- SPIN-CGNN: Improved fixed backbone protein design with contact map-based graph construction and contact graph neural network
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Methods | published 07 Dec 2023 PLOS Computational Biology
- Gate-based quantum computing for protein design
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Research Article | published 12 Apr 2023 PLOS Computational Biology
- Ig-VAE: Generative modeling of protein structure by direct 3D coordinate generation
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Research Article | published 27 Jun 2022 PLOS Computational Biology
- RosettaSurf—A surface-centric computational design approach
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Research Article | published 16 Mar 2022 PLOS Computational Biology
- XENet: Using a new graph convolution to accelerate the timeline for protein design on quantum computers
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Research Article | published 27 Sep 2021 PLOS Computational Biology
- Protein sequence optimization with a pairwise decomposable penalty for buried unsatisfied hydrogen bonds
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Research Article | published 08 Mar 2021 PLOS Computational Biology
- Rosetta design with co-evolutionary information retains protein function
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Research Article | published 19 Jan 2021 PLOS Computational Biology
- 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
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Research Article | published 08 Jun 2020 PLOS Computational Biology
- Multi-state design of flexible proteins predicts sequences optimal for conformational change
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Research Article | published 07 Feb 2020 PLOS Computational Biology
- Rosetta FunFolDes – A general framework for the computational design of functional proteins
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Research Article | published 19 Nov 2018 PLOS Computational Biology
- Integrating linear optimization with structural modeling to increase HIV neutralization breadth
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Research Article | published 16 Feb 2018 PLOS Computational Biology
- Data driven flexible backbone protein design
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Research Article | published 24 Aug 2017 PLOS Computational Biology
- A critical analysis of computational protein design with sparse residue interaction graphs
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Research Article | published 30 Mar 2017 PLOS Computational Biology
- Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity
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Research Article | published 23 Sep 2015 PLOS Computational Biology
https://doi.org/10.1371/journal.pcbi.1004335
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- Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences
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Research Article | published 06 Jul 2015 PLOS Computational Biology
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