From integrative structural biology to cell biology

FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices

(2021) Eitan Lerner et al.   eLife

Integrative/Hybrid Modeling Approaches for Studying Biomolecules

(2020) Ashutosh Srivastava et al.   JOURNAL OF MOLECULAR BIOLOGY

An in-silico human cell model reveals the influence of spatial organization on RNA splicing

(2020) Zhaleh Ghaemi et al.   PLoS Computational Biology

A Multi-Scale Approach to Modeling E. coli Chemotaxis

(2020) Eran Agmon et al.   Entropy

In-cell architecture of the nuclear pore and snapshots of its turnover

(2020) Matteo Allegretti et al.   NATURE

Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry

(2020) Alexander Leitner et al.   STRUCTURE

Using Integrative Modeling Platform to compute, validate, and archive a model of a protein complex structure

(2020) Daniel J. Saltzberg et al.   PROTEIN SCIENCE

Integrative Structure Modeling: Overview and Assessment

(2019) Merav Braitbard et al.   Annual Review of Biochemistry

Glutamine Side Chain 13C═18O as a Nonperturbative IR Probe of Amyloid Fibril Hydration and Assembly

(2019) Haifan Wu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Principles for Integrative Structural Biology Studies

(2019) Michael P. Rout et al.   CELL

Integrative methods in structural biology

(2019) Rob Kaptein et al.   JOURNAL OF BIOMOLECULAR NMR

Archiving and disseminating integrative structure models

(2019) Brinda Vallat et al.   JOURNAL OF BIOMOLECULAR NMR

SSEThread: Integrative threading of the DNA-PKcs sequence based on data from chemical cross-linking and hydrogen deuterium exchange

(2019) Daniel J. Saltzberg et al.   PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY

Integrative Approaches in Structural Biology: A More Complete Picture from the Combination of Individual Techniques

(2019) Linda Cerofolini et al.   Biomolecules

Integrative Modelling of Biomolecular Complexes

(2019) P.I. Koukos et al.   JOURNAL OF MOLECULAR BIOLOGY

Critical assessment of methods of protein structure prediction (CASP)—Round XIII

(2019) Andriy Kryshtafovych et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Federating Structural Models and Data: Outcomes from A Workshop on Archiving Integrative Structures

(2019) Helen M. Berman et al.   STRUCTURE

The Convergence of Markov Chain Monte Carlo Methods: From the Metropolis Method to Hamiltonian Monte Carlo

(2018) Michael Betancourt   ANNALEN DER PHYSIK

Opportunities and Challenges in Building a Spatiotemporal Multi-scale Model of the Human Pancreatic β Cell

(2018) Jitin Singla et al.   CELL

Producing genome structure populations with the dynamic and automated PGS software

(2018) Nan Hua et al.   Nature Protocols

Anticipating innovations in structural biology

(2018) Helen M. Berman et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Development of a Prototype System for Archiving Integrative/Hybrid Structure Models of Biological Macromolecules

(2018) Brinda Vallat et al.   STRUCTURE

In situ architecture of the algal nuclear pore complex

(2018) Shyamal Mosalaganti et al.   Nature Communications

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

Protein Data Bank: the single global archive for 3D macromolecular structure data

(2018) et al.   NUCLEIC ACIDS RESEARCH

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

Optimizing model representation for integrative structure determination of macromolecular assemblies

(2018) Shruthi Viswanath et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How Structural Biologists and the Protein Data Bank Contributed to Recent FDA New Drug Approvals

(2018) John D. Westbrook et al.   STRUCTURE

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

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

MolProbity: More and better reference data for improved all-atom structure validation

(2017) Christopher J. Williams 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

Computational Model Predicts the Effects of Targeting Cellular Metabolism in Pancreatic Cancer

(2017) Mahua Roy et al.   Frontiers in Physiology

2017 publication guidelines for structural modelling of small-angle scattering data from biomolecules in solution: an update

(2017) Jill Trewhella et al.   Acta Crystallographica Section D-Structural Biology

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

(2016) Javier Fernandez-Martinez et al.   CELL

Quantitative FRET studies and integrative modeling unravel the structure and dynamics of biomolecular systems

(2016) Mykola Dimura et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Toward Community Standards and Software for Whole-Cell Modeling

(2016) Dagmar Waltemath et al.   IEEE TRANSACTIONS ON BIOMEDICAL ENGINEERING

Simple rules for passive diffusion through the nuclear pore complex

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

The HADDOCK2.2 Web Server: User-Friendly Integrative Modeling of Biomolecular Complexes

