<i>DADIMODO</i>: a program for refining the structure of multidomain proteins and complexes against small-angle scattering data and NMR-derived restraints

Abstract

DADIMODO is a program for refining atomic models of multidomain proteins or complexes against small-angle X-ray scattering data. Interdomain distance and orientational restraints, such as those derived from NMR measurements, can be included in the optimization process. While domain structures are mainly kept rigid, flexible regions can be user defined. Stepwise generic conformational changes, specified by the user, are applied cyclically in a stochastic optimization algorithm that performs a search in the protein conformation space. The convergence for this genetic algorithm is driven by an adaptable selection pressure. The algorithmic structure guarantees that a physically acceptable full atomic model of the structure is present at all stages of the optimization. A graphical user interface ensures user-friendly handling.