The goal of loop modeling is to predict the native conformation of an internal
stretch of protein backbone. This is an important problem in areas such as
homology modeling, protein design, and structure determination. This benchmark
comprises a standard set of well-curated loops for the purpose of comparing
different loop modeling algorithms. Each algorithm predicts hundreds of
structures for each loop and is judged based on the backbone RMSD between those
predictions and the known structure.
The benchmark is hosted on GitHub. The most recent version can be checked out
using the git <http://git-scm.com/>_ command-line tool::
git clone https://github.com/Kortemme-Lab/loop_modeling.git
The benchmark is only designed to run without modification on the QB3 cluster at UCSF. On that cluster, the commands to run the benchmark will look something like the examples below. The benchmark scripts can work with or without a MySQL server. To use with MySQL::
cd hpc/ucsf/rosetta ./run_benchmark.py B1 benchmarks/kic_no_sfxn_ramp.xml input/mini_rosetta.pdbs --use-database
cd ../../../analysis ./make_report B1
To use without a MySQL server::
cd hpc/ucsf/rosetta ./run_benchmark.py B1 benchmarks/kic_no_sfxn_ramp_disk.xml input/mini_rosetta.pdbs
cd ../../../analysis ./make_report ../hpc/ucsf/rosetta/B1/0/B1.results
More information on what these commands do and how they can be configured is given in the README.rst files in their respective directories.
This archive contains the following directories:
libraries Contains common code used by all the scripts comprising the benchmark.
input Contains the input files for the benchmark.
output These directories are empty by default. This is the default output location for protocols if they are run on the local machine.
output/sample Contains sample output data that can be used to test the analysis script.
analysis Contains the analysis script used to analyze the output of a prediction run. All protocols are expected to produce output in a format compatible with the analysis script.
protocols Contains the scripts needed to run a prediction for each protocol.
hpc Contains scripts that can be used to run the entire benchmark using specific cluster architectures. For practical reasons, a limited number of cluster systems are supported. Please feel free to provide scripts which run the benchmark for your particular cluster system.
This repository contains third party libraries and materials which are distributed under their own terms (see LICENSE-3RD-PARTY). The novel content in this repository is licensed according to LICENSE.
The latest release of this repository: |releasedoi|
.. |releasedoi| image:: https://zenodo.org/badge/doi/10.5281/zenodo.18596.svg
:target: http://dx.doi.org/10.5281/zenodo.18596