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Manuscript Title: MH2c: Characterization of major histocompatibility α-helices - An Information Criterion Approach
Authors: B. Hischenhuber, F. Frommlet, W. Schreiner, B. Knapp
Program title: MH2c (MH helix curves)
Catalogue identifier: AELX_v1_0
Distribution format: tar.gz
Journal reference: Comput. Phys. Commun. 183(2012)1481
Programming language: Matlab.
Computer: Personal computer architectures.
Operating system: Windows, Linux, Mac (all systems on which Matlab can be installed).
RAM: Depends on the trajectory size, min. 1 GB (Matlab)
Keywords: MH, MHC, helix, fitting, comparison, Akaike Information Criterion.
PACS: 87.10.Tf, 87.14.E-, 87.15.bd, 87.15.A-, 87.15hp.
Classification: 2.1, 4.9, 4.14.

External routines: Curve Fitting Toolbox and Statistic Toolbox of Matlab

Nature of problem:
Major histocompatibility (MH) proteins share a similar overall structure. However, identical MH alleles which present different peptides differ by subtle conformational alterations. One hypothesis is that such conformational differences could be another level of T cell regulation. By this software package we present a reliable and systematic way to compare different MH structures to each other.

Solution method:
We tested several fitting approaches on all available experimental crystal structures of MH to obtain an overall picture of how to describe MH helices. For this purpose we transformed all complexes into the same space and applied splines and polynomials of several degrees to them. To draw a general conclusion which method fits them best we employed the "corrected Akaike Information Criterion". The software is applicable for all kinds of helices of biomolecules.

Running time:
Depends on the data, for a single stationary structure the runtime should not exceed a few seconds.