• Article  

      Computational sidechain placement and protein mutagenesis with implicit solvent models 

      Lopes, A.; Alexandrov, A.; Bathelt, C.; Archontis, Georgios Z.; Simonson, T. (2007)
      Structure prediction and computational protein design should benefit from accurate solvent models. We have applied implicit solvent models to two problems that are central to this area. First, we performed sidechain placement ...
    • Article  

      Proteus and the design of ligand binding sites 

      Polydorides, Savvas; Michael, E.; Mignon, D.; Druart, Karen; Archontis, Georgios Z.; Simonson, T. (2016)
      This chapter describes the organization and use of Proteus, a multitool computational suite for the optimization of protein and ligand conformations and sequences, and the calculation of pKα shifts and relative binding ...