ArticlePloS one2012
Using RosettaLigand for small molecule docking into comparative models.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
26 citing papers in PubMed.
- Assessing the Generalizability of Machine Learning and Physics-Based Methods with DNA-Encoded Libraries.Journal of chemical information and modeling · 2026Article
- Assessing the Generalizability of Machine Learning and Physics-Based Methods with DNA-Encoded Libraries.bioRxiv : the preprint server for biology · 2026Article
- Predicting inhibitors of OATP1B1 via heterogeneous OATP-ligand interaction graph neural network (HOLIgraph).Journal of cheminformatics · 2025Article
- Toward high-resolution modeling of small molecule-ion channel interactions.Frontiers in pharmacology · 2024Article
- Introduction to the BioChemical Library (BCL): An Application-Based Open-Source Toolkit for Integrated Cheminformatics and Machine Learning in Computer-Aided Drug Discovery.Frontiers in pharmacology · 2022Article
- Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks.Nature communications · 2021Article
- A practical guide to large-scale docking.Nature protocols · 2021Review
- Interface-based design of the favipiravir-binding site in SARS-CoV-2 RNA-dependent RNA polymerase reveals mutations conferring resistance to chain termination.FEBS letters · 2021Article
- High-throughput rational design of the remdesivir binding site in the RdRp of SARS-CoV-2: implications for potential resistance.iScience · 2021Article
- A structure-based computational workflow to predict liability and binding modes of small molecules to hERG.Scientific reports · 2020Article
- Computational characterization of the glutamate receptor antagonist perampanel and its close analogs: density functional exploration of conformational space and molecular docking study.Journal of molecular modeling · 2019Article
- BCL::MolAlign: Three-Dimensional Small Molecule Alignment for Pharmacophore Mapping.Journal of chemical information and modeling · 2019Article
- Biological and functional relevance of CASP predictions.Proteins · 2018Article
- Inhibitor mechanisms in the S1 binding site of the dopamine transporter defined by multi-site molecular tethering of photoactive cocaine analogs.Biochemical pharmacology · 2017Article
- Ab initio structure determination from prion nanocrystals at atomic resolution by MicroED.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Article
- Assessment of refinement of template-based models in CASP11.Proteins · 2016Article
- Protocols for Molecular Modeling with Rosetta3 and RosettaScripts.Biochemistry · 2016Review
- Hierarchical virtual screening approaches in small molecule drug discovery.Methods (San Diego, Calif.) · 2015Review
- Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Computational small molecule docking into comparative models of proteins is widely used to query protein function and in the development of small molecule therapeutics. We benchmark RosettaLigand docking into comparative models for nine proteins built during CASP8 that contain ligands. We supplement the study with 21 additional protein/ligand complexes to cover a wider space of chemotypes. During a full docking run in 21 of the 30 cases, RosettaLigand successfully found a native-like binding mode among the top ten scoring binding modes. From the benchmark cases we find that careful template selection based on ligand occupancy provides the best chance of success while overall sequence identity between template and target do not appear to improve results. We also find that binding energy normalized by atom number is often less than -0.4 in native-like binding modes.
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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.