Protein–protein docking benchmark version 4.0

By Howook Hwang, Thom Vreven, Joël Janin, Zhiping Weng. Proteins: Structure, Function, and Bioinformatics, 2010

503 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/369743e9f102566314c71a2301fc58169bc8c1d2

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Citations in the corpus

Score_set: A CAPRI benchmark for scoring protein complexes (2014, methodology): “22 But the set of binding modes contained models produced by one docking server, and was not made publicly available.”
A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design (2015, background): “Organizations such as CASP [11] and CAPRI [12] create blind prediction tests for problems in protein structure prediction, protein-protein docking, and other applications, but many questions in the field of macromolecular modeling and design could also benefit from canonical benchmarks such as those”
Docking, scoring, and affinity prediction in CAPRI (2013, background): “…groups were asked to rank these complexes relative to a reference set of 120 natural complexes from a benchmark set for testing docking procedures.36 The natural complexes had known K d values spanning a wide range,37 whereas Baker’s experimental procedure was able to detect binding at a K d of…”
New additions to the ClusPro server motivated by CAPRI (2017, methodology): “…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, respectively.”
Protein–protein docking by fast generalized Fourier transforms on 5D rotational manifolds (2016, unknown): “Execution times of the FMFT sampling algorithm were measured by docking unbound structures of component proteins in 51 enzyme-inhibitor pairs from the established Protein Docking Benchmark [19] (see Table S1).”