``Analysis of domain motions in large proteins'' by K. Hinsen, A. Thomas, and M.J. Field (Proteins 34, 369-382, 1999)
This article describes the domain analysis methods implemented in DomainFinder in detail and discusses several applications.
``Analysis of domain motions by approximate normal mode calculations'' by K. Hinsen (Proteins 33, 417-429, 1998)
This article describes the normal mode calculation technique that allows DomainFinder to treat even large proteins rapidly.
``Harmonicity in slow protein dynamics'' by K. Hinsen, A.J. Petrescu, S. Dellerue, M.C. Bellissent-Funel, and G.R. Kneller (Chem. Phys. 261, 25-37, 2000)
This article describes the improved protein model that is used in DomainFinder 2.0.