(2016) G.C.P. van Zundert et al.   JOURNAL OF MOLECULAR BIOLOGY

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

Molecular architecture of the inner ring scaffold of the human nuclear pore complex

(2016) J. Kosinski et al.   SCIENCE

Insights into HIV-1 proviral transcription from integrative structure and dynamics of the Tat:AFF4:P-TEFb:TAR complex

(2016) Ursula Schulze-Gahmen et al.   eLife

Prion Protein—Antibody Complexes Characterized by Chromatography-Coupled Small-Angle X-Ray Scattering

(2015) Lester Carter et al.   BIOPHYSICAL JOURNAL

Topological Models of Heteromeric Protein Assemblies from Mass Spectrometry: Application to the Yeast eIF3:eIF5 Complex

(2015) Argyris Politis et al.   CHEMISTRY & BIOLOGY

Hybrid methods for macromolecular structure determination: experiment with expectations

(2015) Gunnar F Schröder   CURRENT OPINION IN STRUCTURAL BIOLOGY

Bayesian ensemble refinement by replica simulations and reweighting

(2015) Gerhard Hummer et al.   JOURNAL OF CHEMICAL PHYSICS

A strategy for dissecting the architectures of native macromolecular assemblies

(2015) Yi Shi et al.   NATURE METHODS

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

BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

(2015) Zachary A. King et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Andrej Sali et al.   STRUCTURE

Structure and gating of the nuclear pore complex

(2015) Matthias Eibauer et al.   Nature Communications

Molecular architecture of the yeast Mediator complex

(2015) Philip J Robinson et al.   eLife

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

Structure of a modular polyketide synthase

(2014) Somnath Dutta et al.   NATURE

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

Optimized atomic statistical potentials: assessment of protein interfaces and loops

(2013) Guang Qiang Dong et al.   BIOINFORMATICS

PDBStat: a universal restraint converter and restraint analysis software package for protein NMR

(2013) Roberto Tejero et al.   JOURNAL OF BIOMOLECULAR NMR

Highly Scalable and Memory Efficient Ultra-Coarse-Grained Molecular Dynamics Simulations

(2013) John. M. A. Grime et al.   Journal of Chemical Theory and Computation

Energy barriers and driving forces in tRNA translocation through the ribosome

(2013) Lars V Bock et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Integrative Structural Biology

(2013) A. B. Ward et al.   SCIENCE

Report of the wwPDB Small-Angle Scattering Task Force: Data Requirements for Biomolecular Modeling and the PDB

(2013) Jill Trewhella et al.   STRUCTURE

Recommendations of the wwPDB NMR Validation Task Force

(2013) Gaetano T. Montelione et al.   STRUCTURE

A method for integrative structure determination of protein-protein complexes

(2012) Dina Schneidman-Duhovny et al.   BIOINFORMATICS

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

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

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

BCL::Fold - De Novo Prediction of Complex and Large Protein Topologies by Assembly of Secondary Structure Elements

(2012) Mert Karakaş et al.   PLoS One

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

Outcome of the First Electron Microscopy Validation Task Force Meeting

(2012) Richard Henderson et al.   STRUCTURE

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

(2012) Daniel Russel et al.   PLOS BIOLOGY

UCSF Chimera, MODELLER, and IMP: An integrated modeling system

(2011) Zheng Yang et al.   JOURNAL OF STRUCTURAL BIOLOGY

Structure of the C-terminal domain of Saccharomyces cerevisiae Nup133, a component of the nuclear pore complex

(2011) Parthasarathy Sampathkumar et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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

(2011) Randy J. Read et al.   STRUCTURE

Single-molecule fluorescence spectroscopy maps the folding landscape of a large protein

(2011) Menahem Pirchi et al.   Nature Communications

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

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

Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm

(2010) Sean R. McGuffee et al.   PLoS Computational Biology

Structure and flexibility within proteins as identified through small angle X-ray scattering

(2009) M. Pelikan et al.   GENERAL PHYSIOLOGY AND BIOPHYSICS

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

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

Outcome of a Workshop on Applications of Protein Models in Biomedical Research

(2009) Torsten Schwede et al.   STRUCTURE

Integrating Diverse Data for Structure Determination of Macromolecular Assemblies

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

Macromolecular Modeling with Rosetta

(2008) Rhiju Das et al.   Annual Review of Biochemistry