相关参考文献
注意：仅列出部分参考文献，下载原文获取全部文献信息。Proteome-scale analysis of phase-separated proteins in immunofluorescence images
Chunyu Yu et al.
BRIEFINGS IN BIOINFORMATICS (2021)
Biomolecular Condensates and Cancer
Ann Boija et al.
CANCER CELL (2021)
Machine learning in protein structure prediction
Mohammed AlQuraishi
CURRENT OPINION IN CHEMICAL BIOLOGY (2021)
MobiDB: intrinsically disordered proteins in 2021
Damiano Piovesan et al.
NUCLEIC ACIDS RESEARCH (2021)
Computational resources for identifying and describing proteins driving liquid-liquid phase separation
Rita Pancsa et al.
BRIEFINGS IN BIOINFORMATICS (2021)
Recent Force Field Strategies for Intrinsically Disordered Proteins
Junxi Mu et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2021)
Structural Insights into the Interaction of the Intrinsically Disordered Co-activator TIF2 with Retinoic Acid Receptor Heterodimer (RXR/RAR)
Lucile Senicourt et al.
JOURNAL OF MOLECULAR BIOLOGY (2021)
Biomolecular Condensates and Their Links to Cancer Progression
Danfeng Cai et al.
TRENDS IN BIOCHEMICAL SCIENCES (2021)
Cavin1 intrinsically disordered domains are essential for fuzzy electrostatic interactions and caveola formation
Vikas A. Tillu et al.
NATURE COMMUNICATIONS (2021)
Predicting protein condensate formation using machine learning
Guido van Mierlo et al.
CELL REPORTS (2021)
The genetic landscape for amyloid beta fibril nucleation accurately discriminates familial Alzheimer's disease mutations
Mireia Seuma et al.
ELIFE (2021)
Identifying molecular features that are associated with biological function of intrinsically disordered protein regions
Taraneh Zarin et al.
ELIFE (2021)
In silico prediction of in vitro protein liquid-liquid phase separation experiments outcomes with multi-head neural attention
Daniele Raimondi et al.
BIOINFORMATICS (2021)
Intrachain interaction topology can identify functionally similar intrinsically disordered proteins
Jonathan Huihui et al.
BIOPHYSICAL JOURNAL (2021)
Physics-based computational and theoretical approaches to intrinsically disordered proteins
Joan-Emma Shea et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2021)
A Data-Driven Hydrophobicity Scale for Predicting Liquid-Liquid Phase Separation of Proteins
Thomas Dannenhoffer-Lafage et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2021)
Learning the molecular grammar of protein condensates from sequence determinants and embeddings
Kadi L. Saar et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2021)
Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator
Adrian L. Sanborn et al.
ELIFE (2021)
Refinement of α-Synuclein Ensembles Against SAXS Data: Comparison of Force Fields and Methods
Mustapha Carab Ahmed et al.
FRONTIERS IN MOLECULAR BIOSCIENCES (2021)
On the specificity of protein-protein interactions in the context of disorder
Kaare Teilum et al.
BIOCHEMICAL JOURNAL (2021)
Intrinsically disordered proteins and biomolecular condensates as drug targets
Mateusz Biesaga et al.
CURRENT OPINION IN CHEMICAL BIOLOGY (2021)
Integrative Structural Biology in the Era of Accurate Structure Prediction
Gal Masrati et al.
JOURNAL OF MOLECULAR BIOLOGY (2021)
Learning the protein language: Evolution, structure, and function
Tristan Bepler et al.
CELL SYSTEMS (2021)
Circular dichroism for secondary structure determination of proteins with unfolded domains using a self-organising map algorithm SOMSpec
Adewale Olamoyesan et al.
RSC ADVANCES (2021)
PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins
Tamas Lazar et al.
NUCLEIC ACIDS RESEARCH (2021)
LLPSDB: a database of proteins undergoing liquid-liquid phase separation in vitro
Qian Li et al.
NUCLEIC ACIDS RESEARCH (2020)
PhaSepDB: a database of liquid-liquid phase separation related proteins
Kaiqiang You et al.
NUCLEIC ACIDS RESEARCH (2020)
Physical Principles Underlying the Complex Biology of Intracellular Phase Transitions
Jeong-Mo Choi et al.
Annual Review of Biophysics (2020)
Molecular structure in biomolecular condensates
Ivan Peran et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2020)
Binding without folding - the biomolecular function of disordered polyelectrolyte complexes
Benjamin Schuler et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2020)
Model for disordered proteins with strongly sequence-dependent liquid phase behavior
Antonia Statt et al.
JOURNAL OF CHEMICAL PHYSICS (2020)
Hierarchical Ensembles of Intrinsically Disordered Proteins at Atomic Resolution in Molecular Dynamics Simulations
Lisa M. Pietrek et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)
Maximum Entropy Optimized Force Field for Intrinsically Disordered Proteins
Andrew P. Latham et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)
Improved protein structure prediction using potentials from deep learning
Andrew W. Senior et al.
