Prediction and characterization of enzymatic activities guided by sequence similarity and genome neighborhood networks

Prediction and Biochemical Demonstration of a Catabolic Pathway for the Osmoprotectant Proline Betaine

(2014) R. Kumar et al.   mBio

Identification and characterization of trans -3-hydroxy-l -proline dehydratase and Δ1 -pyrroline-2-carboxylate reductase involved in trans -3-hydroxy-l -proline metabolism of bacteria

(2014) Seiya Watanabe et al.   FEBS Open Bio

Polysaccharides utilization in human gut bacterium Bacteroides thetaiotaomicron: comparative genomics reconstruction of metabolic and regulatory networks

(2013) Dmitry A Ravcheev et al.   BMC GENOMICS

Discovery of new enzymes and metabolic pathways by using structure and genome context

(2013) Suwen Zhao et al.   NATURE

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

Transcriptional regulation of the carbohydrate utilization network in Thermotoga maritima

(2013) Dmitry A. Rodionov et al.   Frontiers in Microbiology

Pythoscape: a framework for generation of large protein similarity networks

(2012) Alan E. Barber et al.   BIOINFORMATICS

Identification of a Humantrans-3-Hydroxy-l-proline Dehydratase, the First Characterized Member of a Novel Family of Proline Racemase-like Enzymes

(2012) Wouter F. Visser et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Identification and Characterization of d-Hydroxyproline Dehydrogenase and Δ1-Pyrroline-4-hydroxy-2-carboxylate Deaminase Involved in Novel l-Hydroxyproline Metabolism of Bacteria

(2012) Seiya Watanabe et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

iMOSFLM: a new graphical interface for diffraction-image processing withMOSFLM

(2011) T. Geoff G. Battye et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Mammalian forebrain ketimine reductase identified as μ-crystallin; potential regulation by thyroid hormones

(2011) André Hallen et al.   JOURNAL OF NEUROCHEMISTRY

InterPro in 2011: new developments in the family and domain prediction database

(2011) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

IMG: the integrated microbial genomes database and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2011) R. Caspi et al.   NUCLEIC ACIDS RESEARCH

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

Determination of 4-hydroxyproline-2-epimerase activity by capillary electrophoresis: A stereoselective platform for inhibitor screening of amino acid isomerases

(2010) Jennilee M. A. Gavina et al.   ELECTROPHORESIS

Catalyzing Racemizations in the Absence of a Cofactor: The Reaction Mechanism in Proline Racemase

(2009) Amir Rubinstein et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

MicrobesOnline: an integrated portal for comparative and functional genomics

(2009) P. S. Dehal et al.   NUCLEIC ACIDS RESEARCH

Using Sequence Similarity Networks for Visualization of Relationships Across Diverse Protein Superfamilies

(2009) Holly J. Atkinson et al.   PLoS One

Arginine racemization by coupled catabolic and anabolic dehydrogenases

(2009) Congran Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cloning and expression of a tauropine dehydrogenase from the marine sponge Suberites domuncula

(2008) Bruna Plese et al.   MARINE BIOLOGY