Browsing by Author "Polydorides, Savvas"

Now showing items 1-6 of 6

    • Article  

      Computational protein design with a generalized born solvent model: Application to asparaginyl-tRNA synthetase 

      Polydorides, Savvas; Amara, Najette; Aubard, C.; Plateau, P.; Simonson, T.; Archontis, Georgios Z. (2011)
      Computational Protein Design (CPD) is a promising method for high throughput protein and ligand mutagenesis. Recently, we developed a CPD method that used a polar-hydrogen energy function for protein interactions and a ...
    • Article  

      Computational protein design: The proteus software and selected applications 

      Simonson, Thomas; Gaillard, Thomas; Mignon, David; Schmidt, am Busch; Lopes, Anne; Amara, Najette; Polydorides, Savvas; Sedano, Audrey; Druart, Karen; Archontis, Georgios Z. (2013)
    • Article  

      Computational protein design: The proteus software and selected applications 

      Simonson, T.; Gaillard, T.; Mignon, D.; Schmidt Am Busch, M.; Lopes, A.; Amara, Najette; Polydorides, Savvas; Sedano, A.; Druart, Karen; Archontis, Georgios Z. (2013)
      We describe an automated procedure for protein design, implemented in a flexible software package, called Proteus. System setup and calculation of an energy matrix are done with the XPLOR modeling program and its sophisticated ...
    • Article  

      Crossreactivity to vinculin and microbes provides a molecular basis for HLA-based protection against rheumatoid arthritis 

      Van Heemst, J.; Jansen, D. T. S. L.; Polydorides, Savvas; Moustakas, Antonis K.; Bax, M.; Feitsma, A. L.; Bontrop-Elferink, D. G.; Baarse, M.; Van Der Woude, D.; Wolbink, G. -J; Rispens, T.; Koning, F.; De Vries, R. R. P.; Papadopoulos, George K.; Archontis, Georgios Z.; Huizinga, T. W.; Toes, R. E. (2015)
      The HLA locus is the strongest risk factor for anti-citrullinated protein antibody (ACPA) + rheumatoid arthritis (RA). Despite considerable efforts in the last 35 years, this association is poorly understood. Here we ...
    • Article  

      Predicting the acid/base behavior of proteins: A constant-pH monte carlo approach with generalized born solvent 

      Aleksandrov, A.; Polydorides, Savvas; Archontis, Georgios Z.; Simonson, T. (2010)
      The acid/base properties of proteins are essential in biochemistry, and proton binding is a valuable reporter on electrostatic interactions. We propose a constant-pH Monte Carlo strategy to compute protonation free energies ...
    • 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 ...