MACiE: a database of enzyme reaction mechanisms. - Gemma L. Holliday; Gail J. Bartlett; Daniel E. Almonacid; Noel M. O'Boyle; Peter Murray-Rust; Janet M. Thornton; John B. O. Mitchell (Bioinform., 2005)

A semiempirical approach to the intra-phycocyanin and inter-phycocyanin fluorescence resonance energy-transfer pathways in phycobilisomes. - Adelio R. Matamala; Daniel E. Almonacid; Maximiliano F. Figueroa; José Martínez-Oyanedel; Marta C. Bunster (J. Comput. Chem., 2007)

MACiE (Mechanism, Annotation and Classification in Enzymes): novel tools for searching catalytic mechanisms. - Gemma L. Holliday; Daniel E. Almonacid; Gail J. Bartlett; Noel M. O'Boyle; James W. Torrance; Peter Murray-Rust; John B. O. Mitchell; Janet M. Thornton (Nucleic Acids Res., 2007)

Quantitative Comparison of Catalytic Mechanisms and Overall Reactions in Convergently Evolved Enzymes: Implications for Classification of Enzyme Function. - Daniel E. Almonacid; Emmanuel R. Yera; John B. O. Mitchell; Patricia C. Babbitt (PLoS Comput. Biol., 2010)

MACiE: exploring the diversity of biochemical reactions. - Gemma L. Holliday; Claudia Andreini; Julia D. Fischer; Syed Asad Rahman; Daniel E. Almonacid; Sophie T. Williams; William R. Pearson (Nucleic Acids Res., 2012)

The Structure-Function Linkage Database. - Eyal Akiva; Shoshana D. Brown; Daniel E. Almonacid; Alan E. Barber II; Ashley F. Custer; Michael A. Hicks 002; Conrad C. Huang; Florian Lauck; Susan T. Mashiyama; Elaine C. Meng; David Mischel; John H. Morris; et al. (Nucleic Acids Res., 2014)