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Updated: Nov 19, 2025

Optimization of Synthetic Proteins: Identification of Interpositional Dependencies Indicating Structurally and/or Functionally Linked Residues
Published on: July 14, 2015
Concerns with computational protein engineering programmes IPRO and OptMAVEn and metabolic pathway engineering
1Department of Chemical Engineering, Pennsylvania State University, University Park, PA 16802-4400, USA.
Abstract:
It has become customary in engineering to require a modelling component in research endeavours. In addition, as the code for these models becomes more byzantine in complexity, it is difficult for reviewers and readers to discern their value and understand the underlying code. This opinion piece summarizes the negative experience of the author with the IPRO and OptMAVEn computational protein engineering models as well as problems with the optStoic metabolic pathway model. In our hands, these models often fail to predict reliable ways to engineer proteins and metabolic pathways.
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