MMDB: annotating protein sequences with Entrez's 3D-structure database. - Yanli Wang; Kenneth J. Addess; Jie Chen 039; Lewis Y. Geer; Jane He; Siqian He; Shennan Lu; Thomas Madej; Aron Marchler-Bauer; Paul A. Thiessen; Naigong Zhang; Stephen H. Bryant (Nucleic Acids Res., 2007)

An improved pairwise decomposable finite-difference Poisson-Boltzmann method for computational protein design. - Christina L. Vizcarra; Naigong Zhang; Shannon A. Marshall; Ned S. Wingreen; Chen Zeng; Stephen L. Mayo (J. Comput. Chem., 2008)

Reference energy extremal optimization: A stochastic search algorithm applied to computational protein design. - Naigong Zhang; Chen Zeng (J. Comput. Chem., 2008)

CDD: specific functional annotation with the Conserved Domain Database. - Aron Marchler-Bauer; John B. Anderson; Farideh Chitsaz; Myra K. Derbyshire; Carol DeWeese-Scott; Jessica H. Fong; Lewis Y. Geer; Renata C. Geer; Noreen R. Gonzales; Marc Gwadz; Siqian He; David I. Hurwitz; et al. (Nucleic Acids Res., 2009)

CDD: a Conserved Domain Database for the functional annotation of proteins. - Aron Marchler-Bauer; Shennan Lu; John B. Anderson; Farideh Chitsaz; Myra K. Derbyshire; Carol DeWeese-Scott; Jessica H. Fong; Lewis Y. Geer; Renata C. Geer; Noreen R. Gonzales; Marc Gwadz; David I. Hurwitz; et al. (Nucleic Acids Res., 2011)

NCBI GEO: archive for functional genomics data sets - update. - Tanya Barrett; Stephen E. Wilhite; Pierre Ledoux; Carlos Evangelista; Irene F. Kim; Maxim Tomashevsky; Kimberly A. Marshall; Katherine H. Phillippy; Patti M. Sherman; Michelle Holko; Andrey Yefanov; Hyeseung Lee; et al. (Nucleic Acids Res., 2013)