PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules. - Daan M. F. van Aalten; Robert P. Bywater; John B. C. Findlay; Manfred Hendlich; Rob W. W. Hooft; Gert Vriend (J. Comput. Aided Mol. Des., 1996)

A comparison of techniques for calculating protein essential dynamics. - Daan M. F. van Aalten; Bert L. de Groot; John B. C. Findlay; Herman J. C. Berendsen; Andrea Amadei (J. Comput. Chem., 1997)

Functional concerted motions in the bovine serum retinol-binding protein. - P.-L. Chau; Daan M. F. van Aalten; Robert P. Bywater; John B. C. Findlay (J. Comput. Aided Mol. Des., 1999)