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A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta
Protocols for Macromolecular Modeling and Design
#MMPMID26335248
Ó Conchúir S
; Barlow KA
; Pache RA
; Ollikainen N
; Kundert K
; O'Meara MJ
; Smith CA
; Kortemme T
PLoS One
2015[]; 10
(9
): e0130433
PMID26335248
show ga
The development and validation of computational macromolecular modeling and
design methods depend on suitable benchmark datasets and informative metrics for
comparing protocols. In addition, if a method is intended to be adopted broadly
in diverse biological applications, there needs to be information on appropriate
parameters for each protocol, as well as metrics describing the expected accuracy
compared to experimental data. In certain disciplines, there exist established
benchmarks and public resources where experts in a particular methodology are
encouraged to supply their most efficient implementation of each particular
benchmark. We aim to provide such a resource for protocols in macromolecular
modeling and design. We present a freely accessible web resource
(https://kortemmelab.ucsf.edu/benchmarks) to guide the development of protocols
for protein modeling and design. The site provides benchmark datasets and metrics
to compare the performance of a variety of modeling protocols using different
computational sampling methods and energy functions, providing a "best practice"
set of parameters for each method. Each benchmark has an associated downloadable
benchmark capture archive containing the input files, analysis scripts, and
tutorials for running the benchmark. The captures may be run with any suitable
modeling method; we supply command lines for running the benchmarks using the
Rosetta software suite. We have compiled initial benchmarks for the resource
spanning three key areas: prediction of energetic effects of mutations, protein
design, and protein structure prediction, each with associated state-of-the-art
modeling protocols. With the help of the wider macromolecular modeling community,
we hope to expand the variety of benchmarks included on the website and continue
to evaluate new iterations of current methods as they become available.
free
free
free
