Ribonucleotide activation by enzyme ribonucleotide reductase: Understanding the role of the enzyme. - Nuno M. F. S. A. Cerqueira; Pedro Alexandrino Fernandes; Leif A. Eriksson; Maria João Ramos (J. Comput. Chem., 2004)

The effect of the sixth sulfur ligand in the catalytic mechanism of periplasmic nitrate reductase. - Nuno M. F. S. A. Cerqueira; P. J. Gonzalez; C. D. Brondino; Maria João Romão; C. C. Romão; Isabel Moura; José J. G. Moura (J. Comput. Chem., 2009)

molUP: A VMD plugin to handle QM and ONIOM calculations using the gaussian software. - Henrique S. Fernandes; Maria João Ramos; Nuno M. F. S. A. Cerqueira (J. Comput. Chem., 2018)

VMD Store-A VMD Plugin to Browse, Discover, and Install VMD Extensions. - Henrique S. Fernandes; Sergio F. Sousa; Nuno M. F. S. A. Cerqueira (J. Chem. Inf. Model., 2019)