ArticleBiophysical journal2006
IPRO: an iterative computational protein library redesign and optimization procedure.
Article in Biophysical journal, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Viral escape-inspired framework for structure-guided dual bait protein biosensor design.PLoS computational biology · 2025Article
- A Practical Guide to Computational Tools for Engineering Biocatalytic Properties.International journal of molecular sciences · 2025Review
- Enzyme Engineering: Performance Optimization, Novel Sources, and Applications in the Food Industry.Foods (Basel, Switzerland) · 2024Review
- Concerns with computational protein engineering programmes IPRO and OptMAVEn and metabolic pathway engineering programme optStoic.Open biology · 2021Article
- Recent advances in automated protein design and its future challenges.Expert opinion on drug discovery · 2018Review
- Pathway design using de novo steps through uncharted biochemical spaces.Nature communications · 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
- Structure-based design of combinatorial mutagenesis libraries.Protein science : a publication of the Protein Society · 2015Article
- Forcefield_NCAA: ab initio charge parameters to aid in the discovery and design of therapeutic proteins and peptides with unnatural amino acids and their application to complement inhibitors of the compstatin family.ACS synthetic biology · 2014Article
- Protein folding and de novo protein design for biotechnological applications.Trends in biotechnology · 2014Review
- OptMAVEn--a new framework for the de novo design of antibody variable region models targeting specific antigen epitopes.PloS one · 2014Article
- Forcefield_PTM:Journal of chemical theory and computation · 2013Article
- An evolution-based approach to De Novo protein design and case study on Mycobacterium tuberculosis.PLoS computational biology · 2013Article
- MAPs: a database of modular antibody parts for predicting tertiary structures and designing affinity matured antibodies.BMC bioinformatics · 2013Article
- Article
- Designing specific protein-protein interactions using computation, experimental library screening, or integrated methods.Protein science : a publication of the Protein Society · 2012Review
- A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions.Structure (London, England : 1993) · 2011Article
- Engineering a protein-protein interface using a computationally designed library.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Computational design of Candida boidinii xylose reductase for altered cofactor specificity.Protein science : a publication of the Protein Society · 2009Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
A number of computational approaches have been developed to reengineer promising chimeric proteins one at a time through targeted point mutations. In this article, we introduce the computational procedure IPRO (iterative protein redesign and optimization procedure) for the redesign of an entire combinatorial protein library in one step using energy-based scoring functions. IPRO relies on identifying mutations in the parental sequences, which when propagated downstream in the combinatorial library, improve the average quality of the library (e.g., stability, binding affinity, specific activity, etc.). Residue and rotamer design choices are driven by a globally convergent mixed-integer linear programming formulation. Unlike many of the available computational approaches, the procedure allows for backbone movement as well as redocking of the associated ligands after a prespecified number of design iterations. IPRO can also be used, as a limiting case, for the redesign of a single or handful of individual sequences. The application of IPRO is highlighted through the redesign of a 16-member library of Escherichia coli/Bacillus subtilis dihydrofolate reductase hybrids, both individually and through upstream parental sequence redesign, for improving the average binding energy. Computational results demonstrate that it is indeed feasible to improve the overall library quality as exemplified by binding energy scores through targeted mutations in the parental sequences.
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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.