Natural-like function in artificial WW domains

By W. P. Russ, Drew M. Lowery, Prashant Mishra, Michael B. Yaffe, Rama Ranganathan. 2005

260 citations recorded by the source corpus.

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

Generating functional protein variants with variational autoencoders (2020, background): “Beyond the identification of sequence variants, computational approaches have enabled the generation of small synthetic protein domains that mimic natural folds while using sequences that are distant from what is seen in nature [4– 6].”
3D structures of membrane proteins from genomic sequencing (2012, positive): “Similarly, evolutionarily coupled pairs may be excellent design elements for engineering new proteins in synthetic biology (Russ et al., 2005) and may have a strategic role in the protein folding process (Fersht, 2008).”
Protein sectors: evolutionary units of three-dimensional structure (2009, background): “…August 21, 2009 ª2009 Elsevier Inc. 781 782 Cell 138, 774–786, August 21, 2009 ª2009 Elsevier Inc. SCA matrix alone to enable the design of artificial proteins that recapitulate the atomic structure and biochemical activity of the WW domain family (Russ et al., 2005; Socolich et al., 2005).”
The spatial architecture of protein function and adaptation (2012, background): “expression of the amino-terminal domain of Escherichia coli RNA polymerase a-subunit fused to the target peptide ligand; and (3) pZE1RM-eGFP (ampicillin resistant), containing the target promoter driving the enhanced green fluorescent protein (eGFP).”
Finding and Leveraging Structure in Learning Problems (2012, methodology): “In the papers [174] and [165], the authors determine, using Statistical Coupling Analysis (SCA), that the residues can be divided into two clusters: the first cluster contains a set of 8 strongly coupled residues and the second cluster contains everything else.”
Graphical Models of Residue Coupling in Protein Families (2008, background): “demonstrated that coupling information enables the design of new, stably folded [35], and functional [32] WW domains.”
Co-evolving residues in membrane proteins (2007, background): “Availability: http://webclu.bio.wzw.tum.de/helixcorr/ Contact: d.frishman@wzw.tum.de Supplementary information: Supplementary data are available at Bioinformatics online.”
Graphical models of residue coupling in protein families (2005, background): “These and similar ideas have been given a significant boost with the promising results of Ranganathan and colleagues [32], [35].”