Application of asymmetric statistical potentials to antibody-protein docking

By Ryan Brenke, David R. Hall, Gwo-Yu Chuang, Stephen R. Comeau, Tanggis Bohnuud, Dmitri Beglov, O. Schueler‐Furman, Sandor Vajda, Dima Kozakov. 2012

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Citations in the corpus

How Good is Automated Protein Docking? (2013, background): “26 The “Other Mode” targets the so-called “other” type of complexes that primarily occur in signal transduction pathways,27 and generally have substantially less perfect shape and electrostatic complementarity than the enzyme–inhibitor complexes.”
Selectivity by Small-Molecule Inhibitors of Protein Interactions Can Be Driven by Protein Surface Fluctuations (2015, unknown): “ROCS represents molecular shape as the sum of Gaussians centered at each atomic position, and can rapidly calculate the near-optimal alignment that maximizes volume overlap between two molecules.”
Performance and its limits in rigid body protein-protein docking (2020, unknown): “Determining the structure of antibody-antigen complexes is an important application of protein docking, and results have been substantially improved by developing a structure based potential specific to these interactions (Brenke et al., 2012).”
The ClusPro web server for protein-protein docking (2017, methodology): “The use of the new potential substantially improved the performance of docking for antibody– protein antigen complexes 54 .”
Antibody i-Patch prediction of the antibody binding site improves rigid local antibody-antigen docking. (2013, methodology): “This may be due to the specific biology of the antibody-binding site, meaning that general docking tools are not ideal for this problem (Sircar and Gray, 2010; de Vries and Bonvin, 2011; Brenke et al., 2012; Li and Kihara, 2012).”
What Method to Use for Protein-Protein Docking? (2019, background): “…ClusPro parameter set for enzyme-inhibitor and “other” type of complexes [24], and the antibody parameterization for antibody-antigen pairs [27] without further training, and obtained acceptable models for 13.7%, 37.3%, and 45.1% of the complexes in the top 1, top 5 and top 10 predictions.”
Modeling and docking antibody structures with Rosetta (2017, methodology): “In particular, there are two fast-Fourier transform (FFT) rigid-body docking approaches that implement antibody-specific energy potentials: PIPER 12 with the antibody-ADARS potential 13 , and ZDOCK 14 with the antibody i-Patch potential 15 .”
New additions to the ClusPro server motivated by CAPRI (2017, background): “…much poorer.13 However, in 2012 we have introduced a special DARS-type potential for this type of interactions, which provided some improvement.16 The last CAPRI evaluation meeting in April 2016 focused on the results of rounds 28–29 and 31–35 that included targets 59–67 and 95–105,…”