AI-based structure prediction empowers integrative structural analysis of human nuclear pores

Cryo-EM structure of the nuclear ring from Xenopus laevis nuclear pore complex

(2022) Gaoxingyu Huang et al.   CELL RESEARCH

8 Å structure of the outer rings of the Xenopus laevis nuclear pore complex obtained by cryo-EM and AI

(2022) Linhua Tai et al.   Protein & Cell

Co-translational assembly orchestrates competing biogenesis pathways

(2022) Maximilian Seidel et al.   Nature Communications

Improved prediction of protein-protein interactions using AlphaFold2

(2022) Patrick Bryant et al.   Nature Communications

Architecture of the cytoplasmic face of the nuclear pore

(2022) Christopher J. Bley et al.   SCIENCE

Architecture of the linker-scaffold in the nuclear pore

(2022) Stefan Petrovic et al.   SCIENCE

Cone-shaped HIV-1 capsids are transported through intact nuclear pores

(2021) Vojtech Zila et al.   CELL

Integrative structural biology in the era of accurate structure prediction

(2021) Gal Masarati et al.   JOURNAL OF MOLECULAR BIOLOGY

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Highly accurate protein structure prediction for the human proteome

(2021) Kathryn Tunyasuvunakool et al.   NATURE

High‐accuracy protein structure prediction in CASP14

(2021) Joana Pereira et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Accurate prediction of protein structures and interactions using a three-track neural network

(2021) Minkyung Baek et al.   SCIENCE

Assessment of protein–protein interfaces in cryo-EM derived assemblies

(2021) Sony Malhotra et al.   Nature Communications

The cellular environment shapes the nuclear pore complex architecture

(2021) Anthony P. Schuller et al.   NATURE

Integrative structural modeling of macromolecular complexes using Assembline

(2021) Vasileios Rantos et al.   Nature Protocols

Applying and improving AlphaFold at CASP14

(2021) John Jumper et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Assessing the accuracy of contact and distance predictions in CASP14

(2021) Victoria Ruiz‐Serra et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Nuclear pores dilate and constrict in cellulo

(2021) Christian E. Zimmerli et al.   SCIENCE

Computed structures of core eukaryotic protein complexes

(2021) Ian R. Humphreys et al.   SCIENCE

Structure of the cytoplasmic ring of the Xenopus laevis nuclear pore complex by cryo-electron microscopy single particle analysis

(2020) Gaoxingyu Huang et al.   CELL RESEARCH

Molecular architecture of the luminal ring of the Xenopus laevis nuclear pore complex

(2020) Yanqing Zhang et al.   CELL RESEARCH

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

(2020) Matteo Allegretti et al.   NATURE

Simulation of FUS Protein Condensates with an Adapted Coarse-Grained Model

(2020) Zakarya Benayad et al.   Journal of Chemical Theory and Computation

The Structure of the Nuclear Pore Complex (An Update)

(2019) Daniel H. Lin et al.   Annual Review of Biochemistry

Structure and Assembly of the Nuclear Pore Complex

(2019) Bernhard Hampoelz et al.   Annual Review of Biophysics

The Dynamic Nature of the Nuclear Envelope

(2018) Paola De Magistris et al.   CURRENT BIOLOGY

Molecular dynamics simulations of carbon nanotube porins in lipid bilayers

(2018) Martin Vögele et al.   FARADAY DISCUSSIONS

Structural and functional analysis of mRNA export regulation by the nuclear pore complex

(2018) Daniel H. Lin et al.   Nature Communications

In situ architecture of the algal nuclear pore complex

(2018) Shyamal Mosalaganti et al.   Nature Communications

Molecular dynamics simulations of carbon nanotube porins in lipid bilayers

(2018) Martin Vögele et al.   FARADAY DISCUSSIONS

Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION

(2018) Takanori Nakane et al.   eLife

ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps

(2018) Tristan Ian Croll   Acta Crystallographica Section D-Structural Biology

Real-space refinement in PHENIX for cryo-EM and crystallography

(2018) Pavel V. Afonine et al.   Acta Crystallographica Section D-Structural Biology

