ArticleJournal of computational chemistry2018
OSPREY 3.0: Open-source protein redesign for you, with powerful new features.
Article in Journal of computational chemistry, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
- A Generative Neuro-Symbolic AI for Protein Sequence Design.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Dynamic-Structure Redesign of Calmodulin Reveals Mechanistic Constraints on Ryr2 Regulation.bioRxiv : the preprint server for biology · 2026Article
- Evaluation of Physics-Based Protein Design Methods for Predicting Single Residue Effects on Peptide Binding Specificities.Journal of computational chemistry · 2025Article
- Predicting Affinity Through Homology (PATH): Interpretable binding affinity prediction with persistent homology.PLoS computational biology · 2025Article
- Protocol for DesigningJournal of computational biology : a journal of computational molecular cell biology · 2024Article
- A comprehensive study of SARS-CoV-2 main protease (Mpro) inhibitor-resistant mutants selected in a VSV-based system.PLoS pathogens · 2024Article
- Locuaz: an in silico platform for protein binders optimization.Bioinformatics (Oxford, England) · 2024Article
- Substrate Turnover Dynamics Guide Ketol-Acid Reductoisomerase Redesign for Increased Specific Activity.ACS catalysis · 2024Article
- Inactivation of cell-free HIV-1 by designing potent peptides based on mutations in the CD4 binding site.Medical & biological engineering & computing · 2024Article
- DexDesign: an OSPREY-based algorithm for designing de novo D-peptide inhibitors.Protein engineering, design & selection : PEDS · 2024Article
- Study of key residues in MERS-CoV and SARS-CoV-2 main proteases for resistance against clinically applied inhibitors nirmatrelvir and ensitrelvir.Npj viruses · 2024Article
- Structure-guided design and cloning of peptide inhibitors targeting CDK9/cyclin T1 protein-protein interaction.Frontiers in pharmacology · 2024Article
- Discovery, characterization, and redesign of potent antimicrobial thanatin orthologs fromJournal of structural biology: X · 2023Article
- A comprehensive study of SARS-CoV-2 main protease (MbioRxiv : the preprint server for biology · 2023Article
- Improved HIV-1 neutralization breadth and potency of V2-apex antibodies by in silico design.Cell reports · 2023Article
- Disruptor: Computational identification of oncogenic mutants disrupting protein-protein and protein-DNA interactions.Communications biology · 2023Article
- Structural evolution of Delta lineage of SARS-CoV-2.International journal of biological macromolecules · 2023Article
- PocketOptimizer 2.0: A modular framework for computer-aided ligand-binding design.Protein science : a publication of the Protein Society · 2023Article
- Design of nanobody-based bispecific constructs byComputational and structural biotechnology journal · 2023Article
- In Silico Analysis of Neutralizing Antibody Epitopes on The Hepatitis C Virus Surface Glycoproteins.Cell journal · 2023Article
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Authors and funding
14 authors.
Funding
Abstract
We present osprey 3.0, a new and greatly improved release of the osprey protein design software. Osprey 3.0 features a convenient new Python interface, which greatly improves its ease of use. It is over two orders of magnitude faster than previous versions of osprey when running the same algorithms on the same hardware. Moreover, osprey 3.0 includes several new algorithms, which introduce substantial speedups as well as improved biophysical modeling. It also includes GPU support, which provides an additional speedup of over an order of magnitude. Like previous versions of osprey, osprey 3.0 offers a unique package of advantages over other design software, including provable design algorithms that account for continuous flexibility during design and model conformational entropy. Finally, we show here empirically that osprey 3.0 accurately predicts the effect of mutations on protein-protein binding. Osprey 3.0 is available at http://www.cs.duke.edu/donaldlab/osprey.php as free and open-source software. © 2018 Wiley Periodicals, Inc.
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