New approach to protein fold recognition based on Delaunay tessellation of protein structure

Conference · Tue Dec 31 04:00:00 EST 1996

OSTI ID:549278

Zheng, W; Cho, S J; Vaisman, I I; Tropsha, A ^[1]

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1. Univ. of North Carolina, Chapel Hill, NC (United States)

We propose new algorithms for sequence-structure compatibility (fold recognition) searches in multidimensional sequence-structure space. Individual amino acid residues in protein structures are represented by their C{sup {alpha}} atoms; thus each protein is described as a collection of points in three-dimensional space. Delaunay tessellation of a protein generates an aggregate of space-filling, irregular tetrahedra, or Delaunay simplices. Statistical analysis of quadruplet residue compositions of all Delaunay simplices in a representative dataset of protein structures leads to a novel four body contact residue potential expressed as log likelihood factor q. The q factors are calculated for native 20 letter amino acid alphabet and several reduced alphabets. Two sequence structure compatibility functions are computed as (i) the sum of q factors for all Delaunay simplices in a given protein, or (ii) 3D-1D Delaunay tessellation profiles where the individual residue profile value is calculated as the sum of q factors for all simplices that share this vertex residue. Both threading functions have been implemented in structure-recognizes-sequence and sequence-recognizes-structure protocols for protein fold recognition. We find that both profile and total score based threading functions can distinguish both the native fold from incorrect folds for a sequence, and the native sequence from non-native sequences for a fold. 25 refs., 4 figs., 1 tab.

• OSTI ID: 549278
• Report Number(s): CONF-970132--
• Country of Publication: United States
• Language: English

Related Subjects

55 BIOLOGY AND MEDICINE
BASIC STUDIES
99 GENERAL AND MISCELLANEOUS
ALGORITHMS
AMINO ACIDS
COMPATIBILITY
DNA SEQUENCING
ELECTRIC POTENTIAL
ELECTRONIC STRUCTURE
MATHEMATICAL MODELS
NUMERICAL ANALYSIS
PROTEIN STRUCTURE
PROTEINS
STATISTICS
STRUCTURAL MODELS
STRUCTURE-ACTIVITY RELATIONSHIPS
THREE-DIMENSIONAL CALCULATIONS