IMPROVED CALCULATIONS OF COMPACTNESS AND A REEVALUATION OF CONTINUOUSCOMPACT UNITS

A new method for calculating compactness (Z) that uses look-up table-b ased algorithms for area and volume computations is introduced. These algorithms can be used in any iterative area or volume calculation, ar e more than 1000 times faster than the original algorithms, and have e qual or better precision. With the faster algorithms it is now possibl e to calculate the compactness of all continuous units in a protein, a nd 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 a s well as 12 additional proteins. This method is robust, and yields si milar units even when applied to coordinates of protein crystals grown under different experimental conditions.