ArticlePloS one2020
Assessing multiple score functions in Rosetta for drug discovery.
Article in PloS one, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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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
19 citing papers in PubMed.
- Structure-guided compound prioritization strategy for virtual screening identifies putative binders for the nuclear receptor LRH-1.bioRxiv : the preprint server for biology · 2026Article
- A Hybrid Physics-Deep Learning Framework for Combinatorial De Novo Design of Small-Molecule Binding Proteins.bioRxiv : the preprint server for biology · 2026Article
- High-throughput screening identifies a trafficking corrector for long QT syndrome-associated KCNQ1 variants.JCI insight · 2026Article
- Ultra-large library screening with an evolutionary algorithm in Rosetta (REvoLd).Communications chemistry · 2025Article
- A generalizable deep learning framework for structure-based protein-ligand affinity ranking.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- High Throughput Screening Identifies a Small Molecule Trafficking Corrector for Long-QT Syndrome Associated KCNQ1 Variants.bioRxiv : the preprint server for biology · 2025Article
- Genomics-informed drug-repurposing strategy identifies two therapeutic targets for preventing liver disease associated with metabolic dysfunction.American journal of human genetics · 2025Article
- Cholesterol allosteric modulation of the oxytocin receptor.Biophysical journal · 2025Article
- Energy metric prediction for double insertion mutants via the RoseNet deep learning framework.Bioinformatics advances · 2025Article
- Article
- Recent Advances in Automated Structure-Based De Novo Drug Design.Journal of chemical information and modeling · 2024Review
- Toward high-resolution modeling of small molecule-ion channel interactions.Frontiers in pharmacology · 2024Article
- Docking cholesterol to integral membrane proteins with Rosetta.PLoS computational biology · 2023Article
- Single amino acid residue mediates reciprocal specificity in two mosquito odorant receptors.eLife · 2022Article
- Protocol for iterative optimization of modified peptides bound to protein targets.Journal of computer-aided molecular design · 2022Article
- Neural Upscaling from Residue-Level Protein Structure Networks to Atomistic Structures.Biomolecules · 2021Article
- Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks.Nature communications · 2021Article
- Co-occurring gain-of-function mutations in HER2 and HER3 modulate HER2/HER3 activation, oncogenesis, and HER2 inhibitor sensitivity.Cancer cell · 2021Article
- General Purpose Structure-Based Drug Discovery Neural Network Score Functions with Human-Interpretable Pharmacophore Maps.Journal of chemical information and modeling · 2021Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Rosetta is a computational software suite containing algorithms for a wide variety of macromolecular structure prediction and design tasks including small molecule protocols commonly used in drug discovery or enzyme design. Here, we benchmark RosettaLigand score functions and protocols in comparison to results of other software recently published in the Comparative Assessment of Score Functions (CASF-2016). The CASF-2016 benchmark covers a wide variety of tests including scoring and ranking multiple compounds against a target, ligand docking of a small molecule to a target, and virtual screening to extract binders from a compound library. Direct comparison to the score functions provided by CASF-2016 results shows that the original RosettaLigand score function ranks among the top software for scoring, ranking, docking and screening tests. Most notably, the RosettaLigand score function ranked 2/34 among other report score functions in CASF-2016. We additionally perform a ligand docking test with full sampling to mimic typical use cases. Despite improved performance of newer score functions in canonical protein structure prediction and design, we demonstrate here that more recent Rosetta score functions have reduced performance across all small molecule benchmarks. The tests described here have also been uploaded to the Rosetta scientific benchmarking server and will be run weekly to track performance as the code is continually being developed.
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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.