Conformational buffering underlies functional selection in intrinsically disordered protein regions

Host diversification is concurrent with linear motif evolution in a Mastadenovirus hub protein

(2022) Juliana Glavina et al.   JOURNAL OF MOLECULAR BIOLOGY

ColabFold: making protein folding accessible to all

(2022) Milot Mirdita et al.   NATURE METHODS

Quantification of Conformational Entropy Unravels Effect of Disordered Flanking Region in Coupled Folding and Binding

(2021) Frederik Friis Theisen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Valence and patterning of aromatic residues determine the phase behavior of prion-like domains

(2020) Erik W. Martin et al.   SCIENCE

Dissecting the Functional Contributions of the Intrinsically Disordered C-terminal Tail of Bacillus subtilis FtsZ

(2020) Megan C. Cohan et al.   JOURNAL OF MOLECULAR BIOLOGY

Allostery of multidomain proteins with disordered linkers

(2020) Qiaojing Huang et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Intrinsically Disordered Regions Direct Transcription Factor In Vivo Binding Specificity

(2020) Sagie Brodsky et al.   MOLECULAR CELL

Intrinsically disordered linkers control tethered kinases via effective concentration

(2020) Mateusz Dyla et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MMseqs2 desktop and local web server app for fast, interactive sequence searches

(2019) M Mirdita et al.   BIOINFORMATICS

Temporal dynamics of adenovirus 5 gene expression in normal human cells

(2019) Leandro Crisostomo et al.   PLoS One

Proteome-wide signatures of function in highly diverged intrinsically disordered regions

(2019) Taraneh Zarin et al.   eLife

Combinatorial diversity of Syk recruitment driven by its multivalent engagement with FcεRIγ

(2019) Timothy Travers et al.   MOLECULAR BIOLOGY OF THE CELL

Interplay of Protein Disorder in Retinoic Acid Receptor Heterodimer and Its Corepressor Regulates Gene Expression

(2019) Tiago N. Cordeiro et al.   STRUCTURE

Effective concentrations enforced by intrinsically disordered linkers are governed by polymer physics

(2019) Charlotte S. Sørensen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

IUPred2A: context-dependent prediction of protein disorder as a function of redox state and protein binding

(2018) Bálint Mészáros et al.   NUCLEIC ACIDS RESEARCH

Short linear motif core and flanking regions modulate retinoblastoma protein binding affinity and specificity

(2018) Nicolás Palopoli et al.   PROTEIN ENGINEERING DESIGN & SELECTION

Hacking the Cell: Network Intrusion and Exploitation by Adenovirus E1A

(2018) Cason R. King et al.   mBio

Interplay between sequence, structure and linear motifs in the adenovirus E1A hub protein

(2018) Juliana Glavina et al.   VIROLOGY

Realistic Ensemble Models of Intrinsically Disordered Proteins Using a Structure-Encoding Coil Database

(2018) Alejandro Estaña et al.   STRUCTURE

Control of transcriptional activity by design of charge patterning in the intrinsically disordered RAM region of the Notch receptor

(2017) Kathryn P. Sherry et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Intrinsically disordered linkers determine the interplay between phase separation and gelation in multivalent proteins

(2017) Tyler S Harmon et al.   eLife

ATSAS 2.8: a comprehensive data analysis suite for small-angle scattering from macromolecular solutions

(2017) D. Franke et al.   JOURNAL OF APPLIED CRYSTALLOGRAPHY

Structural and Dynamic Characterization of the Molecular Hub Early Region 1A (E1A) from Human Adenovirus

(2016) Tomáš Hošek et al.   CHEMISTRY-A EUROPEAN JOURNAL

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

ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules

(2016) Haim Ashkenazy et al.   NUCLEIC ACIDS RESEARCH

Cryptic sequence features within the disordered protein p27Kip1regulate cell cycle signaling

(2016) Rahul K. Das et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping the interactions of adenoviral E1A proteins with the p160 nuclear receptor coactivator binding domain of CBP

(2016) Peter Haberz et al.   PROTEIN SCIENCE

Targeting the Two Oncogenic Functional Sites of the HPV E6 Oncoprotein with a High-Affinity Bivalent Ligand

(2015) Juan Ramirez et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

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

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

Plasticity of an Ultrafast Interaction between Nucleoporins and Nuclear Transport Receptors

(2015) Sigrid Milles et al.   CELL

Convergent evolution and mimicry of protein linear motifs in host–pathogen interactions

(2015) Lucía Beatriz Chemes et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Relating sequence encoded information to form and function of intrinsically disordered proteins

(2015) Rahul K Das et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Intrinsically Disordered C-Terminal Tails of E . coli Single-Stranded DNA Binding Protein Regulate Cooperative Binding to Single-Stranded DNA

