Optimizing energy functions for protein–protein interface design

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Scientific Benchmarks for Guiding Macromolecular Energy Function Improvement (2013, methodology): “, 2012), the ORBIT energy function (Sharabi et al., 2010), and the SCWRL energy function (Shapovalov & Dunbrack, 2011).”
Contacts-based prediction of binding affinity in protein–protein complexes (2015, background): “…Aloy and Russell, 2006 ; Beltrao et al., 2007 ; Kiel et al., 2008 ; Dell’Orco, 2009 ), but also for other applications such as protein engineering ( Kortemme et al., 2004 ; Sharabi et al., 2011 ), computational mutagenesis ( Ben-Shimon and Eisenstein, 2010 ), and docking ( Halperin et al., 2002 ).”
A general-purpose protein design framework based on mining sequence–structure relationships in known protein structures (2018, methodology): “the Mayo lab (5, 6), PROTEUS by Simonson and co-workers (7), and FoldX by Serrano and colleagues (8).”
Protein engineering by highly parallel screening of computationally designed variants (2016, methodology): “…interaction interfaces to enhance interaction affinity ( 24 , 25 ) prompted the development of scoring functions specific for protein interface design, whereby energy terms of existing functions were reweighted or a reduced set of terms focused on electrostatics and solvation were used ( 26 – 28 ).”