Integrative structure modeling with the Integrative Modeling Platform

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

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

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

(2017) Paula Upla et al.   STRUCTURE

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

(2017) Stephen K. Burley et al.   STRUCTURE

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

(2016) Javier Fernandez-Martinez et al.   CELL

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

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

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

(2015) Jie Luo et al.   MOLECULAR CELL

Microtubule nucleation at the centrosome and beyond

(2015) Sabine Petry et al.   NATURE CELL BIOLOGY

A strategy for dissecting the architectures of native macromolecular assemblies

(2015) Yi Shi et al.   NATURE METHODS

Centrosome function and assembly in animal cells

(2015) Paul T. Conduit et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

(2015) Andrej Sali et al.   STRUCTURE

Molecular architecture of the yeast Mediator complex

(2015) Philip J Robinson et al.   eLife

Structured illumination with particle averaging reveals novel roles for yeast centrosome components during duplication

(2015) Shannon Burns et al.   eLife

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

(2014) Jan P. Erzberger et al.   CELL

Uncertainty in integrative structural modeling

(2014) Dina Schneidman-Duhovny et al.   CURRENT OPINION IN STRUCTURAL 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

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

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

Matching Cross-linked Peptide Spectra: Only as Good as the Worse Identification

(2013) Michael J. Trnka et al.   MOLECULAR & CELLULAR PROTEOMICS

Integrative Structural Biology

(2013) A. B. Ward et al.   SCIENCE

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

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

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

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

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

Structure-Function Analysis of the C-terminal Domain of CNM67, a Core Component of theSaccharomyces cerevisiaeSpindle Pole Body

(2011) Vadim A. Klenchin et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Statistical Potential for Modeling and Ranking of Protein–Ligand Interactions

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

Iwr1 Directs RNA Polymerase II Nuclear Import

(2011) Elmar Czeko et al.   MOLECULAR CELL

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

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

Architecture of the RNA polymerase II–TFIIF complex revealed by cross-linking and mass spectrometry

(2010) Zhuo Angel Chen et al.   EMBO JOURNAL

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

Publish your computer code: it is good enough

(2010) Nick Barnes   NATURE

Computational science: ...Error

(2010) Zeeya Merali   NATURE

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

EMDataBank.org: unified data resource for CryoEM

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

Enhanced Sampling in the Well-Tempered Ensemble

(2010) M. Bonomi et al.   PHYSICAL REVIEW LETTERS

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

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

Accessible Reproducible Research

(2010) J. P. Mesirov   SCIENCE

The Nuclear Pore Complex and Nuclear Transport

(2010) S. R. Wente et al.   Cold Spring Harbor Perspectives in Biology

The structural dynamics of macromolecular processes

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

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

Evidence for a Shared Nuclear Pore Complex Architecture That Is Conserved from the Last Common Eukaryotic Ancestor

(2009) Jeffrey A. DeGrasse et al.   MOLECULAR & CELLULAR PROTEOMICS

What recent ribosome structures have revealed about the mechanism of translation

(2009) T. Martin Schmeing et al.   NATURE

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

Multiple Subunit Fitting into a Low-Resolution Density Map of a Macromolecular Complex Using a Gaussian Mixture Model

(2008) Takeshi Kawabata   BIOPHYSICAL JOURNAL

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