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)

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)

A sequence and structural study of transmembrane helices. - Robert P. Bywater; David Thomas; Gert Vriend (J. Comput. Aided Mol. Des., 2001)

Ab initio modelling of the N-terminal domain of the secretin receptors. - William R. Taylor; Robin E. J. Munro; Kjell Petersen; Robert P. Bywater (Comput. Biol. Chem., 2003)

De Novo Generation of Molecular Structures Using Optimization To Select Graphs on a Given Lattice. - Robert P. Bywater; Thomas A. Poulsen; Peter Røgen; Poul G. Hjorth (J. Chem. Inf. Model., 2004)

Drug design for ever, from hype to hope. - G. Seddon; Valère Lounnas; Ross McGuire; T. van den Bergh; Robert P. Bywater; Laerte Oliveira; Gert Vriend (J. Comput. Aided Mol. Des., 2012)