Recognition specificity, or sequence tolerance, protocols predict the tolerated sequence space for a given protein-protein interface or protein domain. This sequence tolerance benchmark measures the recapitulation of a reference distribution over a sequence space given the conformation of a prototypical sequence.
This benchmark includes:
This protocol capture is based off the original captures from the Smith & Kortemme papers listed above however most of the output directories have been excluded here to reduce the size of the repository. The full output of a successful run can be found in the RosettaCommons repositories and at http://kortemmelab.ucsf.edu/data/.
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 benchmark is hosted on GitHub. The most recent version can be checked out using the git command-line tool:
git clone https://github.com/Kortemme-Lab/sequence-tolerance.git
This archive contains the following directories:
This repository contains one protocol which can be used to run the benchmark. We welcome the inclusion of more protocols. Please contact if you wish to contribute towards the repository.
Each protocol is accompanied by specific documentation in its protocol directory.
Created by: Colin A. Smith 1
Software suite: Rosetta
Protocol directory: protocols/backrub_seqtol
Smith, CA, Kortemme, T. Structure-Based Prediction of the Peptide Sequence Space Recognized by Natural and Synthetic PDZ Domains. 2010. J Mol Biol 402(2):460-74. doi: 10.1016/j.jmb.2010.07.032.
Smith, CA, Kortemme, T. Predicting the Tolerated Sequences for Proteins and Protein Interfaces Using RosettaBackrub Flexible Backbone Design. 2011. PLoS ONE 6(7):e20451. doi: 10.1371/journal.pone.0020451.
The same set of analysis scripts is used by all protocols. Conceptually, the analysis scripts should be a black box that is separated from the output of each protocol by an interface. Currently, the scripts are tied particularly to the Rosetta protocol included herein however we are happy to make the scripts more modular once another protocol is added to the benchmark capture.
The analysis scripts generates four metrics which can be used to evaluate the results of the sequence tolerance simulations as well as a series of plots. The scripts are described in more detail in analysis/README.rst.
The original version of this protocol capture was developed and tested for Rosetta 3.2. Any errors in the current version above are likely to be our fault rather than that of the original author. Please contact with any issues which may arise.↩