ArticleBiochemistry2011
Design of native-like proteins through an exposure-dependent environment potential.
Article in Biochemistry, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 7 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
7 citing papers in PubMed, 13 citations in OpenAlex.
- Combining Rosetta Sequence Design with Protein Language Model Predictions Using Evolutionary Scale Modeling (ESM) as Restraint.ACS synthetic biology · 2024Article
- New computational protein design methods for de novo small molecule binding sites.PLoS computational biology · 2020Article
- Finding the needle in the haystack: towards solving the protein-folding problem computationally.Critical reviews in biochemistry and molecular biology · 2018Review
- Computational design of membrane proteins using RosettaMembrane.Protein science : a publication of the Protein Society · 2018Article
- Computational design of protein-small molecule interfaces.Journal of structural biology · 2014Article
- Energy functions in de novo protein design: current challenges and future prospects.Annual review of biophysics · 2013Review
- Article
Corrections and comments
- Erratum issued
Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
We hypothesize that the degree of surface exposure of amino acid side chains within a globular, soluble protein has been optimized in evolution, not only to minimize the solvation free energy of the monomeric protein but also to prevent protein aggregation. This effect needs to be taken into account when engineering proteins de novo. We test this hypothesis through addition of a knowledge-based, exposure-dependent energy term to the RosettaDesign solvation potential [Lazaridis, T., and Karplus, M. (1999) Proteins 35, 133-152]. Correlation between amino acid type and surface exposure is determined from a representative set of experimental protein structures. The amino acid solvent accessible surface area (SASA) is estimated with a neighbor vector measure that increases in accuracy compared to the neighbor count measure while remaining pairwise decomposable [Durham, E., et al. (2009) J. Mol. Model. 15, 1093-1108]. Benchmarking of this potential in protein design displays a 3.2% improvement in the overall sequence recovery and an 8.5% improvement in recovery of amino acid types tolerated in evolution.
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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.