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Calculation of resolution dependent Matthews Probabilities

 


MATTPROB is an updated, parameter free estimator calulating normalized probabilities for the occurrence of multimerization states. Originally the estimator was based on a 2003 survey of Vm (Matthews coefficient) and solvent content (Vs) distribution of about 11,000 non-redundant crystallographic PDB entries (Kantardjieff and Rupp, Protein Science 12:1865-1871, 2003). The 2013 data set has grow to over 60000 entires and the program can be used with the 2013 parametrized version or the new kernel estimator, which allows any given resolution range to be entered without the need to use binned data. The absence of binning and a 6x larger learning test set can give more accurate results.

Higher packing density and this lower solvent content significantly correlate with increasing resolution and can be used to provide a more refined probability for the occurrence of a certain oligomerization state. The program thus accepts resolution as additional information to select the proper probability distribution. The assumption is that observed resolution represents an estimate for the lower limit for crystal quality, i.e., crystals obviously diffract to at least this value (but could also diffract better). It must be understood that the answers are always relative probabilities based on our current state of knowledge and that no clear answer may result in certain cases.

One can also enter the molecular data for one monomer and select its known multimerization state, in case you know what basic multimer unit you are looking for. For example, if your known molecular unit is a trimer, you may want to look for 3-mer, 6-mer, 9-mer etc. Note that crystallographic axes coinciding with multimer axes can result in improbably low Vm for a single multimer unit. Whenever possible, use the correct molecular weight based on the sequnce and not the estimated value based on residue number.

The results are represented in tabular form at the top of the output followed by two graphs showing the normalized probability distributions (resolution corrected and all PDB data) against Vm and Vs, respectively.    

We would appreciate citation of the two following references when using this program in published work:

The old parameterized fit function and parameter files from 2003 and 2013 are also available for download.

For developers, the implemenation and the link to the data filed for the kernel estimator can be found in the Computational Crystallography Newsletter 15, January 2015.


Unit cell

a   b   c   ()     
al    be    ga    (deg)

Sample type:

Data resolution: (Useful range 1.2 - 3.5, reliable mostly for proteins)

Basic multimer unit: 

Spacegroup or spacegroup number: (List of allowed SG symbols)

Select molecular weight option: is    

Select method and data file

You can use this local app or the EXPASY protparam tool to compute the actual mol weight from sequence.

 
 

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