Archiving and disseminating integrative structure models

Principles for Integrative Structural Biology Studies

(2019) Michael P. Rout et al.   CELL

Integrative Structure Determination of Protein Complexes by Inferred Structural Equivalence

(2018) Ignacia Echeverria et al.   BIOPHYSICAL JOURNAL

Prediction of enzymatic pathways by integrative pathway mapping

(2018) Sara Calhoun et al.   eLife

Integrative structure and functional anatomy of a nuclear pore complex

(2018) Seung Joong Kim et al.   NATURE

Architecture of Pol II(G) and molecular mechanism of transcription regulation by Gdown1

(2018) Miki Jishage et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Rev7 dimerization is important for assembly and function of the Rev1/Polζ translesion synthesis complex

(2018) Alessandro A. Rizzo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural dynamics of the E6AP/UBE3A-E6-p53 enzyme-substrate complex

(2018) Carolin Sailer et al.   Nature Communications

The proteasome-interacting Ecm29 protein disassembles the 26S proteasome in response to oxidative stress

(2017) Xiaorong Wang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Molecular Details Underlying Dynamic Structures and Regulation of the Human 26S Proteasome

(2017) Xiaorong Wang et al.   MOLECULAR & CELLULAR PROTEOMICS

The molecular architecture of the yeast spindle pole body core determined by Bayesian integrative modeling

(2017) Shruthi Viswanath et al.   MOLECULAR BIOLOGY OF THE CELL

Integrative structure modeling with the Integrative Modeling Platform

(2017) Benjamin Webb et al.   PROTEIN SCIENCE

Xplor-NIH for molecular structure determination from NMR and other data sources

(2017) Charles D. Schwieters et al.   PROTEIN SCIENCE

UCSF ChimeraX: Meeting modern challenges in visualization and analysis

(2017) Thomas D. Goddard et al.   PROTEIN SCIENCE

OneDep: Unified wwPDB System for Deposition, Biocuration, and Validation of Macromolecular Structures in the PDB Archive

(2017) Jasmine Y. Young et al.   STRUCTURE

Molecular Architecture of the Major Membrane Ring Component of the Nuclear Pore Complex

(2017) Paula Upla et al.   STRUCTURE

Validation of Structures in the Protein Data Bank

(2017) Swanand Gore et al.   STRUCTURE

PDB-Dev: a Prototype System for Depositing Integrative/Hybrid Structural Models

(2017) Stephen K. Burley et al.   STRUCTURE

Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors

(2017) François Serra et al.   PLoS Computational Biology

Structure and Function of the Nuclear Pore Complex Cytoplasmic mRNA Export Platform

(2016) Javier Fernandez-Martinez et al.   CELL

Simple rules for passive diffusion through the nuclear pore complex

(2016) Benjamin L. Timney et al.   JOURNAL OF CELL BIOLOGY

A Residue-Resolved Bayesian Approach to Quantitative Interpretation of Hydrogen–Deuterium Exchange from Mass Spectrometry: Application to Characterizing Protein–Ligand Interactions

(2016) Daniel J. Saltzberg et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structure of Complement C3(H2O) Revealed By Quantitative Cross-Linking/Mass Spectrometry And Modeling

(2016) Zhuo A. Chen et al.   MOLECULAR & CELLULAR PROTEOMICS

FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles

(2016) Dina Schneidman-Duhovny et al.   NUCLEIC ACIDS RESEARCH

Slide-and-exchange mechanism for rapid and selective transport through the nuclear pore complex

(2016) Barak Raveh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population-based 3D genome structure analysis reveals driving forces in spatial genome organization

(2016) Harianto Tjong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extension of the sasCIF format and its applications for data processing and deposition

(2016) Michael Kachala et al.   JOURNAL OF APPLIED CRYSTALLOGRAPHY

Serum Albumin Domain Structures in Human Blood Serum by Mass Spectrometry and Computational Biology

(2015) Adam Belsom et al.   MOLECULAR & CELLULAR PROTEOMICS

Architecture of the Human and Yeast General Transcription and DNA Repair Factor TFIIH

(2015) Jie Luo et al.   MOLECULAR CELL

A strategy for dissecting the architectures of native macromolecular assemblies

(2015) Yi Shi et al.   NATURE METHODS

NMR Exchange Format: a unified and open standard for representation of NMR restraint data

(2015) Aleksandras Gutmanas et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Assessing the limits of restraint-based 3D modeling of genomes and genomic domains

(2015) Marie Trussart et al.   NUCLEIC ACIDS RESEARCH

EMDataBank unified data resource for 3DEM

(2015) Catherine L. Lawson et al.   NUCLEIC ACIDS RESEARCH

Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop

(2015) Andrej Sali et al.   STRUCTURE

Integrative Modeling of Biomolecular Complexes: HADDOCKing with Cryo-Electron Microscopy Data

(2015) Gydo C.P. van Zundert et al.   STRUCTURE

NMR Exchange Format: a unified and open standard for representation of NMR restraint data

(2015) Aleksandras Gutmanas et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Molecular architecture of the yeast Mediator complex

(2015) Philip J Robinson et al.   eLife

Molecular Architecture of the 40S⋅eIF1⋅eIF3 Translation Initiation Complex

(2014) Jan P. Erzberger et al.   CELL

Molecular Architecture of Photoreceptor Phosphodiesterase Elucidated by Chemical Cross-Linking and Integrative Modeling

