Systems biology of the structural proteome

A streamlined ribosome profiling protocol for the characterization of microorganisms

(2015) Haythem Latif et al.   BIOTECHNIQUES

Model-driven discovery of underground metabolic functions inEscherichia coli

(2015) Gabriela I. Guzmán et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantifying Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation of Cellular Resources

(2014) Gene-Wei Li et al.   CELL

Network-level architecture and the evolutionary potential of underground metabolism

(2014) R. A. Notebaart et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predicting microbial growth

(2014) J. Monk et al.   SCIENCE

Metabolic Resource Allocation in Individual Microbes Determines Ecosystem Interactions and Spatial Dynamics

(2014) William R. Harcombe et al.   Cell Reports

Global Patterns of Protein Domain Gain and Loss in Superkingdoms

(2014) Arshan Nasir et al.   PLoS Computational Biology

Engineered thermostable fungal Cel6A and Cel7A cellobiohydrolases hydrolyze cellulose efficiently at elevated temperatures

(2013) Indira Wu et al.   BIOTECHNOLOGY AND BIOENGINEERING

Antibacterial mechanisms identified through structural systems pharmacology

(2013) Roger L Chang et al.   BMC Systems Biology

COBRApy: COnstraints-Based Reconstruction and Analysis for Python

(2013) Ali Ebrahim et al.   BMC Systems Biology

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

(2013) Jaina Mistry et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Structural Systems Biology Evaluation of Metabolic Thermotolerance in Escherichia coli

(2013) R. L. Chang et al.   SCIENCE

Ab Initio structure prediction for Escherichia coli: towards genome-wide protein structure modeling and fold assignment

(2013) Dong Xu et al.   Scientific Reports

Directed Evolution of Xylose Isomerase for Improved Xylose Catabolism and Fermentation in the Yeast Saccharomyces cerevisiae

(2012) Sun-Mi Lee et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions

(2012) Jeffrey D Orth et al.   BMC Systems Biology

Engineering specialized metabolic pathways—is there a room for enzyme improvements?

(2012) Arren Bar-Even et al.   CURRENT OPINION IN BIOTECHNOLOGY

Classification of Ligand Molecules in PDB with Fast Heuristic Graph Match Algorithm COMPLIG

(2012) Mihoko Saito et al.   JOURNAL OF MOLECULAR BIOLOGY

Structure-based prediction of protein–protein interactions on a genome-wide scale

(2012) Qiangfeng Cliff Zhang et al.   NATURE

Three-dimensional reconstruction of protein networks provides insight into human genetic disease

(2012) Xiujuan Wang et al.   NATURE BIOTECHNOLOGY

The RCSB Protein Data Bank: new resources for research and education

(2012) Peter W. Rose et al.   NUCLEIC ACIDS RESEARCH

Network Context and Selection in the Evolution to Enzyme Specificity

(2012) H. Nam et al.   SCIENCE

In silico method for modelling metabolism and gene product expression at genome scale

(2012) Joshua A. Lerman et al.   Nature Communications

A Structural Systems Biology Approach for Quantifying the Systemic Consequences of Missense Mutations in Proteins

(2012) Tammy M. K. Cheng et al.   PLoS Computational Biology

Quantitative, High-Resolution Proteomics for Data-Driven Systems Biology

(2011) Jürgen Cox et al.   Annual Review of Biochemistry

A comprehensive protein-centric ID mapping service for molecular data integration

(2011) H. Huang et al.   BIOINFORMATICS

ProDy: Protein Dynamics Inferred from Theory and Experiments

(2011) A. Bakan et al.   BIOINFORMATICS

How Do Thermophilic Proteins and Proteomes Withstand High Temperature?

(2011) Lucas Sawle et al.   BIOPHYSICAL JOURNAL

A computational exploration of bacterial metabolic diversity identifying metabolic interactions and growth-efficient strain communities

(2011) Eleftheria Tzamali et al.   BMC Systems Biology

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011

(2011) J. D. Orth et al.   Molecular Systems Biology

Physical limits of cells and proteomes

(2011) K. A. Dill et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pre-calculated protein structure alignments at the RCSB PDB website: Fig. 1.

(2010) Andreas Prlić et al.   BIOINFORMATICS

Dynamic flux balance modeling of microbial co-cultures for efficient batch fermentation of glucose and xylose mixtures

(2010) Timothy J. Hanly et al.   BIOTECHNOLOGY AND BIOENGINEERING

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions

(2010) Jan Schellenberger et al.   BMC BIOINFORMATICS

Emergent cooperation in microbial metabolism

(2010) Edwin H Wintermute et al.   Molecular Systems Biology

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

I-TASSER: a unified platform for automated protein structure and function prediction

(2010) Ambrish Roy et al.   Nature Protocols

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

History of biological metal utilization inferred through phylogenomic analysis of protein structures

(2010) C. L. Dupont et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Environments that Induce Synthetic Microbial Ecosystems

(2010) Niels Klitgord et al.   PLoS Computational Biology

Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model

(2010) Roger L. Chang et al.   PLoS Computational Biology

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Metabolic investigation of host/pathogen interaction using MS2-infected Escherichia coli

(2009) Rishi Jain et al.   BMC Systems Biology

Predicting melting temperature directly from protein sequences

(2009) Tienhsiung Ku et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Biocharts: a visual formalism for complex biological systems

(2009) H. Kugler et al.   Journal of the Royal Society Interface

The Pfam protein families database

(2009) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Three-Dimensional Structural View of the Central Metabolic Network of Thermotoga maritima

(2009) Y. Zhang et al.   SCIENCE

Proteome Organization in a Genome-Reduced Bacterium

(2009) S. Kuhner et al.   SCIENCE

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization

(2009) Ines Thiele et al.   PLoS Computational Biology

Probing the functional tolerance of the b subunit of Escherichia coli ATP synthase for sequence manipulation through a chimera approach

(2008) Yumin Bi et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

The origin and evolution of modern metabolism

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

Reconstruction of biochemical networks in microorganisms

(2008) Adam M. Feist et al.   NATURE REVIEWS MICROBIOLOGY

BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009

(2008) A. Chang et al.   NUCLEIC ACIDS RESEARCH