From the resolution revolution to evolution: structural insights into the evolutionary relationships between vesicle coats and the nuclear pore

(2018) Martin Beck et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Integrative structure and functional anatomy of a nuclear pore complex

(2018) Seung Joong Kim et al.   NATURE

BUMPy: A Model-Independent Tool for Constructing Lipid Bilayers of Varying Curvature and Composition

(2018) Kevin J. Boyd et al.   Journal of Chemical Theory and Computation

A self-inhibitory interaction within Nup155 and membrane binding are required for nuclear pore complex formation

(2017) Paola De Magistris et al.   JOURNAL OF CELL SCIENCE

Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4 Å

(2017) Beata Turoňová et al.   JOURNAL OF STRUCTURAL BIOLOGY

Automated tilt series alignment and tomographic reconstruction in IMOD

(2017) David N. Mastronarde et al.   JOURNAL OF STRUCTURAL BIOLOGY

Implementation of a cryo-electron tomography tilt-scheme optimized for high resolution subtomogram averaging

(2017) Wim J.H. Hagen et al.   JOURNAL OF STRUCTURAL BIOLOGY

Landscape of nuclear transport receptor cargo specificity

(2017) Marie‐Therese Mackmull et al.   Molecular Systems Biology

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

(2017) Ali Punjani et al.   NATURE METHODS

Postmitotic nuclear pore assembly proceeds by radial dilation of small membrane openings

(2017) Shotaro Otsuka et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Integrative structure modeling with the Integrative Modeling Platform

(2017) Benjamin Webb et al.   PROTEIN SCIENCE

UCSF ChimeraX: Meeting modern challenges in visualization and analysis

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

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

(2017) Paula Upla et al.   STRUCTURE

Postmitotic nuclear pore assembly proceeds by radial dilation of small membrane openings

(2017) Shotaro Otsuka et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The flexibility and dynamics of the tubules in the endoplasmic reticulum

(2017) Pantelis Georgiades et al.   Scientific Reports

Excessive aggregation of membrane proteins in the Martini model

(2017) Matti Javanainen et al.   PLoS One

Architecture of the yeast Elongator complex

(2016) Maria I Dauden et al.   EMBO REPORTS

The Multiple Faces of Disordered Nucleoporins

(2016) Edward A. Lemke   JOURNAL OF MOLECULAR BIOLOGY

The nuclear pore complex: understanding its function through structural insight

(2016) Martin Beck et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Architecture of the symmetric core of the nuclear pore

(2016) D. H. Lin et al.   SCIENCE

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

(2016) J. Kosinski et al.   SCIENCE

Visualizing the molecular sociology at the HeLa cell nuclear periphery

(2016) J. Mahamid et al.   SCIENCE

Interactome Mapping Reveals the Evolutionary History of the Nuclear Pore Complex

(2016) Samson O. Obado et al.   PLOS BIOLOGY

Nup153 Recruits the Nup107-160 Complex to the Inner Nuclear Membrane for Interphasic Nuclear Pore Complex Assembly

(2015) Benjamin Vollmer et al.   DEVELOPMENTAL CELL

Nuclear pore proteins and the control of genome functions

(2015) Arkaitz Ibarra et al.   GENES & DEVELOPMENT

Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations

(2015) Tsjerk A. Wassenaar et al.   Journal of Chemical Theory and Computation

CTFFIND4: Fast and accurate defocus estimation from electron micrographs

(2015) Alexis Rohou et al.   JOURNAL OF STRUCTURAL BIOLOGY

In situ structural analysis of the human nuclear pore complex

(2015) Alexander von Appen et al.   NATURE

Linker Nups connect the nuclear pore complex inner ring with the outer ring and transport channel

(2015) Jessica Fischer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Atomic structure of the Y complex of the nuclear pore

(2015) Kotaro Kelley et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Architecture of the fungal nuclear pore inner ring complex

(2015) T. Stuwe et al.   SCIENCE

Linker Nups connect the nuclear pore complex inner ring with the outer ring and transport channel

(2015) Jessica Fischer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Atomic structure of the Y complex of the nuclear pore

