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Predicting immunoglobulin‐like hypervariable loops
Author(s) -
Vasmatzis George,
Brower Richard,
Delisi Charles
Publication year - 1994
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.360341211
Subject(s) - chemistry , cartesian coordinate system , constraint (computer aided design) , simulated annealing , algorithm , monte carlo method , atom (system on chip) , computer science , geometry , mathematics , statistics , embedded system
A two‐stage method is developed to search the conformational space of small protein segments for low energy structures. Central features of the method are efficient procedures for generating small, eight‐backbone atom, local moves in Cartesian coordinates and for introducing geometric constraints in adaptable Monte Carlo procedures. This allows natural implementation of an adaptive simulated annealing algorithm, which achieves an effective trade‐off between speed and acceptance ratio. The method is applied to the calculation of various immunoglobulin loops. We also develop data base derived rules for identifying constraint conditions, and show that the incorporation of an identified side‐chain constraint allows a 1.2 Å all‐backbone atom rms deviation prediction of a 9 residue long L1 loop. © 1994 John Wiley & Sons, Inc.