Abstract
Structure-based drug design is frequently used to accelerate the development of small-molecule therapeutics. Although substantial progress has been made in X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy, the availability of high-resolution structures is limited owing to the frequent inability to crystallize or obtain sufficient NMR restraints for large or flexible proteins. Computational methods can be used to both predict unknown protein structures and model ligand interactions when experimental data are unavailable. This paper describes a comprehensive and detailed protocol using the Rosetta modeling suite to dock small-molecule ligands into comparative models. In the protocol presented here, we review the comparative modeling process, including sequence alignment, threading and loop building. Next, we cover docking a small-molecule ligand into the protein comparative model. In addition, we discuss criteria that can improve ligand docking into comparative models. Finally, and importantly, we present a strategy for assessing model quality. The entire protocol is presented on a single example selected solely for didactic purposes. The results are therefore not representative and do not replace benchmarks published elsewhere. We also provide an additional tutorial so that the user can gain hands-on experience in using Rosetta. The protocol should take 5–7 h, with additional time allocated for computer generation of models.
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Acknowledgements
We thank J. Smith, as well as R. Levinson, for testing the protocol and for their helpful comments. Work in the Meiler laboratory is supported through grants from the National Institutes of Health (R01 GM080403, R01 MH090192) and the National Science Foundation (Career 0742762).
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All authors contributed equally to this work. All authors wrote substantial portions of the main text, the figures and the supplementary information. S.A.C. proposed the composition of the work for the benefit of the scientific community, tested the presented protocol and managed submission. S.L.D. wrote instructions on how to install the software, generated the comparative models, wrote data-processing scripts and managed references. S.H.D. wrote the supplementary glossary and was responsible for overall editing of the work. G.H.L. wrote the RosettaLigand program in its present form. D.P.N. carefully read through the manuscript for consistency and accuracy and helped in the analysis of the generated models. E.D.N. also generated comparative models, performed all of the ligand docking and performed the data analysis. J.R.W. contributed several figures, data-processing scripts, specialty movers, wrote large sections of the tutorial and managed references. J.H.S. tested the protocol, wrote the Troubleshooting section and edited the manuscript for clarity. J.M. helped define the scope of the work and guided the process of establishing the protocol.
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Supplementary information
Supplementary Discussion
Discussion of clustering using Rosetta, Using Constraints as Filters in RosettaScripts, Installing Rosetta 3.4, Testing Rosetta, and Glossary. (PDF 676 kb)
Supplementary Data
A zipped file that contains example input files, command lines, and output files that the user can download. This tutorial is provided to allow the user to gain handson experience with docking small molecules into comparative models with Rosetta. (ZIP 16433 kb)
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Combs, S., DeLuca, S., DeLuca, S. et al. Small-molecule ligand docking into comparative models with Rosetta. Nat Protoc 8, 1277–1298 (2013). https://doi.org/10.1038/nprot.2013.074
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DOI: https://doi.org/10.1038/nprot.2013.074
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