Renal function in newly diagnosed multiple myeloma—a demographic study of 1353 patients

LM Knudsen, E Hippe, M Hjorth… - European journal of …, 1994 - Wiley Online Library
This study describes the occurrence of renal failure among 1353 newly diagnosed cases of
multiple myeloma. Renal function was evaluated by serum creatinine concentration in 1353 …

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 …

Contrastive learning on protein embeddings enlightens midnight zone

M Heinzinger, M Littmann, I Sillitoe… - NAR genomics and …, 2022 - academic.oup.com
Experimental structures are leveraged through multiple sequence alignments, or more
generally through homology-based inference (HBI), facilitating the transfer of information …

OB-fold domains: a snapshot of the evolution of sequence, structure and function

V Arcus - Current opinion in structural biology, 2002 - Elsevier
The OB-fold is found in all three kingdoms and is well represented in both sequence and
structural databases. The OB-fold is a five-stranded closed β barrel and the majority of OB …

Widespread position-specific conservation of synonymous rare codons within coding sequences

JL Chaney, A Steele, R Carmichael… - PLoS computational …, 2017 - journals.plos.org
Synonymous rare codons are considered to be sub-optimal for gene expression because
they are translated more slowly than common codons. Yet surprisingly, many protein coding …

The origin, evolution and structure of the protein world

G Caetano-Anollés, M Wang… - Biochemical …, 2009 - portlandpress.com
Contemporary protein architectures can be regarded as molecular fossils, historical imprints
that mark important milestones in the history of life. Whereas sequences change at a …

Gene Loss Rather Than Gene Gain Is Associated with a Host Jump from Monocots to Dicots in the Smut Fungus Melanopsichium pennsylvanicum

R Sharma, B Mishra, F Runge… - Genome biology and …, 2014 - academic.oup.com
Smut fungi are well-suited to investigate the ecology and evolution of plant pathogens, as
they are strictly biotrophic, yet cultivable on media. Here we report the genome sequence of …

Emergence of diverse biochemical activities in evolutionarily conserved structural scaffolds of proteins

V Anantharaman, L Aravind, EV Koonin - Current opinion in chemical …, 2003 - Elsevier
Comparative analysis of numerous protein structures that have become available in the past
few years, combined with genome comparison, has yielded new insights into the evolution …

Extending CATH: increasing coverage of the protein structure universe and linking structure with function

AL Cuff, I Sillitoe, T Lewis, AB Clegg… - Nucleic acids …, 2010 - academic.oup.com
Abstract CATH version 3.3 (class, architecture, topology, homology) contains 128 688
domains, 2386 homologous superfamilies and 1233 fold groups, and reflects a major focus …

SoyDB: a knowledge database of soybean transcription factors

Z Wang, M Libault, T Joshi, B Valliyodan, HT Nguyen… - BMC Plant …, 2010 - Springer
Background Transcription factors play the crucial rule of regulating gene expression and
influence almost all biological processes. Systematically identifying and annotating …