[Biojava-dev] AFPChain getSimilarity function

[Ambikesh Jayal]

Dear Andreas,

Thanks. I will have a look a the functions you mentioned. What about the
functions AFPChain.getSimilarity() getSimilarity1(), getSimilarity2()? I
thought they were the main functions for finding similarity between the two
structures.

I am new to genetics and protein structure similarity measures. Do you know
of any easy to understand paper that will give me a deeper insight into
protein structure matching?

Thanks
Ambi.


On Thu, Jan 6, 2011 at 4:15 AM, Andreas Prlic <andreas at sdsc.edu> wrote:

> Hi Ambikesh,
>
> Sorry for the lack of documentation... will add javadoc for this as
> well as set a page up on the wiki.
>
> There are a few methods that provide access to various scores. If you
> want to compare the similarity between the two structures,  probably
> the most important values to look at are:
>
> getNrEQR()  the number of structurally equivalent residues
>
> getTotalRMSDOpt() the RMSD of the alignment
>
> getProbability() the Probability of the alignment (FATCAT) or the Z-score
> (CE)
>
> getTMScore() returns the TM-score
>
>  Does that make more sense?
>
> Andreas
>
>
>
> On Wed, Jan 5, 2011 at 10:06 AM, Ambikesh Jayal <ambi1999 at gmail.com>
> wrote:
> > Hi,
> > Is there a document that explains the purpose of different functions in
> the
> > AFPChain class? Basically I am interested to find how similar two protein
> > structures are. The following four functions seem to be returning values
> > indicating similarity but I am not sure what is the main difference
> between
> > them. So it will be helpful if someone can explain.
> > org.biojava.bio.structure.align.model.AFPChain
> > getSimilarity()
> > getSimilarity1()
> > getSimilarity2()
> > getAlignScore()
> > I ran the CE and FATCAT algorithms for two proteins and got the following
> > results. Not sure how to interpret them. Any help?
> > CE, name1 = "1cdg.A"; name2 = "1tim.B";
> > **** afpChain.getSimilarity() 0.1951219512195122
> > **** afpChain.getSimilarity1() 30
> > **** afpChain.getSimilarity2() 83
> > **** afpChain.getAlignScore()693.7852267498898
> >
> >
> > FATCAT, name1 = "1cdg.A"; name2 = "1tim.B";
> > **** afpChain.getSimilarity() 0.17647058823529413
> > **** afpChain.getSimilarity1() 21
> > **** afpChain.getSimilarity2() 58
> > **** afpChain.getAlignScore()186.61939969257776
> >
> >
> >
> >
> > FATCAT name1 = "1cdg.A"; name2 = "1cdg.A";
> > **** afpChain.getSimilarity() 1.0
> > **** afpChain.getSimilarity1() 100
> > **** afpChain.getSimilarity2() 100
> > **** afpChain.getAlignScore()2040.0
> >
> > Kind Regards,
> > Ambi
>