Algorithmic Determination of Core Positions in the VL and VH Domains of Immunoglobulin Molecules
- 1 January 1998
- journal article
- research article
- Published by Mary Ann Liebert Inc in Journal of Computational Biology
- Vol. 5 (3) , 467-477
- https://doi.org/10.1089/cmb.1998.5.467
Abstract
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 Cα(I) – Cα(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 Cα atom positions for the VL and VH domains. Applications of the core sets are described.Keywords
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