ArticleBiophysical journal2008
Toward full-sequence de novo protein design with flexible templates for human beta-defensin-2.
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Rigorous Computational and Experimental Investigations on MDM2/MDMX-Targeted Linear and Macrocyclic Peptides.Molecules (Basel, Switzerland) · 2019Article
- CATS (Coordinates of Atoms by Taylor Series): protein design with backbone flexibility in all locally feasible directions.Bioinformatics (Oxford, England) · 2017Article
- Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences.PLoS computational biology · 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
- Derivation of ligands for the complement C3a receptor from the C-terminus of C5a.European journal of pharmacology · 2014Article
- De novo design and experimental characterization of ultrashort self-associating peptides.PLoS computational biology · 2014Article
- De novo peptide design and experimental validation of histone methyltransferase inhibitors.PloS one · 2014Article
- An evolution-based approach to De Novo protein design and case study on Mycobacterium tuberculosis.PLoS computational biology · 2013Article
- Protein WISDOM: a workbench for in silico de novo design of biomolecules.Journal of visualized experiments : JoVE · 2013Article
- Systematic optimization model and algorithm for binding sequence selection in computational enzyme design.Protein science : a publication of the Protein Society · 2013Article
- Increasing sequence diversity with flexible backbone protein design: the complete redesign of a protein hydrophobic core.Structure (London, England : 1993) · 2012Article
- De novo peptide design with C3a receptor agonist and antagonist activities: theoretical predictions and experimental validation.Journal of medicinal chemistry · 2012Article
- Molecular dynamics in drug design: new generations of compstatin analogs.Chemical biology & drug design · 2012Article
- Assessment of flexible backbone protein design methods for sequence library prediction in the therapeutic antibody Herceptin-HER2 interface.Protein science : a publication of the Protein Society · 2011Article
- Computational design of the lasso peptide antibiotic microcin J25.Protein engineering, design & selection : PEDS · 2011Article
- Discovery of entry inhibitors for HIV-1 via a new de novo protein design framework.Biophysical journal · 2010Article
- New compstatin variants through two de novo protein design frameworks.Biophysical journal · 2010Article
- Computational methods for de novo protein design and its applications to the human immunodeficiency virus 1, purine nucleoside phosphorylase, ubiquitin specific protease 7, and histone demethylases.Current drug targets · 2010Review
- Computer-aided design of functional protein interactions.Nature chemical biology · 2009Review
- A search for energy minimized sequences of proteins.PloS one · 2009Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
In this article, we introduce and apply our de novo protein design framework, which observes true backbone flexibility, to the redesign of human beta-defensin-2, a 41-residue cationic antimicrobial peptide of the innate immune system. The flexible design templates are generated using molecular dynamics simulations with both Generalized Born implicit solvation and explicit water molecules. These backbone templates were employed in addition to the x-ray crystal structure for designing human beta-defensin-2. The computational efficiency of our framework was demonstrated with the full-sequence design of the peptide with flexible backbone templates, corresponding to the mutation of all positions except the native cysteines.
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Registered trials
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