Nucleotide binding database NBDB – a collection of sequence motifs with specific protein-ligand interactions

Expanded microbial genome coverage and improved protein family annotation in the COG database

(2014) Michael Y. Galperin et al.   NUCLEIC ACIDS RESEARCH

Bacterial second messengers, cGMP and c-di-GMP, in a quest for regulatory dominance

(2013) Mark Gomelsky et al.   EMBO JOURNAL

Exploring the evolution of protein function in Archaea

(2012) Alexander Goncearenco et al.   BMC EVOLUTIONARY BIOLOGY

Computational reconstruction of primordial prototypes of elementary functional loops in modern proteins

(2011) Alexander Goncearenco et al.   BIOINFORMATICS

Divergence and Convergence in Enzyme Evolution

(2011) Michael Y. Galperin et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

MACiE: exploring the diversity of biochemical reactions

(2011) Gemma L. Holliday et al.   NUCLEIC ACIDS RESEARCH

Cofactor-binding sites in proteins of deviating sequence: Comparative analysis and clustering in torsion angle, cavity, and fold space

(2011) Björn Stegemann et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The CoFactor database: organic cofactors in enzyme catalysis

(2010) Julia D. Fischer et al.   BIOINFORMATICS

Prototypes of elementary functional loops unravel evolutionary connections between protein functions

(2010) Alexander Goncearenco et al.   BIOINFORMATICS

The Structures and Physicochemical Properties of Organic Cofactors in Biocatalysis

(2010) Julia D. Fischer et al.   JOURNAL OF MOLECULAR BIOLOGY

Modular architecture of nucleotide-binding pockets

(2010) Pier Federico Gherardini et al.   NUCLEIC ACIDS RESEARCH

Origins and evolution of modern biochemistry: insights from genomes and molecular structure

(2008) Gustavo Caetano-Anolles   Frontiers in Bioscience-Landmark

The origin and evolution of modern metabolism

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

InterPro: the integrative protein signature database

(2008) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments

(2008) L. Xie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA