ArticleNature protocols2013
Small-molecule ligand docking into comparative models with Rosetta.
Article in Nature protocols, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 86 papers.
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Who cites it
86 citing papers in PubMed.
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- Identification and Evaluation of Benzimidazole- Agonists of Innate Immune Receptor NOD2.ACS infectious diseases · 2026Article
- Prioritizing Neuroactive Ligands Using Motif-Guided Virtual Discovery and Zebrafish Profiling.bioRxiv : the preprint server for biology · 2026Article
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- Small Molecule Modulation of MHC-I Surface Expression: A Click Chemistry-Based Discovery Approach.Journal of medicinal chemistry · 2025Article
- Luminescent Properties and Cytotoxic Activity of 2-phenylbenzoxazole Fluorosulfate Derivatives.International journal of molecular sciences · 2025Article
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- Enhanced discovery of bacterial laccase-like multicopper oxidase through computer simulation and metagenomic analysis of industrial wastewater.FEBS open bio · 2025Article
- Cloning, Characterization, and Computer-Aided Evolution of a Thermostable Laccase of the DUF152 Family From Klebsiella michiganensis.Proteins · 2025Article
- Maltodextrin transport in the extremely thermophilic, lignocellulose degrading bacteriumJournal of bacteriology · 2025Article
- Patulin Detoxification by Evolutionarily Divergent Reductases ofJournal of agricultural and food chemistry · 2025Article
- Computational Engineering of siderocalin to modulate its binding affinity to the antihypertension drug candesartan.Journal of structural biology · 2025Article
- Insurmountable antagonism of human mu opioid receptors by buprenorphine is due to hemi-equilibrium.European journal of pharmacology · 2025Article
26 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors.
Funding
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.