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Updated: May 14, 2026

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
Published on: July 25, 2013
The protein local optimization program and G-protein-coupled receptors: loop restoration and applications to homology
Dahlia A Goldfeld1, Richard A Friesner
1Department of Chemistry, Columbia University, New York, USA. dag2115@columbia.edu
Abstract:
The protein local optimization program (PLOP) uses sophisticated sampling algorithms and a highly refined physics-based energy function to restore loops within a protein structure. In this chapter, we highlight some of the recent successes we have had with PLOP restoring long loops in their native environment as well as the intra- and extracellular loops of four G-protein-coupled receptors. This includes the very long second extracellular loops of bovine rhodopsin and the turkey β1- and human β2-adrenergic receptors. We then provide an extremely detailed description of PLOP's algorithms, as well as a sample file and explicit keywords so that a new user can successfully run PLOP.
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