ArticlePloS one2015
Enhancements to the Rosetta Energy Function Enable Improved Identification of Small Molecules that Inhibit Protein-Protein Interactions.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 25 citations in OpenAlex.
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- Computer-Aided Designing Peptide Inhibitors of Human Hematopoietic Prostaglandin D2 Synthase Combined Molecular Docking and Molecular Dynamics Simulation.Molecules (Basel, Switzerland) · 2023Article
- Computational design of a synthetic PD-1 agonist.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Machine learning classification can reduce false positives in structure-based virtual screening.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Modulating Integrin αIIbβ3 Activity through Mutagenesis of Allosterically Regulated Intersubunit Contacts.Biochemistry · 2019Article
- Rational re-design ofRSC advances · 2019Article
- Rotamer Libraries for the High-Resolution Design of β-Amino Acid Foldamers.Structure (London, England : 1993) · 2017Article
- Computational tools help improve protein stability but with a solubility tradeoff.The Journal of biological chemistry · 2017Article
- "Solvent hydrogen-bond occlusion": A new model of polar desolvation for biomolecular energetics.Journal of computational chemistry · 2017Article
- The fungal natural product azaphilone-9 binds to HuR and inhibits HuR-RNA interaction in vitro.PloS one · 2017Article
- Protocols for Molecular Modeling with Rosetta3 and RosettaScripts.Biochemistry · 2016Review
- Ultra-High-Throughput Structure-Based Virtual Screening for Small-Molecule Inhibitors of Protein-Protein Interactions.Journal of chemical information and modeling · 2016Article
- Introduction to the Rosetta Special Collection.PloS one · 2015Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Protein-protein interactions are among today's most exciting and promising targets for therapeutic intervention. To date, identifying small-molecules that selectively disrupt these interactions has proven particularly challenging for virtual screening tools, since these have typically been optimized to perform well on more "traditional" drug discovery targets. Here, we test the performance of the Rosetta energy function for identifying compounds that inhibit protein interactions, when these active compounds have been hidden amongst pools of "decoys." Through this virtual screening benchmark, we gauge the effect of two recent enhancements to the functional form of the Rosetta energy function: the new "Talaris" update and the "pwSHO" solvation model. Finally, we conclude by developing and validating a new weight set that maximizes Rosetta's ability to pick out the active compounds in this test set. Looking collectively over the course of these enhancements, we find a marked improvement in Rosetta's ability to identify small-molecule inhibitors of protein-protein interactions.
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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.