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Prediction of side-chain conformations in proteins - Protein folding

Prediction of side-chain conformations in proteins - Protein folding

The prediction of the conformation of the side-chains on a fixed backbone can be considered a sub-problem of the Protein Folding problem. We have developed work on this subject using physical models based on the Self-Consistent Mean Field Algorithm (SCMFA). In particular, we developed a Flexible Rotamer Model (FRM) and a theoretical framework that allowed us to derive a side-chain modelling method superior to the best found in the literature at the time. Moreover, the FRM solved some of the practical problems that were presented in these methods.


A Flexible Rotamer Model representation for a Trp residue (Mendes et al. (1999), Proteins, 37, 530-543).

Relevant publications:
  • Mendes, J., Soares, C.M., Carrondo, M.A. (1999) "Improvement of side-chain modelling in proteins with the Self-Consistent Mean Field Theory method based on an analysis of the factors influencing prediction", Biopolymers, 50, 111-131
  • Mendes, J., Baptista, A. M. and Carrondo, M. A., Soares, C. M. (1999) "Improved modelling of side-chains in proteins with rotamer-based methods: a flexible rotamer model.", Proteins, 37, 530-543
  • Burke, D.F., Deane, C.M., Nagarajaram, H.A., Campillo, N., Martin-Martinez, M., Mendes, J., Molina, F., Perry, J., Reddy, B.V.B., Soares, C.M., Steward, R.E., Williams, M., Carrondo, M.A., Blundell, T.L., Mizuguchi, K. (1999) "An iterative structure-assisted approach to sequence alignment and comparative modelling", Proteins, Suppl 3, 55-60
  • Mendes, J., Nagarajaram, H.A., Soares, C.M., Blundell, T.L., Carrondo, M.A. (2001) "Incorporing a knowledge-based bias into an energy-based side-chain modelling method: application to comparative modelling of protein structure", Biopolymers, 59, 72-86
  • Mendes, J., Baptista, A.M, Carrondo, M.A., Soares, C.M. (2001) "Implicit solvation in the Self-Consistent Mean Field Theory method: side-chain modelling and prediction of folding free energies of protein mutants", J.Comp.Aid.Mol.Des. , 15, 721-740


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