NATURE (2020)
Biophysical prediction of protein-peptide interactions and signaling networks using machine learning
Joseph M. Cunningham et al.
NATURE METHODS (2020)
Improved protein structure prediction using predicted interresidue orientations
Jianyi Yang et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)
Valence and patterning of aromatic residues determine the phase behavior of prion-like domains
Erik W. Martin et al.
SCIENCE (2020)
Emerging Features of Linear Motif-Binding Hub Proteins
Nathan Jespersen et al.
TRENDS IN BIOCHEMICAL SCIENCES (2020)
Biomolecular Phase Separation: From Molecular Driving Forces to Macroscopic Properties
Gregory L. Dignon et al.
Annual Review of Physical Chemistry (2020)
Deep Dive into Machine Learning Models for Protein Engineering
Yuting Xu et al.
JOURNAL OF CHEMICAL INFORMATION AND MODELING (2020)
Hydropathy Patterning Complements Charge Patterning to Describe Conformational Preferences of Disordered Proteins
Wenwei Zheng et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2020)
Mechanism of Coupled Folding-upon-Binding of an Intrinsically Disordered Protein
Paul Robustelli et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2020)
Combining molecular dynamics simulations with small-angle X-ray and neutron scattering data to study multi-domain proteins in solution
Andreas Haahr Larsen et al.
PLoS Computational Biology (2020)
A High-Throughput Screen for Transcription Activation Domains Reveals Their Sequence Features and Permits Prediction by Deep Learning
Ariel Erijman et al.
MOLECULAR CELL (2020)
Deep mutational scanning reveals the structural basis for α-synuclein activity
Robert W. Newberry et al.
NATURE CHEMICAL BIOLOGY (2020)
Robust Sequence Determinants of α-Synuclein Toxicity in Yeast Implicate Membrane Binding
Robert W. Newberry et al.
ACS CHEMICAL BIOLOGY (2020)
IDRMutPred: predicting disease-associated germline nonsynonymous single nucleotide variants (nsSNVs) in intrinsically disordered regions
Jing-Bo Zhou et al.
BIOINFORMATICS (2020)
New analysis pipeline for high-throughput domain-peptide affinity experiments improves SH2 interaction data
Tom Ronan et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2020)
Machine Learning Force Fields and Coarse-Grained Variables in Molecular Dynamics: Application to Materials and Biological Systems
Paraskevi Gkeka et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)
Protein-Protein Interactions Mediated by Intrinsically Disordered Protein Regions Are Enriched in Missense Mutations
Eric T. C. Wong et al.
BIOMOLECULES (2020)
Interactions by Disorder - A Matter of Context
Katrine Bugge et al.
FRONTIERS IN MOLECULAR BIOSCIENCES (2020)
Predicting Secondary Structure Propensities in IDPs Using Simple Statistics from Three-Residue Fragments
Alejandro Estana et al.
JOURNAL OF MOLECULAR BIOLOGY (2020)
Analytical Theory for Sequence-Specific Binary Fuzzy Complexes of Charged Intrinsically Disordered Proteins
Alan N. Amin et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2020)
Systematic Discovery of Short Linear Motifs Decodes Calcineurin Phosphatase Signaling
Callie P. Wigington et al.
MOLECULAR CELL (2020)
Using deep mutational scanning to benchmark variant effect predictors and identify disease mutations
Benjamin J. Livesey et al.
MOLECULAR SYSTEMS BIOLOGY (2020)
Protein Databases Related to Liquid-Liquid Phase Separation
Qian Li et al.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2020)
Learning peptide recognition rules for alow-specificityprotein
Lucas C. Wheeler et al.
PROTEIN SCIENCE (2020)
ODiNPred: comprehensive prediction of protein order and disorder
Rupashree Dass et al.
SCIENTIFIC REPORTS (2020)
High-Throughput Discovery and Characterization of Human Transcriptional Effectors
Josh Tycko et al.
CELL (2020)
Phase Separation as a Missing Mechanism for Interpretation of Disease Mutations
Brian Tsang et al.
CELL (2020)
Coarse graining molecular dynamics with graph neural networks
Brooke E. Husic et al.
JOURNAL OF CHEMICAL PHYSICS (2020)
Widespread occurrence of the droplet state of proteins in the human proteome
Maarten Hardenberg et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)
A Machine Learning Protocol for Predicting Protein Infrared Spectra
Sheng Ye et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2020)
An Information-Theory-Based Approach for Optimal Model Reduction of Biomolecules
Marco Giulini et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2020)
Deep Learning in Protein Structural Modeling and Design
Wenhao Gao et al.
PATTERNS (2020)
Charge pattern affects the structure and dynamics of polyampholyte condensates
Milan Kumar Hazra et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2020)
DrLLPS: a data resource of liquid-liquid phase separation in eukaryotes
Wanshan Ning et al.
NUCLEIC ACIDS RESEARCH (2020)
Structural Characterization of N-WASP Domain V Using MD Simulations with NMR and SAXS Data
Maud Chan-Yao-Chong et al.
