ArticleBiophysical journal2007
Extending Iterative Protein Redesign and Optimization (IPRO) in protein library design for ligand specificity.
Article in Biophysical journal, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
14 citing papers in PubMed.
- A Practical Guide to Computational Tools for Engineering Biocatalytic Properties.International journal of molecular sciences · 2025Review
- Rapid characterization of secreted recombinant proteins by native mass spectrometry.Communications biology · 2018Article
- A review of computational tools for design and reconstruction of metabolic pathways.Synthetic and systems biotechnology · 2017Review
- Computational Redesign of Acyl-ACP Thioesterase with Improved Selectivity toward Medium-Chain-Length Fatty Acids.ACS catalysis · 2017Article
- Forcefield_PTM:Journal of chemical theory and computation · 2013Article
- Engineering dynamic pathway regulation using stress-response promoters.Nature biotechnology · 2013Article
- MAPs: a database of modular antibody parts for predicting tertiary structures and designing affinity matured antibodies.BMC bioinformatics · 2013Article
- Predictive Bcl-2 family binding models rooted in experiment or structure.Journal of molecular biology · 2012Article
- Restriction enzyme-free construction of random gene mutagenesis libraries in Escherichia coli.Analytical biochemistry · 2012Article
- Brønsted-Evans-Polanyi relationships for C-C bond forming and C-C bond breaking reactions in thiamine-catalyzed decarboxylation of 2-keto acids using density functional theory.Journal of molecular modeling · 2012Article
- Engineering a protein-protein interface using a computationally designed library.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Design and directed evolution of a dideoxy purine nucleoside phosphorylase.Protein engineering, design & selection : PEDS · 2010Article
- Computational design of Candida boidinii xylose reductase for altered cofactor specificity.Protein science : a publication of the Protein Society · 2009Article
- OptGraft: A computational procedure for transferring a binding site onto an existing protein scaffold.Protein science : a publication of the Protein Society · 2009Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In this article we extend the Iterative Protein Redesign and Optimization (IPRO) framework for the design of protein libraries with targeted ligand specificity. Mutations that minimize the binding energy with the desired ligand are identified. At the same time explicit constraints are introduced that maintain the binding energy for all decoy ligands above a threshold necessary for successful binding. The proposed framework is demonstrated by computationally altering the effector binding specificity of the bacterial transcriptional regulatory protein AraC, belonging to the AraC/XylS family of transcriptional regulators for different unnatural ligands. The obtained results demonstrate the importance of systematically suppressing the binding energy for competing ligands. Pinpointing a small set of mutations within the binding pocket greatly improves the difference in binding energies between targeted and decoy ligands, even when they are very similar.
Indexed as
Identifiers
What OpenQuestion holds
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.