To cite bio3d in publications use:

  Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

A BibTeX entry for LaTeX users is

  @Article{,
    author = {Grant B.J. and Rodrigues A.P.C. and ElSawy K.M. and McCammon J.A. and Caves L.S.D.},
    title = {Bio3D: An R package for the comparative analysis of protein structures.},
    journal = {Bioinformatics},
    year = {2006},
    volume = {22},
    pages = {2695--2696},
    month = {Nov},
    organization = {University of California, San Diego, La Jolla, CA 92093, USA.},
  }

Original article and updates are available from
http://thegrantlab.org/bio3d/