A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design

摘要: The development and validation of computational macromolecular modeling design methods depend on suitable benchmark datasets informative metrics for comparing protocols. In addition, if a method is intended to be adopted broadly in diverse biological applications, there needs information appropriate parameters each protocol, as well describing the expected accuracy compared experimental data. certain disciplines, exist established benchmarks public resources where experts particular methodology are encouraged supply their most efficient implementation benchmark. We aim provide such resource protocols design. present freely accessible web (https://kortemmelab.ucsf.edu/benchmarks) guide protein site provides compare performance variety using different sampling energy functions, providing “best practice” set method. Each has an associated downloadable capture archive containing input files, analysis scripts, tutorials running captures may run with any method; we command lines Rosetta software suite. have compiled initial spanning three key areas: prediction energetic effects mutations, design, structure prediction, state-of-the-art With help wider community, hope expand included website continue evaluate new iterations current they become available.