An integrative computational model for large-scale identification of metalloproteins in microbial genomes: a focus on iron–sulfur cluster proteins

Regularization Paths for Generalized Linear Models via Coordinate Descent

(2015) Jerome Friedman et al.   Journal of Statistical Software

Active-site models for complexes of quinolinate synthase with substrates and intermediates

(2013) Erika V. Soriano et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

The catalytic mechanism for aerobic formation of methane by bacteria

(2013) Siddhesh S. Kamat et al.   NATURE

Two Fe-S clusters catalyze sulfur insertion by radical-SAM methylthiotransferases

(2013) Farhad Forouhar et al.   Nature Chemical Biology

Biochemical Similarities and Differences between the Catalytic [4Fe-4S] Cluster Containing Fumarases FumA and FumB from Escherichia coli

(2013) Barbara M. A. van Vugt-Lussenburg et al.   PLoS One

Protein fractionation and detection for metalloproteomics: challenges and approaches

(2012) James P. Barnett et al.   ANALYTICAL AND BIOANALYTICAL CHEMISTRY

Studies of Inhibitor Binding to the [4Fe-4S] Cluster of Quinolinate Synthase

(2012) Alice Chan et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Biosynthesis of F0, Precursor of the F420 Cofactor, Requires a Unique Two Radical-SAM Domain Enzyme and Tyrosine as Substrate

(2012) Laure Decamps et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Metals in biology: defining metalloproteomes

(2011) Steven M Yannone et al.   CURRENT OPINION IN BIOTECHNOLOGY

Reannotation of the genome sequence of Clostridium difficile strain 630

(2011) M. Monot et al.   JOURNAL OF MEDICAL MICROBIOLOGY

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

SufD and SufC ATPase Activity Are Required for Iron Acquisition during in Vivo Fe-S Cluster Formation on SufB

(2010) Avneesh Saini et al.   BIOCHEMISTRY

From array-based hybridization of Helicobacter pylori isolates to the complete genome sequence of an isolate associated with MALT lymphoma

(2010) Jean-Michel Thiberge et al.   BMC GENOMICS

Metalloproteomics: forward and reverse approaches in metalloprotein structural and functional characterization

(2010) Wuxian Shi et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

S-Adenosylmethionine-dependent radical-based modification of biological macromolecules

(2010) Mohamed Atta et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Iron-Sulfur (Fe-S) Cluster Assembly

(2010) Silke Wollers et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Microbial metalloproteomes are largely uncharacterized

(2010) Aleksandar Cvetkovic et al.   NATURE

Development of Tools and Database for Analysis of Metal Binding Sites in Protein

(2010) Bhusan Kumar Kuntal et al.   PROTEIN AND PEPTIDE LETTERS

Metalloproteomes: A Bioinformatic Approach

(2009) Claudia Andreini et al.   ACCOUNTS OF CHEMICAL RESEARCH

Pyrroloquinoline Quinone Biogenesis: Demonstration That PqqE fromKlebsiella pneumoniaeIs a RadicalS-Adenosyl-l-methionine Enzyme

(2009) Stephen R. Wecksler et al.   BIOCHEMISTRY

Genome sequence ofVibrio splendidus: an abundant planctonic marine species with a large genotypic diversity

(2009) Frédérique Le Roux et al.   ENVIRONMENTAL MICROBIOLOGY

Identification and Characterization of a Novel Member of the Radical AdoMet Enzyme Superfamily and Implications for the Biosynthesis of the Hmd Hydrogenase Active Site Cofactor

(2009) S. E. McGlynn et al.   JOURNAL OF BACTERIOLOGY

Elastic-net regularization in learning theory

(2009) Christine De Mol et al.   JOURNAL OF COMPLEXITY

Bioinformatics in bioinorganic chemistry

(2009) Ivano Bertini et al.   Metallomics

Function and biogenesis of iron–sulphur proteins

(2009) Roland Lill   NATURE

Metalloproteins and metal sensing

(2009) Kevin J. Waldron et al.   NATURE

The Universal Protein Resource (UniProt) in 2010

(2009)   NUCLEIC ACIDS RESEARCH

Fast and accurate automatic structure prediction with HHpred

(2009) Andrea Hildebrand et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

NeMeSys: a biological resource for narrowing the gap between sequence and function in the human pathogen Neisseria meningitidis

(2009) Christophe Rusniok et al.   GENOME BIOLOGY

Iron–sulfur cluster biosynthesis in bacteria: Mechanisms of cluster assembly and transfer

(2008) Marc Fontecave et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

The iscS gene deficiency affects the expression of pyrimidine metabolism genes

(2008) Hisaaki Mihara et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Prediction of zinc-binding sites in proteins from sequence

(2008) Nanjiang Shu et al.   BIOINFORMATICS

MetalDetector: a web server for predicting metal-binding sites and disulfide bridges in proteins from sequence

(2008) M. Lippi et al.   BIOINFORMATICS

Metallomics and metalloproteomics

(2008) W. Shi et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

The Radical SAM Superfamily

(2008) Perry A. Frey et al.   CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY

Reconstitution of ThiC in thiamine pyrimidine biosynthesis expands the radical SAM superfamily

(2008) Abhishek Chatterjee et al.   Nature Chemical Biology

How do bacterial cells ensure that metalloproteins get the correct metal?

(2008) Kevin J. Waldron et al.   NATURE REVIEWS MICROBIOLOGY

SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny

(2008) Derek Wilson et al.   NUCLEIC ACIDS RESEARCH

HAMAP: a database of completely sequenced microbial proteome sets and manually curated microbial protein families in UniProtKB/Swiss-Prot

(2008) T. Lima et al.   NUCLEIC ACIDS RESEARCH

InterPro: the integrative protein signature database

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

Comparative Analysis of Acinetobacters: Three Genomes for Three Lifestyles

(2008) David Vallenet et al.   PLoS One

A newly discovered role for iron-sulfur clusters

(2008) P. C. Dos Santos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA