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R. Norel, D. Petrey and B. Honig, “Pudge: A Flexible, Interactive Server for Protein Structure Prediction,” Nucleic Acids Research, Vol. 38, Suppl. 2, 2010, pp. W550-554.
http://dx.doi.org/10.1093/nar/gkq475

has been cited by the following article:

• TITLE: A Method to Predict Amino Acids at Proximity of Beta-Sheet Axes from Protein Sequences

  AUTHORS: Antonin Guilloux, Bernard Caudron, Jean-Luc Jestin

  KEYWORDS: Polypeptide Chain; Protein Structure; Topology; Beta-Strand; Folding; Amino Acid; Structure Prediction

  JOURNAL NAME: Applied Mathematics, Vol.5 No.1, January 2, 2014

  ABSTRACT: A general and elementary protein folding step was described in a previous article. Energy conservation during this folding step yielded an equation with remarkable solutions over the field of rational numbers. Sets of sequences optimized for folding were derived. In this work, a geometrical analysis of protein beta-sheet backbone structures allows the definition of positions of topological interest. They correspond to amino acids’ alpha carbons located on a unique axis crossing all beta-sheet’s strands or at proximity of this axis defined here. These positions of topological interest are shown to be highly correlated with the absence of sequences optimized for folding. Applications in protein structure prediction for the quality assessment of structural models are envisioned.