Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently

A Currin, N Swainston, PJ Day, DB Kell - Chemical Society Reviews, 2015 - pubs.rsc.org
The amino acid sequence of a protein affects both its structure and its function. Thus, the
ability to modify the sequence, and hence the structure and activity, of individual proteins in …

A review of methods available to estimate solvent-accessible surface areas of soluble proteins in the folded and unfolded states

S Ausaf Ali, M Imtaiyaz Hassan, A Islam… - Current Protein and …, 2014 - benthamdirect.com
Solvent accessible surface area (SASA) of proteins has always been considered as a
decisive factor in protein folding and stability studies. It is defined as the surface …

BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes

MC Jespersen, B Peters, M Nielsen… - Nucleic acids …, 2017 - academic.oup.com
Antibodies have become an indispensable tool for many biotechnological and clinical
applications. They bind their molecular target (antigen) by recognizing a portion of its …

NetSurfP‐2.0: Improved prediction of protein structural features by integrated deep learning

MS Klausen, MC Jespersen, H Nielsen… - Proteins: Structure …, 2019 - Wiley Online Library
The ability to predict local structural features of a protein from the primary sequence is of
paramount importance for unraveling its function in absence of experimental structural …

GPS 5.0: an update on the prediction of kinase-specific phosphorylation sites in proteins

C Wang, H Xu, S Lin, W Deng, J Zhou… - Genomics …, 2020 - academic.oup.com
In eukaryotes, protein phosphorylation is specifically catalyzed by numerous protein kinases
(PKs), faithfully orchestrates various biological processes, and reversibly determines cellular …

Systematic functional annotation of somatic mutations in cancer

PKS Ng, J Li, KJ Jeong, S Shao, H Chen, YH Tsang… - Cancer cell, 2018 - cell.com
The functional impact of the vast majority of cancer somatic mutations remains unknown,
representing a critical knowledge gap for implementing precision oncology. Here, we report …

Retraction of DNA-bound type IV competence pili initiates DNA uptake during natural transformation in Vibrio cholerae

CK Ellison, TN Dalia, A Vidal Ceballos, JCY Wang… - Nature …, 2018 - nature.com
Natural transformation is a broadly conserved mechanism of horizontal gene transfer in
bacterial species that can shape evolution and foster the spread of antibiotic resistance …

A highly conserved program of neuronal microexons is misregulated in autistic brains

M Irimia, RJ Weatheritt, JD Ellis, NN Parikshak… - Cell, 2014 - cell.com
Alternative splicing (AS) generates vast transcriptomic and proteomic complexity. However,
which of the myriad of detected AS events provide important biological functions is not well …

Uncovering global SUMOylation signaling networks in a site-specific manner

IA Hendriks, RCJ D'souza, B Yang… - Nature structural & …, 2014 - nature.com
SUMOylation is a reversible post-translational modification essential for genome stability.
Using high-resolution MS, we have studied global SUMOylation in human cells in a site …

Obstruction of pilus retraction stimulates bacterial surface sensing

CK Ellison, J Kan, RS Dillard, DT Kysela, A Ducret… - Science, 2017 - science.org
It is critical for bacteria to recognize surface contact and initiate physiological changes
required for surface-associated lifestyles. Ubiquitous microbial appendages called pili are …