Conformational and oligomeric states of SPOP from small-angle X-ray scattering and molecular dynamics simulations

Conformational ensembles of intrinsically disordered proteins and flexible multidomain proteins

(2022) F. Emil Thomasen et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Improving Martini 3 for Disordered and Multidomain Proteins

(2022) F. Emil Thomasen et al.   Journal of Chemical Theory and Computation

REGALS: a general method to deconvolve X-ray scattering data from evolving mixtures

(2021) Steve P. Meisburger et al.   IUCrJ

Martini 3: a general purpose force field for coarse-grained molecular dynamics

(2021) Paulo C. T. Souza et al.   NATURE METHODS

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Structure and Energetics of GTP- and GDP-Tubulin Isodesmic Self-Association

(2021) Asaf Shemesh et al.   ACS Chemical Biology

Refining conformational ensembles of flexible proteins against small-angle x-ray scattering data

(2021) Francesco Pesce et al.   BIOPHYSICAL JOURNAL

Accurate model of liquid–liquid phase behavior of intrinsically disordered proteins from optimization of single-chain properties

(2021) Giulio Tesei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Author Correction: SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution

(2020) Andreas Haahr Larsen et al.   PLoS Computational Biology

Array programming with NumPy

(2020) Charles R. Harris et al.   NATURE

UCSF ChimeraX : Structure visualization for researchers, educators, and developers

(2020) Eric F. Pettersen et al.   PROTEIN SCIENCE

The ubiquitin ligase adaptor SPOP in cancer

(2019) Matthew J. Cuneo et al.   FEBS Journal

HOOMD-blue: A Python package for high-performance molecular dynamics and hard particle Monte Carlo simulations

(2019) Joshua A. Anderson et al.   COMPUTATIONAL MATERIALS SCIENCE

Protein Network Structure Enables Switching between Liquid and Gel States

(2019) Jeremy D. Schmit et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Cancer Mutations of the Tumor Suppressor SPOP Disrupt the Formation of Active, Phase-Separated Compartments

(2018) Jill J. Bouchard et al.   MOLECULAR CELL

Opposing effects of cancer-type-specific SPOP mutants on BET protein degradation and sensitivity to BET inhibitors

(2017) Hana Janouskova et al.   NATURE MEDICINE

Structural Analysis of Multi-component Amyloid Systems by Chemometric SAXS Data Decomposition

(2017) Fátima Herranz-Trillo et al.   STRUCTURE

Pepsi-SAXS: an adaptive method for rapid and accurate computation of small-angle X-ray scattering profiles

(2017) Sergei Grudinin et al.   Acta Crystallographica Section D-Structural Biology

Higher‐order oligomerization promotes localization of SPOP to liquid nuclear speckles

(2016) Melissa R Marzahn et al.   EMBO JOURNAL

Multiple Weak Linear Motifs Enhance Recruitment and Processivity in SPOP-Mediated Substrate Ubiquitination

(2016) Wendy K. Pierce et al.   JOURNAL OF MOLECULAR BIOLOGY

SPOP-containing complex regulates SETD2 stability and H3K36me3-coupled alternative splicing

(2016) Kun Zhu et al.   NUCLEIC ACIDS RESEARCH

Genomic Correlates of Immune-Cell Infiltrates in Colorectal Carcinoma

(2016) Marios Giannakis et al.   Cell Reports

Structure, Dynamics, Assembly, and Evolution of Protein Complexes

(2015) Joseph A. Marsh et al.   Annual Review of Biochemistry

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

(2015) Robert T. McGibbon et al.   BIOPHYSICAL JOURNAL

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

Ubiquitylome analysis identifies dysregulation of effector substrates in SPOP-mutant prostate cancer

(2014) J.-P. P. Theurillat et al.   SCIENCE

Destruction of Full-Length Androgen Receptor by Wild-Type SPOP, but Not Prostate-Cancer-Associated Mutants

(2014) Jian An et al.   Cell Reports

Structural basis of high-order oligomerization of the cullin-3 adaptor SPOP

(2013) Laura K. van Geersdaele et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models

(2013) Tsjerk A. Wassenaar et al.   Journal of Chemical Theory and Computation

Prostate cancer-associated mutations in speckle-type POZ protein (SPOP) regulate steroid receptor coactivator 3 protein turnover

(2013) C. Geng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mutational and expressional analyses ofSPOP, a candidate tumor suppressor gene, in prostate, gastric and colorectal cancers

(2012) Min S. Kim et al.   APMIS

Exome sequencing of serous endometrial tumors identifies recurrent somatic mutations in chromatin-remodeling and ubiquitin ligase complex genes

(2012) Matthieu Le Gallo et al.   NATURE GENETICS

Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma

(2012) Michael Krauthammer et al.   NATURE GENETICS

Adaptor Protein Self-Assembly Drives the Control of a Cullin-RING Ubiquitin Ligase

(2012) Wesley J. Errington et al.   STRUCTURE

The Evolution of Multimeric Protein Assemblages

(2011) M. Lynch   MOLECULAR BIOLOGY AND EVOLUTION

Tumor-suppressor role for the SPOP ubiquitin ligase in signal-dependent proteolysis of the oncogenic co-activator SRC-3/AIB1

(2011) C Li et al.   ONCOGENE

Structures of SPOP-Substrate Complexes: Insights into Molecular Architectures of BTB-Cul3 Ubiquitin Ligases

(2009) Min Zhuang et al.   MOLECULAR CELL

Multiple Ser/Thr-rich degrons mediate the degradation of Ci/Gli by the Cul3-HIB/SPOP E3 ubiquitin ligase

(2009) Qing Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cullin-RING ubiquitin ligases: global regulation and activation cycles

(2008) Dimple R Bosu et al.   Cell Division