural alignment and multiple structural alignment.
- VMD
- SSM
- CE
- Dali
- Deep View
... And many many more!
For example see...