General concepts underlying ACORN, a computer program for the solution of protein structures

Abstract

ACORN has been shown to be a successful program for the solution of small and medium-size protein structures, when data at atomic resolution or better are available. At the heart of ACORN lies a density modification method called DDM (Dynamic Density Modification). DDM operates on any density map containing a minimum of information. Its action is to progressively enhance positive features of the map and to reduce, at the same time, undesired noise and bias towards very small values. This is indeed a feature claimed by other density modification procedures. The effectiveness of the procedure arises from the fact that the shape of DDM's modification curve is one of a restricted class of functions, whose properties will be described. The importance of a proper weighting scheme will also be considered. Tests on a few structures will help to clarify the theoretical concepts involved as well as to make clear the potential applications and limits of the program.