ArticleMethods in enzymology2013
OSPREY: protein design with ensembles, flexibility, and provable algorithms.
Article in Methods in enzymology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 55 papers.
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Who cites it
55 citing papers in PubMed.
- Entropy quantum computing for fixed-backbone protein design.Scientific reports · 2026Article
- The open-source Masala software suite: Facilitating rapid methods development for synthetic heteropolymer design.bioRxiv : the preprint server for biology · 2025Article
- Enzyme Engineering: Performance Optimization, Novel Sources, and Applications in the Food Industry.Foods (Basel, Switzerland) · 2024Review
- Article
- An end-to-end deep learning method for protein side-chain packing and inverse folding.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Molecular Dynamics Methods for Antibody Design.Methods in molecular biology (Clifton, N.J.) · 2023Article
- On the Rapid Calculation of Binding Affinities for Antigen and Antibody Design and Affinity Maturation Simulations.Antibodies (Basel, Switzerland) · 2022Article
- ECNet is an evolutionary context-integrated deep learning framework for protein engineering.Nature communications · 2021Article
- De Novo Protein Design for Novel Folds Using Guided Conditional Wasserstein Generative Adversarial Networks.Journal of chemical information and modeling · 2020Article
- New computational protein design methods for de novo small molecule binding sites.PLoS computational biology · 2020Article
- Novel, provable algorithms for efficient ensemble-based computational protein design and their application to the redesign of the c-Raf-RBD:KRas protein-protein interface.PLoS computational biology · 2020Article
- A general-purpose protein design framework based on mining sequence-structure relationships in known protein structures.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Development and applications of artificial symmetrical proteins.Computational and structural biotechnology journal · 2020Review
- Toward Broad Spectrum Dihydrofolate Reductase Inhibitors Targeting Trimethoprim Resistant Enzymes Identified in Clinical Isolates of Methicillin ResistantACS infectious diseases · 2019Article
- Protein Design by Provable Algorithms.Communications of the ACM · 2019Article
- rstoolbox - a Python library for large-scale analysis of computational protein design data and structural bioinformatics.BMC bioinformatics · 2019Article
- Combining Mutational Signatures, Clonal Fitness, and Drug Affinity to Define Drug-Specific Resistance Mutations in Cancer.Cell chemical biology · 2018Article
- OSPREY 3.0: Open-source protein redesign for you, with powerful new features.Journal of computational chemistry · 2018Article
- Fast design of arbitrary length loops in proteins using InteractiveRosetta.BMC bioinformatics · 2018Article
- Computational Feasibility of an Exhaustive Search of Side-Chain Conformations in Protein-Protein Docking.Journal of computational chemistry · 2018Article
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11 authors.
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Abstract
unlabelledWe have developed a suite of protein redesign algorithms that improves realistic in silico modeling of proteins. These algorithms are based on three characteristics that make them unique: (1) improved flexibility of the protein backbone, protein side-chains, and ligand to accurately capture the conformational changes that are induced by mutations to the protein sequence; (2) modeling of proteins and ligands as ensembles of low-energy structures to better approximate binding affinity; and (3) a globally optimal protein design search, guaranteeing that the computational predictions are optimal with respect to the input model. Here, we illustrate the importance of these three characteristics. We then describe OSPREY, a protein redesign suite that implements our protein design algorithms. OSPREY has been used prospectively, with experimental validation, in several biomedically relevant settings. We show in detail how OSPREY has been used to predict resistance mutations and explain why improved flexibility, ensembles, and provability are essential for this application. AVAILABILITY: OSPREY is free and open source under a Lesser GPL license. The latest version is OSPREY 2.0. The program, user manual, and source code are available at www.cs.duke.edu/donaldlab/software.php. CONTACT: osprey@cs.duke.edu.
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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.