Protein structure prediction

[DarkStar]

Hi everyone,

Protein structure is a complex thing...and also confusing!

 

I was going through literature about protein structure prediction.

If given a primary sequence of a protein, how can secondary structure be reliably predicted? I am aware of tendency of aa to be associated with different secondary structures, is there a specific algorithm used for calculation of secondary structure?

 

Is there any other way to model a protein structure based on primary sequence besides homology modelling?

 

Thanks in advance for input and also for reading this!

[CharonY]

Your last question first:

Is there any other way to model a protein structure based on primary sequence besides homology modelling?

 

If you want to have tertiary structures, to date there are not many promising approaches.

 

There are plenty algorithms for the prediction of secondary structures, though. For a collection of mostly older tools check expasy.ch

Some use a combination of various algorithms like e.g.:

Wallner et al. Nucleic Acids Res. 2007 Jul 1;35(Web Server issue):W369-74. Epub 2007 Jun 21.

 

Ideally just search for papers in which prediction tools are presented and either they will describe the algorithm as well as the underlying prediction theory or you can check the references of said papers to get the information.

[Psycho]

Hi everyone,

Protein structure is a complex thing...and also confusing!

 

I was going through literature about protein structure prediction.

If given a primary sequence of a protein, how can secondary structure be reliably predicted? I am aware of tendency of aa to be associated with different secondary structures, is there a specific algorithm used for calculation of secondary structure?

 

Is there any other way to model a protein structure based on primary sequence besides homology modelling?

 

Thanks in advance for input and also for reading this!

Not really, the main thing the primary structure will show is its evolutionary relationship to other proteins, however certain areas will have large quantities of polar or non-polar amino acids as well areas will these alternating which may give you an incite into the structure or placement in the protein.