Some information about protein structure can be obtained by using Nuclear Magnetic Resonance (NMR) techniques, but they provide only a sparse set of distances between atoms in a protein. The Molecular Distance Geometry Problem (MDGP) consists in determining the three-dimensional structure of a molecule using a set of known distances between some atoms. Recently, a Branch and Prune (BP) algorithm was proposed to calculate the backbone of a protein, based on a discrete formulation for the MDGP. We present an extension of the BP algorithm that can calculate not only the protein backbone, but the whole three-dimensional structure of proteins. © 2013 Inderscience Enterprises Ltd.93261270Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E., The protein data bank (2000) Nucleic Acids Research, 28, pp. 235-242Biswas, P., Toh, K.C., Ye, Y., A distributed sdp approach for large-scale noisy anchor-free graph realization with applications to molecular conformation (2008) SIAM Journal on Scientific Computing, 30, pp. 1251-1277Carvalho, R.S., Lavor, C., Protti, F., Extending the geometric buildup algorithm for the molecular distance geometry problem (2008) Information Processing Letters, 108, pp. 234-237Creighton, T., (1993) Proteins: Structures and Molecular Properties, , 2nd ed., W.H. Freeman, New YorkDong, Q., Wu, Z., A linear-time algorithm for solving the molecular distance geometry problem with exact interatomic distances (2002) Journal of Global Optimization, 22, pp. 365-375Lavor, C., Lee, J., Lee-St John, A., Liberti, L., Mucherino, A., Sviridenko, M., Discretization orders for distance geometry problems (2010) Optimization Letters, , DOI: 10.1007/s11590-011-0302-6Lavor, C., Liberti, L., Maculan, N., (2006) The Discretizable Molecular Distance Geometry Problem, , arXiv:q-bio/0608012v1Lavor, C., Liberti, L., Maculan, N., (2009) Molecular Distance Geometry Problem, Encyclopedia of Optimization, pp. 2305-2311. , 2nd ed., Springer, New YorkLavor, C., Liberti, L., Maculan, N., Mucherino, A., Recent advances on the discretizable molecular distance geometry problem (2011) European Journal of Operational Research, , DOI: 10.1016/j.ejor.2011.11.007Lavor, C., Liberti, L., Maculan, N., Mucherino, A., The discretizable molecular distance geometry problem (2012) Computational Optimization and Applications, , DOI: 10.1007/s 10589-011-9402-9406Liberti, L., Lavor, C., Maculan, N., A branch-and-prune algorithm for the molecular distance geometry problem (2008) International Transactions in Operational Research, 15, pp. 1-17Liberti, L., Lavor, C., Maculan, N., Molecular distance geometry methods: From continuous to discrete (2011) International Transactions in Operational Research, 18, pp. 33-51Saxe, J.B., Embeddability of weighted graphs in k-space is strongly np-hard (1979) Proceedings of 17th Allerton Conference in Communications, Control and Computing, pp. 480-489. , Monticello, ILSchlick, T., (2002) Molecular Modeling and Simulation: An Interdisciplinary Guide, , Springer, New YorkWu, D., Wu, Z., An updated geometric build-up algorithm for solving the molecular distance geometry problem with sparse distance data (2007) Journal of Global Optimization, 37, pp. 661-673Wu, D., Wu, Z., Yuan, Y., Rigid versus unique determination of protein structures with geometric buildup (2008) Optimization Letters, 2, pp. 319-331