Research

Table of Contents

  • Environment Specific Substitution Score (ESSS)
  • FREAD, a database search loop structure prediction
  • Contact Profile
  • ConFREAD, FREAD with the Contact Profiles
  • Environment Specific Substitution Score (ESSS)

    The Environment Specific Substitution Score Tables were constructed by observing the frequencies of amino acid substitutions in the loops of homologous proteins extracted from the HOMSTRAD database. FREAD uses "environments" described by the six dihedral angle areas (([phi, psi] -> [(-180, 180), (-180, 180)]: 1) [(-180, 0), (-90, 80)]; 2) [(-110, 0), (-180, -90) (100, 180)]; 3) [(-180, -110), (-180, -90) (100, 180)]; 4) [(-180, 0), (80, 100)]; 5) [(20, 140), (-40, 80)]; 6) the rest).

    Recently we found that the protein loop structure prediction problem can be regarded as a local problem: When it is physically and geometrically constrained (typically by anchor regions, the terminal regions of the loop), sequence similarity quantified by ESSS is a primary determinant of the local loop structure (typically ESSS over 25).

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    FREAD, a database search loop structure prediction

    The basic assumption of FREAD is that local sequence similarity may determine the backbone structure of a local protein structure if it is constrained within anchor structures.

    FREAD predicts loops according to the following criteria:

  • C-alpha separation of anchor structures
  • Samudrala-Moult statistical potential energy
  • Local sequence similarity measured by environment specific substitution tables (specified by dihedral angles) Anchor structure match

    FREAD gives extremely accurate results regardless of loop length if the query is identifiable in the database.

    For more details, please visit FREAD Website

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    Contact Profile


    Since protein loops are located in protein's surface, they often have functional roles and interact with other objects. The contact profile method makes use of the contact information induced by interactions (defined by inter-atomic distances).

    The above example is from an antibody structure, PDB code 1XF2 chain B and H. The two chains share 100% identical seuqneces. However, because of the different interaction with the DNA present in the picture, they have different contact patterns. The structural differences are shown in the regions where the contacts are different.

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    ConFREAD, FREAD with the Contact Profiles


    ConFREAD is a sub-version of FREAD - FREAD accompannied with the contact profile method. ConFREAD is especially powerful to predict antibody complementarity determining regions.

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    © Design by Andreas Viklund and modified by Yoonjoo Choi
    Last updated 26/Nov/2010