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Announcement

  • 08/2010
      -Peeling3D is launched

  • 25/02/2009
      -Peeling2 is moved

  • 10/02/2006
      -Peeling2 launched

  • 19/01/2005
      -Peeling launched

Peeling a protein

This method take an input pdb file and peel it.



Browse for your 3D structure file (pdb file format):




Note that data older than 7 days are deleted.

Options

  Prune tree This parameter allow control the overall quality of splitting.
With this parameter activated, program stop peeling if a splitting event produce only protein units (PUs) having a compaction index (CI) inferior to a given cut-off. CI is an entropy derived measure focuses on contacts intra PU vs extra PU. A weak value (<0.2) specifie a PU unit extended, a high value (>0.5)a unit of type compact : 		YesNo
CI cut-off:
  Choose a specific R-value :Modify R value for increase or decrease the importance of splitting. A hight R value imply a hight level of splitting. R is an entropy derived correlation based on contat between PU. This index quantifies globally the dependance of PUs in terms of contact.
  Minimal size of protein unit :Minimal size of protein unit allowed by algorithm.
  Minimal size of secondary structures :This parameter allow to avoid cutting continuous secondary structure of a given lenght. Under this size value, continuous secondary structure were not splitted.
  Take into account only regular
     secondary structure for Peeling :With this parameter activated only contacts between regular secondary structure are taken into account in peeling process. Contribution of others contacts in computation of R-value and Partition Index are drastically reduced. 		YesNo
  Cut-off distance between atom :This value is the reference distance in Angstrom separating Calpha. This parameter D0 was used in logistic function to derive contact matrix into contact probability matrix used in peeling algrithm. High delfa value implied more distant contact taken into accounts to compute logistic fonction (see Gelly et al. 2006 for more explanation).
  Delta parameter in logistic function :Delta parameter used in logistic function (see Gelly et al. 2006 for more explanation).
  Maximal size of protein unit :The peeling process is stopped if all PUs are smaller than this size. A value of 0 seems that this value is not used, i.e. the protein peeling is performed without constraints on the maximal size of protein unit.
  


References


Gelly JC, de Brevern AG
Protein Peeling 3D: New tools for analyzing protein structures
Bioinformatics 2011 Jan 1;27(1):132-3.

Faure G., Bornot A., de Brevern A.G.
Analysis of protein contacts into Protein Units
Biochimie 2009 91(7):876-87.

Gelly JC, de Brevern AG, Hazout S.
'Protein Peeling': an approach for splitting a 3D protein structure into compact fragments.
Bioinformatics. 2006 Jan 15;22(2):129-33. Epub 2005 Nov 14.

Gelly JC, Etchebest C, Hazout S, de Brevern AG.
Protein Peeling 2: a web server to convert protein structures into series of protein units.
Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W75-8.