The role of structural bioinformatics resources in the era of integrative structural biology

Vivaldi: Visualization and validation of biomacromolecular NMR structures from the PDB

(2013) Pieter M. S. Hendrickx et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Notes of a protein crystallographer: on the high-resolution structure of the PDB growth rate

(2012) Cele Abad-Zapatero   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Implementing an X-ray validation pipeline for the Protein Data Bank

(2012) Swanand Gore et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

PDB_REDO: constructive validation, more than just looking for errors

(2012) Robbie P. Joosten et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

On the need for an international effort to capture, share and use crystallization screening data

(2012) Janet Newman et al.   Acta Crystallographica Section F-Structural Biology and Crystallization Communications

The 2010 cryo-em modeling challenge

(2012) Steven J. Ludtke et al.   BIOPOLYMERS

A new understanding of the decoding principle on the ribosome

(2012) Natalia Demeshkina et al.   NATURE

Structural basis of highly conserved ribosome recycling in eukaryotes and archaea

(2012) Thomas Becker et al.   NATURE

The 2.8 Å crystal structure of the dynein motor domain

(2012) Takahide Kon et al.   NATURE

OMERO: flexible, model-driven data management for experimental biology

(2012) Chris Allan et al.   NATURE METHODS

Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy

(2012) Raju Tomer et al.   NATURE METHODS

Data management challenges in three-dimensional EM

(2012) Ardan Patwardhan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

SIFTS: Structure Integration with Function, Taxonomy and Sequences resource

(2012) Sameer Velankar et al.   NUCLEIC ACIDS RESEARCH

Decoding in the Absence of a Codon by tmRNA and SmpB in the Ribosome

(2012) C. Neubauer et al.   SCIENCE

Blind Testing of Routine, Fully Automated Determination of Protein Structures from NMR Data

(2012) Antonio Rosato et al.   STRUCTURE

Outcome of the First Electron Microscopy Validation Task Force Meeting

(2012) Richard Henderson et al.   STRUCTURE

The Protein Data Bank at 40: Reflecting on the Past to Prepare for the Future

(2012) Helen M. Berman et al.   STRUCTURE

The Protein Data Bank in Europe (PDBe): bringing structure to biology

(2011) Sameer Velankar et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Macromolecular complexes in crystals and solutions

(2011) Evgeny Krissinel   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Overview of theCCP4 suite and current developments

(2011) Martyn D. Winn et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

The ribosome as a molecular machine: the mechanism of tRNA–mRNA movement in translocation

(2011) Marina V. Rodnina et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Rotation and structure of FoF1-ATP synthase

(2011) D. Okuno et al.   JOURNAL OF BIOCHEMISTRY

Electron tomography of plant thylakoid membranes

(2011) B. Daum et al.   JOURNAL OF EXPERIMENTAL BOTANY

How mutations in tRNA distant from the anticodon affect the fidelity of decoding

(2011) T Martin Schmeing et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format

(2011) A. R. Kinjo et al.   NUCLEIC ACIDS RESEARCH

PDBe: Protein Data Bank in Europe

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

Reorganizing the protein space at the Universal Protein Resource (UniProt)

(2011)   NUCLEIC ACIDS RESEARCH

NRG-CING: integrated validation reports of remediated experimental biomolecular NMR data and coordinates in wwPDB

(2011) J. F. Doreleijers et al.   NUCLEIC ACIDS RESEARCH

The IntAct molecular interaction database in 2012

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

Database resources of the National Center for Biotechnology Information

(2011) E. W. Sayers et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2012

(2011) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

The Pfam protein families database

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

Macromolecular organization of ATP synthase and complex I in whole mitochondria

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

A New Generation of Crystallographic Validation Tools for the Protein Data Bank

(2011) Randy J. Read et al.   STRUCTURE

PHENIX: a comprehensive Python-based system for macromolecular structure solution

(2010) Paul D. Adams et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Imaging cellular architecture with X-rays

(2010) Carolyn A Larabell et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Straightforward and complete deposition of NMR data to the PDBe

(2010) Christopher J. Penkett et al.   JOURNAL OF BIOMOLECULAR NMR

The Three-Dimensional Organization of Polyribosomes in Intact Human Cells

(2010) Florian Brandt et al.   MOLECULAR CELL

Safeguarding the integrity of protein archive

(2010) Helen M. Berman et al.   NATURE

PDBe: Protein Data Bank in Europe

(2010) S. Velankar et al.   NUCLEIC ACIDS RESEARCH

Extending CATH: increasing coverage of the protein structure universe and linking structure with function

(2010) A. L. Cuff et al.   NUCLEIC ACIDS RESEARCH

EMDataBank.org: unified data resource for CryoEM

(2010) C. L. Lawson et al.   NUCLEIC ACIDS RESEARCH

Reactome: a database of reactions, pathways and biological processes

(2010) D. Croft et al.   NUCLEIC ACIDS RESEARCH

MolProbity: all-atom structure validation for macromolecular crystallography

(2009) Vincent B. Chen et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Cryo-electron tomography in biology and medicine

(2009) Roman I. Koning et al.   ANNALS OF ANATOMY-ANATOMISCHER ANZEIGER

The Native 3D Organization of Bacterial Polysomes

(2009) Florian Brandt et al.   CELL

The European Bioinformatics Institute's data resources

(2009) Catherine Brooksbank et al.   NUCLEIC ACIDS RESEARCH

OLDERADO: On-line database of ensemble representatives and domains

(2009) Lawrence A. Kelley et al.   PROTEIN SCIENCE

Single-particle reconstruction of biological macromolecules in electron microscopy – 30 years

(2009) Joachim Frank   QUARTERLY REVIEWS OF BIOPHYSICS

Ion-Abrasion Scanning Electron Microscopy Reveals Surface-Connected Tubular Conduits in HIV-Infected Macrophages

(2009) Adam E. Bennett et al.   PLoS Pathogens

BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions

(2008) John L. Markley et al.   JOURNAL OF BIOMOLECULAR NMR

Molecular architecture of native HIV-1 gp120 trimers

(2008) Jun Liu et al.   NATURE

Reactome knowledgebase of human biological pathways and processes

(2008) L. Matthews et al.   NUCLEIC ACIDS RESEARCH

InterPro: the integrative protein signature database

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