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Improved calculations of compactness and a reevaluation of continuous compact units
Author(s) -
Zehfus Micheal H.
Publication year - 1993
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.340160307
Subject(s) - compact space , algorithm , computation , volume (thermodynamics) , computer science , table (database) , mathematics , data mining , physics , mathematical analysis , quantum mechanics
A new method for calculating compactness ( Z ) that uses look‐up table‐based algorithms for area and volume computations is introduced. These algorithms can be used in any iterative area orvolume calculation, are more than 1000 times faster than the originalalgorithms, and have equal or better precision. With the faster algorithms it is now possible to calculate the compactness of all continuous units in a protein, and to precisely locate the optimal compact units without the screening functions and limited resolution used previously. These methods have been incorporated into a fully automatic domain finding algorithm, and this method has been applied to the 21 proteins originally analyzed as well as 12 additional proteins. This method is robust, and yields similar units even when applied to coordinates of protein crystals grown under different experimental conditions. © 1993 Wiley‐Liss, Inc.