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J Comput Biol. 1998 Fall;5(3):467-77.

Algorithmic determination of core positions in the VL and VH domains of immunoglobulin molecules.

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Department of Mathematics, Rutgers University, New Brunswick, NJ 08903, USA.


We introduce a new algorithmic method for identifying the geometrical core of proteins that does not require the usual superposition of structures. A geometrical core is defined as the set of residues such that the C alpha (I) - C alpha (J) atom distances are identical in all structures of the protein family under study, where I and J are secondary structure positions in the structural units--strands, loops, or parts of them. The result of applying the algorithm to 53 Ig structures leads to the identification of two geometrical core sets of C alpha atom positions for the VL and VH domains. Applications of the core sets are described.

[Indexed for MEDLINE]

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