Protein families and their evolution—a structural perspective

CA Orengo, JM Thornton - Annu. Rev. Biochem., 2005 - annualreviews.org
▪ Abstract We can now assign about two thirds of the sequences from completed genomes to
as few as 1400 domain families for which structures are known and thus more ancient …

Pfam 10 years on: 10 000 families and still growing

SJ Sammut, RD Finn, A Bateman - Briefings in bioinformatics, 2008 - academic.oup.com
Classifications of proteins into groups of related sequences are in some respects like a
periodic table for biology, allowing us to understand the underlying molecular biology of any …

Protein superfamily evolution and the last universal common ancestor (LUCA)

JAG Ranea, A Sillero, JM Thornton… - Journal of Molecular …, 2006 - Springer
By exploiting three-dimensional structure comparison, which is more sensitive than
conventional sequence-based methods for detecting remote homology, we have identified a …

Evolution of protein superfamilies and bacterial genome size

JAG Ranea, DWA Buchan, JM Thornton… - Journal of molecular …, 2004 - Elsevier
We present the structural annotation of 56 different bacterial species based on the
assignment of genes to 816 evolutionary superfamilies in the CATH domain structure …

The evolutionary history of protein domains viewed by species phylogeny

S Yang, PE Bourne - PloS one, 2009 - journals.plos.org
Background Protein structural domains are evolutionary units whose relationships can be
detected over long evolutionary distances. The evolutionary history of protein domains …

Progress towards mapping the universe of protein folds

A Grant, D Lee, C Orengo - Genome biology, 2004 - Springer
Although the precise aims differ between the various international structural genomics
initiatives currently aiming to illuminate the universe of protein folds, many selectively target …

Understanding the molecular machinery of genetics through 3D structures

RA Laskowski, JM Thornton - Nature Reviews Genetics, 2008 - nature.com
Detailed knowledge of the three-dimensional structures of biological molecules has had an
enormous impact on all areas of biological science, including genetics, as structure can …

Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches

JM Chandonia, SE Brenner - PROTEINS: Structure, Function …, 2005 - Wiley Online Library
Structural genomics is an international effort to determine the three‐dimensional shapes of
all important biological macromolecules, with a primary focus on proteins. Target proteins …

Universal sharing patterns in proteomes and evolution of protein fold architecture and life

G Caetano-Anolles, D Caetano-Anolles - Journal of molecular evolution, 2005 - Springer
Protein evolution is imprinted in both the sequence and the structure of evolutionary building
blocks known as protein domains. These domains share a common ancestry and can be …

CRTC1/MAML2 gain-of-function interactions with MYC create a gene signature predictive of cancers with CREB–MYC involvement

AL Amelio, M Fallahi, FX Schaub… - Proceedings of the …, 2014 - National Acad Sciences
Chimeric oncoproteins created by chromosomal translocations are among the most common
genetic mutations associated with tumorigenesis. Malignant mucoepidermoid salivary gland …