Metabolite–enzyme coevolution: from single enzymes to metabolic pathways and networks
L Noda-Garcia, W Liebermeister… - Annual Review of …, 2018 - annualreviews.org
How individual enzymes evolved is relatively well understood. However, individual enzymes
rarely confer a physiological advantage on their own. Judging by its current state, the …
rarely confer a physiological advantage on their own. Judging by its current state, the …
Computational approaches to predict protein functional families and functional sites
Understanding the mechanisms of protein function is indispensable for many biological
applications, such as protein engineering and drug design. However, experimental …
applications, such as protein engineering and drug design. However, experimental …
Revealing unexplored sequence-function space using sequence similarity networks
The rapidly expanding number of protein sequences found in public databases can improve
our understanding of how protein functions evolve. However, our current knowledge of …
our understanding of how protein functions evolve. However, our current knowledge of …
Multi-omics data integration analysis identifies the spliceosome as a key regulator of DNA double-strand break repair
DNA repair by homologous recombination (HR) is critical for the maintenance of genome
stability. Germline and somatic mutations in HR genes have been associated with an …
stability. Germline and somatic mutations in HR genes have been associated with an …
Exploring the sequence, function, and evolutionary space of protein superfamilies using sequence similarity networks and phylogenetic reconstructions
Integrative computational methods can facilitate the discovery of new protein functions and
enzymatic reactions by enabling the observation and investigation of complex sequence …
enzymatic reactions by enabling the observation and investigation of complex sequence …
General strategies for using amino acid sequence data to guide biochemical investigation of protein function
EN Kennedy, CA Foster, SA Barr… - Biochemical Society …, 2022 - portlandpress.com
The rapid increase of '-omics' data warrants the reconsideration of experimental strategies to
investigate general protein function. Studying individual members of a protein family is likely …
investigate general protein function. Studying individual members of a protein family is likely …
New computational approaches to understanding molecular protein function
JS Fetrow, PC Babbitt - PLoS Computational Biology, 2018 - journals.plos.org
Function is like beauty—its definition lies in the eye of the beholder or, in this case, the
researcher. At the broadest level, we define organismal function—the function that the …
researcher. At the broadest level, we define organismal function—the function that the …
An atlas of peroxiredoxins created using an active site profile-based approach to functionally relevant clustering of proteins
AF Harper, JB Leuthaeuser, PC Babbitt… - PLoS Computational …, 2017 - journals.plos.org
Peroxiredoxins (Prxs or Prdxs) are a large protein superfamily of antioxidant enzymes that
rapidly detoxify damaging peroxides and/or affect signal transduction and, thus, have roles …
rapidly detoxify damaging peroxides and/or affect signal transduction and, thus, have roles …
PASV: Automatic protein partitioning and validation using conserved residues
Background Increasingly, researchers use protein-coding genes from targeted PCR
amplification or direct metagenomic sequencing in community and population ecology …
amplification or direct metagenomic sequencing in community and population ecology …
Isofunctional clustering and conformational analysis of the arsenate reductase superfamily reveals nine distinct clusters
Arsenate reductase (ArsC) is a superfamily of enzymes that reduce arsenate. Due to active
site similarities, some ArsC can function as low-molecular weight protein tyrosine …
site similarities, some ArsC can function as low-molecular weight protein tyrosine …