(2015) Alexander G. Kozlov et al.   JOURNAL OF MOLECULAR BIOLOGY

Effects of Linker Length and Transient Secondary Structure Elements in the Intrinsically Disordered Notch RAM Region on Notch Signaling

(2015) Kathryn P. Sherry et al.   JOURNAL OF MOLECULAR BIOLOGY

Conformation and Dynamics of the Troponin I C-Terminal Domain: Combining Single-Molecule and Computational Approaches for a Disordered Protein Region

(2015) Lauren Ann Metskas et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Multiple Cross-Species Transmission Events of Human Adenoviruses (HAdV) during Hominine Evolution

(2015) Eileen Hoppe et al.   MOLECULAR BIOLOGY AND EVOLUTION

DNA tumor virus oncogenes antagonize the cGAS-STING DNA-sensing pathway

(2015) L. Lau et al.   SCIENCE

An intrinsically disordered linker plays a critical role in bacterial cell division

(2015) P.J. Buske et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Advanced ensemble modelling of flexible macromolecules using X-ray solution scattering

(2015) Giancarlo Tria et al.   IUCrJ

Versatile sample environments and automation for biological solution X-ray scattering experiments at the P12 beamline (PETRA III, DESY)

(2015) Clement E. Blanchet et al.   JOURNAL OF APPLIED CRYSTALLOGRAPHY

Classification of Intrinsically Disordered Regions and Proteins

(2014) Robin van der Lee et al.   CHEMICAL REVIEWS

A Million Peptide Motifs for the Molecular Biologist

(2014) Peter Tompa et al.   MOLECULAR CELL

Frustration in biomolecules

(2014) Diego U. Ferreiro et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Use of Host-like Peptide Motifs in Viral Proteins Is a Prevalent Strategy in Host-Virus Interactions

(2014) Tzachi Hagai et al.   Cell Reports

Rapid Evolution of Virus Sequences in Intrinsically Disordered Protein Regions

(2014) Leonid Gitlin et al.   PLoS Pathogens

Accurate SAXS Profile Computation and its Assessment by Contrast Variation Experiments

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

Folding of a Cyclin Box

(2013) Lucía B. Chemes et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Modulation of allostery by protein intrinsic disorder

(2013) Allan Chris M. Ferreon et al.   NATURE

Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues

(2013) R. K. Das et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure-based model of allostery predicts coupling between distant sites

(2012) P. Weinkam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A core subunit of Polycomb repressive complex 1 is broadly conserved in function but not primary sequence

(2012) L. Y. Beh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Polymer scaling laws of unfolded and intrinsically disordered proteins quantified with single-molecule spectroscopy

(2012) H. Hofmann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Prediction of Hydrodynamic and Other Solution Properties of Rigid Proteins from Atomic- and Residue-Level Models

(2011) A. Ortega et al.   BIOPHYSICAL JOURNAL

Evolution and disorder

(2011) Celeste J Brown et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Rosetta FlexPepDock web server—high resolution modeling of peptide–protein interactions

(2011) Nir London et al.   NUCLEIC ACIDS RESEARCH

Crystal structure of the unliganded retinoblastoma protein pocket domain

(2011) Eva Rose M. Balog et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Sequence Determinants of Compaction in Intrinsically Disordered Proteins

(2010) Joseph A. Marsh et al.   BIOPHYSICAL JOURNAL

Sequence-Specific Random Coil Chemical Shifts of Intrinsically Disordered Proteins

(2010) Kamil Tamiola et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Net charge per residue modulates conformational ensembles of intrinsically disordered proteins

(2010) A. H. Mao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Charge interactions can dominate the dimensions of intrinsically disordered proteins

(2010) S. Muller-Spath et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How viruses hijack cell regulation

(2010) Norman E. Davey et al.   TRENDS IN BIOCHEMICAL SCIENCES

Jalview Version 2--a multiple sequence alignment editor and analysis workbench

(2009) A. M. Waterhouse et al.   BIOINFORMATICS

Semiflexible chains in confined spaces

(2009) Greg Morrison et al.   PHYSICAL REVIEW E

Structural basis for subversion of cellular control mechanisms by the adenoviral E1A oncoprotein

(2009) J. C. Ferreon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The effects of conformational heterogeneity on the binding of the Notch intracellular domain to effector proteins: a case of biologically tuned disorder

(2008) Angela Bertagna et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

ABSINTH: A new continuum solvation model for simulations of polypeptides in aqueous solutions

(2008) Andreas Vitalis et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Do viral proteins possess unique biophysical features?

(2008) Nobuhiko Tokuriki et al.   TRENDS IN BIOCHEMICAL SCIENCES