(2015) Kotaro Kelley et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests

(2013) Valerio Mariani et al.   BIOINFORMATICS

Integrated Structural Analysis of the Human Nuclear Pore Complex Scaffold

(2013) Khanh Huy Bui et al.   CELL

Cell type-specific nuclear pores: a case in point for context-dependent stoichiometry of molecular machines

(2013) A. Ori et al.   Molecular Systems Biology

Dimerization and direct membrane interaction of Nup53 contribute to nuclear pore complex assembly

(2012) Benjamin Vollmer et al.   EMBO JOURNAL

Dynamo: A flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments

(2012) Daniel Castaño-Díez et al.   JOURNAL OF STRUCTURAL BIOLOGY

RELION: Implementation of a Bayesian approach to cryo-EM structure determination

(2012) Sjors H.W. Scheres   JOURNAL OF STRUCTURAL BIOLOGY

Molecular basis for Nup37 and ELY5/ELYS recruitment to the nuclear pore complex

(2012) S. Bilokapic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structural evolution of the membrane-coating module of the nuclear pore complex

(2012) X. Liu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Human Nuclear Pore Complex as Revealed by Cryo-Electron Tomography

(2012) Tal Maimon et al.   STRUCTURE

Membrane-Elasticity Model of Coatless Vesicle Budding Induced by ESCRT Complexes

(2012) Bartosz Różycki et al.   PLoS Computational Biology

Overview of theCCP4 suite and current developments

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

Insight into Structure and Assembly of the Nuclear Pore Complex by Utilizing the Genome of a Eukaryotic Thermophile

(2011) Stefan Amlacher et al.   CELL

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

(2011) Naveen Michaud-Agrawal et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Structural and functional analysis of an essential nucleoporin heterotrimer on the cytoplasmic face of the nuclear pore complex

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

Features and development ofCoot

(2010) P. Emsley et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

iAlign: a method for the structural comparison of protein–protein interfaces

(2010) Mu Gao et al.   BIOINFORMATICS

The nuclear pore complex: bridging nuclear transport and gene regulation

(2010) Caterina Strambio-De-Castillia et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The nuclear pore complex protein ALADIN is anchored via NDC1 but not via POM121 and GP210 in the nuclear envelope

(2009) Barbara Kind et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

The transmembrane nucleoporin NDC1 is required for targeting of ALADIN to nuclear pore complexes

(2009) Yusuke Yamazumi et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Tissue-specific expression and subcellular localization of ALADIN, the absence of which causes human triple A syndrome

(2009) A-Ri Cho et al.   EXPERIMENTAL AND MOLECULAR MEDICINE

Role of the Ndc1 interaction network in yeast nuclear pore complex assembly and maintenance

(2009) Evgeny Onischenko et al.   JOURNAL OF CELL BIOLOGY

Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition

(2009) Xavier Periole et al.   Journal of Chemical Theory and Computation

Molecular architecture of the Nup84–Nup145C–Sec13 edge element in the nuclear pore complex lattice

(2009) Stephen G Brohawn et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

MM-align: a quick algorithm for aligning multiple-chain protein complex structures using iterative dynamic programming

(2009) Srayanta Mukherjee et al.   NUCLEIC ACIDS RESEARCH

Structure of a trimeric nucleoporin complex reveals alternate oligomerization states

(2009) V. Nagy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

fdrtool: a versatile R package for estimating local and tail area-based false discovery rates

(2008) K. Strimmer   BIOINFORMATICS

On the Octagonal Structure of the Nuclear Pore Complex: Insights from Coarse-Grained Models

(2008) Christopher Wolf et al.   BIOPHYSICAL JOURNAL

The MARTINI Coarse-Grained Force Field: Extension to Proteins

(2008) Luca Monticelli et al.   Journal of Chemical Theory and Computation

A Fence-like Coat for the Nuclear Pore Membrane

(2008) Erik W. Debler et al.   MOLECULAR CELL

Structural Basis of the Nic96 Subcomplex Organization in the Nuclear Pore Channel

(2008) Nils Schrader et al.   MOLECULAR CELL