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Bioinformatics Vol. 19 no. 12 2003
Pages 1540-1548
© 2003 Oxford University Press

Development of a four-body statistical pseudo-potential to discriminate native from non-native protein conformations

Bala Krishnamoorthy 1 and Alexander Tropsha 2,*

1 Department of Operations Research, CB 3180, UNC Chapel Hill, NC 27599, USA
2 Laboratory for Molecular Modeling, School of Pharmacy, UNC Chapel Hill, NC 27599, USA

Received on September 28, 2002 ; revised on November 26, 2002 ; accepted on February 20, 2003

Motivation: Most scoring functions used in protein fold recognition employ two-body (pseudo) potential energies. The use of higher-order terms may improve the performance of current algorithms.

Methods: Proteins are represented by the side chain centroids of amino acids. Delaunay tessellation of this representation defines all sets of nearest neighbor quadruplets of amino acids. Four-body contact scoring function (log likelihoods of residue quadruplet compositions) is derived by the analysis of a diverse set of proteins with known structures. A test protein is characterized by the total score calculated as the sum of the individual log likelihoods of composing amino acid quadruplets.

Results: The scoring function distinguishes native from partially unfolded or deliberately misfolded structures. It also discriminates between pre- and post-transition state and native structures in the folding simulations trajectory of Chymotrypsin Inhibitor 2 (CI2).

Availability: All codes are written in C/C++. Programs are available from the authors on request..

Contact: alex_tropsha{at}unc.edu

* To whom correspondence should be addressed.


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