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Calculation procedure

PepLook™ calculates 106 to 107 random structures iterating a Boltzmann-stochastic procedure. For all details, please refer to the publication submitted

Structures are generated by random combination of phi/psi values. They are selected on energy criteria (van der Waals, electrostatic plus hydrophobicity terms). The 99 structures of lower energy are saved as the ”good structures”.

The best structure among the good ones is named the Prime: its structure stability is scored by a MFP ratio that evaluates the quality of the intramolecular interactions. The highest the score, the best the stability: a score at 50% or lower is an indication of low stability.

A peptide can fluctuate between diverse structures, the magnitude of this fluctuation is an index of disorder. The RMS [A] scores the disorder, hence the structure diversity. It compares all good structures to the Prime and maps variability along the sequence. A score up to 1.5 is an index of order, higher than 1.5 it is an index of disorder.

Which files are provided?

Results will be provided in 4 files for each medium:

• __pho_01_099_prime.pdb

The pdb coordinates of the Prime.

• __pho_01_099.pdb

The pdb coordinates of the good population (up to 99 structures).

• __pho_AA_MFP.xls

This file gives the secondary structure, the MFP score and the RMS[A] of all structures. A fragment of the file is shown here:

Structure Nb: All good structures are listed in rank order: 1 is the Prime. The peptide sequence is in the three letter code. In the different lines, aa# is the residue number, Sec.St. the secondary structure, C is random coil, H3, 3-10 helix, Ha alpha helix, B beta structure as detailed in Thomas et al ¹. Ref [MFP] is the MFP reference value, E [MFP] is the peptide MFP value, % is the ratio of E/Ref, RMS[A] is the backbone RMS on a window of 9 residues.
For the Prime structure, the RMS[A] is the mean RMS of all structures versus the Prime, for the other structures (2 to up to 99) it is the value of the individual structure versus the Prime.

• __pho_rms.txt

The matrix of all atoms RMS of all structures, the first line and column refer to the Prime

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