The Frustratometer is an algorithm inspired by Energy Landscape Theory that aims at quantifying the degree of local frustration manifested in protein molecules. Frustration provides insight to the proteins biological behavior by analyzing how the energy is distributed in protein structures and how mutations or conformational changes shift the energy distributions. Sites of high local frustration often indicate biologically important regions such as binding or allosteric sites. Minimally frustrated linkages constitute a stable folding core of the molecule. In collaboration with Peter Wolynes and Elizabeth Komives.
An R package for frustration calculations can be found in github.
NGOME is an algorithm for the prediction of spontaneous non-enzymatic deamidation of internal asparagine residues in proteins. Asparagine deamidation is modulated by protein local sequence, secondary structure and hydrogen bonding.NGOME makes use of sequence-based predictions of secondary structure and intrinsic disorder and does not require a protein structure. NGOME may help the user identify deamidation-prone asparagine residues that may act as a molecular clock for the regulation of protein function and turnover. In collaboration with Leonardo G. Alonso.