MANET 3.0: Hierarchy and modularity in evolving metabolic networks

Mechanism and Catalytic Site Atlas (M-CSA): a database of enzyme reaction mechanisms and active sites

(2017) António J M Ribeiro et al.   NUCLEIC ACIDS RESEARCH

A Dynamic Model for the Evolution of Protein Structure

(2016) Guy Tal et al.   JOURNAL OF MOLECULAR EVOLUTION

BRENDA in 2017: new perspectives and new tools in BRENDA

(2016) Sandra Placzek et al.   NUCLEIC ACIDS RESEARCH

Global Patterns of Protein Domain Gain and Loss in Superkingdoms

(2014) Arshan Nasir et al.   PLoS Computational Biology

PDBsum additions

(2013) Tjaart A. P. de Beer et al.   NUCLEIC ACIDS RESEARCH

Structural Phylogenomics Reveals Gradual Evolutionary Replacement of Abiotic Chemistries by Protein Enzymes in Purine Metabolism

(2013) Kelsey Caetano-Anollés et al.   PLoS One

The evolutionary history of protein fold families and proteomes confirms that the archaeal ancestor is more ancient than the ancestors of other superkingdoms

(2012) Kyung Mo Kim et al.   BMC EVOLUTIONARY BIOLOGY

Giant viruses coexisted with the cellular ancestors and represent a distinct supergroup along with superkingdoms Archaea, Bacteria and Eukarya

(2012) Arshan Nasir et al.   BMC EVOLUTIONARY BIOLOGY

Structural phylogenomics uncovers the early and concurrent origins of cysteine biosynthesis and iron-sulfur proteins

(2012) Hong-Yu Zhang et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Ribosomal History Reveals Origins of Modern Protein Synthesis

(2012) Ajith Harish et al.   PLoS One

The Enzymatic and Metabolic Capabilities of Early Life

(2012) Aaron David Goldman et al.   PLoS One

Protein Domain Structure Uncovers the Origin of Aerobic Metabolism and the Rise of Planetary Oxygen

(2012) Kyung Mo Kim et al.   STRUCTURE

Biphasic patterns of diversification and the emergence of modules

(2012) Jay Mittenthal et al.   Frontiers in Genetics

The Phylogenomic Roots of Modern Biochemistry: Origins of Proteins, Cofactors and Protein Biosynthesis

(2011) Gustavo Caetano-Anollés et al.   JOURNAL OF MOLECULAR EVOLUTION

The NCBI Taxonomy database

(2011) S. Federhen   NUCLEIC ACIDS RESEARCH

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Annotation of Protein Domains Reveals Remarkable Conservation in the Functional Make up of Proteomes Across Superkingdoms

(2011) Arshan Nasir et al.   Genes

The evolution and functional repertoire of translation proteins following the origin of life

(2010) Aaron D Goldman et al.   Biology Direct

Proteome Evolution and the Metabolic Origins of Translation and Cellular Life

(2010) Derek Caetano-Anollés et al.   JOURNAL OF MOLECULAR EVOLUTION

A Universal Molecular Clock of Protein Folds and Its Power in Tracing the Early History of Aerobic Metabolism and Planet Oxygenation

(2010) Minglei Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

The origin, evolution and structure of the protein world

(2009) Gustavo Caetano-Anollés et al.   BIOCHEMICAL JOURNAL

The Evolutionary Mechanics of Domain Organization in Proteomes and the Rise of Modularity in the Protein World

(2009) Minglei Wang et al.   STRUCTURE

The conservation and evolutionary modularity of metabolism

(2009) José M Peregrín-Alvarez et al.   GENOME BIOLOGY

The origin and evolution of modern metabolism

(2008) Gustavo Caetano-Anollés et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Network ‘Small-World-Ness’: A Quantitative Method for Determining Canonical Network Equivalence

(2008) Mark D. Humphries et al.   PLoS One