ArticlePloS one2011
A generic program for multistate protein design.
Article in PloS one, 2011. 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, 101 citations in OpenAlex.
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- An integrative approach to protein sequence design through multiobjective optimization.bioRxiv : the preprint server for biology · 2024Article
- A general computational design strategy for stabilizing viral class I fusion proteins.Nature communications · 2024Article
- Sparks of function by de novo protein design.Nature biotechnology · 2024Review
- GPCRome-wide analysis of G-protein-coupling diversity using a computational biology approach.Nature communications · 2023Article
- Reconfigurable asymmetric protein assemblies through implicit negative design.Science (New York, N.Y.) · 2022Article
- De novo metalloprotein design.Nature reviews. Chemistry · 2022Article
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- Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design.Biochemistry · 2021Review
- Protein sequence design by conformational landscape optimization.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Structural basis for peptide substrate specificities of glycosyltransferase GalNAc-T2.ACS catalysis · 2021Article
- Computational design and experimental optimization of protein binders with prospects for biomedical applications.Protein engineering, design & selection : PEDS · 2021Review
- Rosetta design with co-evolutionary information retains protein function.PLoS computational biology · 2021Article
- Rosetta:MSF:NN: Boosting performance of multi-state computational protein design with a neural network.PloS one · 2021Article
- Macromolecular modeling and design in Rosetta: recent methods and frameworks.Nature methods · 2020Review
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Some protein design tasks cannot be modeled by the traditional single state design strategy of finding a sequence that is optimal for a single fixed backbone. Such cases require multistate design, where a single sequence is threaded onto multiple backbones (states) and evaluated for its strengths and weaknesses on each backbone. For example, to design a protein that can switch between two specific conformations, it is necessary to to find a sequence that is compatible with both backbone conformations. We present in this paper a generic implementation of multistate design that is suited for a wide range of protein design tasks and demonstrate in silico its capabilities at two design tasks: one of redesigning an obligate homodimer into an obligate heterodimer such that the new monomers would not homodimerize, and one of redesigning a promiscuous interface to bind to only a single partner and to no longer bind the rest of its partners. Both tasks contained negative design in that multistate design was asked to find sequences that would produce high energies for several of the states being modeled. Success at negative design was assessed by computationally redocking the undesired protein-pair interactions; we found that multistate design's accuracy improved as the diversity of conformations for the undesired protein-pair interactions increased. The paper concludes with a discussion of the pitfalls of negative design, which has proven considerably more challenging than positive design.
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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.