(2014) Xiaohui Zeng-Elmore et al.   JOURNAL OF MOLECULAR BIOLOGY

Determining Protein Complex Structures Based on a Bayesian Model ofin VivoFörster Resonance Energy Transfer (FRET) Data

(2014) Massimiliano Bonomi et al.   MOLECULAR & CELLULAR PROTEOMICS

Integrative Structure–Function Mapping of the Nucleoporin Nup133 Suggests a Conserved Mechanism for Membrane Anchoring of the Nuclear Pore Complex

(2014) Seung Joong Kim et al.   MOLECULAR & CELLULAR PROTEOMICS

Molecular Architecture and Function of the SEA Complex, a Modulator of the TORC1 Pathway

(2014) Romain Algret et al.   MOLECULAR & CELLULAR PROTEOMICS

Structural Characterization by Cross-linking Reveals the Detailed Architecture of a Coatomer-related Heptameric Module from the Nuclear Pore Complex

(2014) Yi Shi et al.   MOLECULAR & CELLULAR PROTEOMICS

SASBDB, a repository for biological small-angle scattering data

(2014) Erica Valentini et al.   NUCLEIC ACIDS RESEARCH

Cys-Scanning Disulfide Crosslinking and Bayesian Modeling Probe the Transmembrane Signaling Mechanism of the Histidine Kinase, PhoQ

(2014) Kathleen S. Molnar et al.   STRUCTURE

Accurate SAXS Profile Computation and its Assessment by Contrast Variation Experiments

(2013) Dina Schneidman-Duhovny et al.   BIOPHYSICAL JOURNAL

Integrative Structural Biology

(2013) A. B. Ward et al.   SCIENCE

Recommendations of the wwPDB NMR Validation Task Force

(2013) Gaetano T. Montelione et al.   STRUCTURE

SAXS Merge: an automated statistical method to merge SAXS profiles using Gaussian processes

(2013) Yannick G. Spill et al.   JOURNAL OF SYNCHROTRON RADIATION

A method for integrative structure determination of protein-protein complexes

(2012) Dina Schneidman-Duhovny et al.   BIOINFORMATICS

Structure–function mapping of a heptameric module in the nuclear pore complex

(2012) Javier Fernandez-Martinez et al.   JOURNAL OF CELL BIOLOGY

Atomic model of the type III secretion system needle

(2012) Antoine Loquet et al.   NATURE

A toolkit and benchmark study for FRET-restrained high-precision structural modeling

(2012) Stanislav Kalinin et al.   NATURE METHODS

Assembly of macromolecular complexes by satisfaction of spatial restraints from electron microscopy images

(2012) J. Velazquez-Muriel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular architecture of the 26S proteasome holocomplex determined by an integrative approach

(2012) K. Lasker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies

(2012) Daniel Russel et al.   PLOS BIOLOGY

Statistical Potential for Modeling and Ranking of Protein–Ligand Interactions

(2011) Hao Fan et al.   Journal of Chemical Information and Modeling

An Efficient Protocol for NMR-Spectroscopy-Based Structure Determination of Protein Complexes in Solution

(2010) Bernd Simon et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Macromolecular docking restrained by a small angle X-ray scattering profile

(2010) Dina Schneidman-Duhovny et al.   JOURNAL OF STRUCTURAL BIOLOGY

Integrative Structure Modeling of Macromolecular Assemblies from Proteomics Data

(2010) Keren Lasker et al.   MOLECULAR & CELLULAR PROTEOMICS

The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules

(2010) Davide Baù et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

FoXS: a web server for rapid computation and fitting of SAXS profiles

(2010) D. Schneidman-Duhovny et al.   NUCLEIC ACIDS RESEARCH

Determining macromolecular assembly structures by molecular docking and fitting into an electron density map

(2010) Keren Lasker et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The structural dynamics of macromolecular processes

(2009) Daniel Russel et al.   CURRENT OPINION IN CELL BIOLOGY

The NMR restraints grid at BMRB for 5,266 protein and nucleic acid PDB entries

(2009) Jurgen F. Doreleijers et al.   JOURNAL OF BIOMOLECULAR NMR

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Inferential Optimization for Simultaneous Fitting of Multiple Components into a CryoEM Map of Their Assembly

(2009) Keren Lasker et al.   JOURNAL OF MOLECULAR BIOLOGY

Comprehensive Molecular Structure of the Eukaryotic Ribosome

(2009) Derek J. Taylor et al.   STRUCTURE

Molecular Electron Microscopy: State of the Art and Current Challenges

(2008) Henning Stahlberg et al.   ACS Chemical Biology

Integrating Diverse Data for Structure Determination of Macromolecular Assemblies

(2008) Frank Alber et al.   Annual Review of Biochemistry

Cryo-electron tomography of cells: connecting structure and function

(2008) Vladan Lučić et al.   HISTOCHEMISTRY AND CELL BIOLOGY

Subnanometer-resolution electron cryomicroscopy-based domain models for the cytoplasmic region of skeletal muscle RyR channel

(2008) I. I. Serysheva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiple Conformations of E. coli Hsp90 in Solution: Insights into the Conformational Dynamics of Hsp90

(2008) Kristin A. Krukenberg et al.   STRUCTURE

Crystallographic Conformers of Actin in a Biologically Active Bundle of Filaments

(2007) Yao Cong et al.   JOURNAL OF MOLECULAR BIOLOGY