BIOPHYSICAL JOURNAL (2019)
Matter over mind: Liquid phase separation and neurodegeneration
Shana Elbaum-Garfinkle
JOURNAL OF BIOLOGICAL CHEMISTRY (2019)
Biophysical and Mechanistic Models for Disease-Causing Protein Variants
Amelie Stein et al.
TRENDS IN BIOCHEMICAL SCIENCES (2019)
Fitting Corrections to an RNA Force Field Using Experimental Data
Andrea Cesari et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)
Evolution of All-Atom Protein Force Fields to Improve Local and Global Properties
Gul H. Zerze et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2019)
Gain-of-Function Mutations: An Emerging Advantage for Cancer Biology
Yongsheng Li et al.
TRENDS IN BIOCHEMICAL SCIENCES (2019)
End-to-End Differentiable Learning of Protein Structure
Mohammed AlQuraishi
CELL SYSTEMS (2019)
The PCNA interaction motifs revisited: thinking outside the PIP-box
Andreas Prestel et al.
CELLULAR AND MOLECULAR LIFE SCIENCES (2019)
Entropy and Information within Intrinsically Disordered Protein Regions
Iva Pritisanac et al.
ENTROPY (2019)
Deep-learning contact-map guided protein structure prediction in CASP13
Wei Zheng et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2019)
Proteome-wide signatures of function in highly diverged intrinsically disordered regions
Taraneh Zarin et al.
ELIFE (2019)
Bayesian-Maximum-Entropy Reweighting of IDP Ensembles Based on NMR Chemical Shifts
Ramon Crehuet et al.
ENTROPY (2019)
SAXS-Restrained Ensemble Simulations of Intrinsically Disordered Proteins with Commitment to the Principle of Maximum Entropy
Markus R. Hermann et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)
SESCA: Predicting Circular Dichroism Spectra from Protein Molecular Structures
Gabor Nagy et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2019)
Intrinsically disordered proteins and structured proteins with intrinsically disordered regions have different functional roles in the cell
Antonio Deiana et al.
PLOS ONE (2019)
Distance-based protein folding powered by deep learning
Jinbo Xu
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)
Information theoretic measures for quantifying sequence-ensemble relationships of intrinsically disordered proteins
Megan C. Cohan et al.
PROTEIN ENGINEERING DESIGN & SELECTION (2019)
Interplay of Protein Disorder in Retinoic Acid Receptor Heterodimer and Its Corepressor Regulates Gene Expression
Tiago N. Cordeiro et al.
STRUCTURE (2019)
Elucidating the Molecular Determinants of Aβ Aggregation with Deep Mutational Scanning
Vanessa E. Gray et al.
G3-GENES GENOMES GENETICS (2019)
Leveraging New Definitions of the LxVP SLiM To Discover Novel Calcineurin Regulators and Substrates
Brooke L. Brauer et al.
ACS CHEMICAL BIOLOGY (2019)
Unified rational protein engineering with sequence-based deep representation learning
Ethan C. Alley et al.
NATURE METHODS (2019)
Effective concentrations enforced by intrinsically disordered linkers are governed by polymer physics
Charlotte S. Sorensen et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)
Recent developments in deep learning applied to protein structure prediction
Shaun M. Kandathil et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2019)
Critical assessment of methods of protein structure prediction (CASP)-Round XIII
Andriy Kryshtafovych et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2019)
The mutational landscape of a prion-like domain
Benedetta Bolognesi et al.
NATURE COMMUNICATIONS (2019)
Modeling aspects of the language of life through transfer-learning protein sequences
Michael Heinzinger et al.
BMC BIOINFORMATICS (2019)
Friend or foePost-translational modifications as regulators of phase separation and RNP granule dynamics
Mario Hofweber et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2019)
Comparative Exploratory Analysis of Intrinsically Disordered Protein Dynamics Using Machine Learning and Network Analytic Methods
Gianmarc Grazioli et al.
FRONTIERS IN MOLECULAR BIOSCIENCES (2019)
Using Small-Angle Scattering Data and Parametric Machine Learning to Optimize Force Field Parameters for Intrinsically Disordered Proteins
Omar Demerdash et al.
FRONTIERS IN MOLECULAR BIOSCIENCES (2019)
Quality and bias of protein disorder predictors
Jakob T. Nielsen et al.
SCIENTIFIC REPORTS (2019)
A growth hormone receptor SNP promotes lung cancer by impairment of SOCS2-mediated degradation
Y. Chhabra et al.
ONCOGENE (2018)
Machine Learning Methods for X-Ray Scattering Data Analysis from Biomacromolecular Solutions
Daniel Franke et al.
BIOPHYSICAL JOURNAL (2018)
How Hard It Is Seeing What Is in Front of Your Eyes
David S. Eisenberg
CELL (2018)
The Eukaryotic Proteome Is Shaped by E3 Ubiquitin Ligases Targeting C-Terminal Degrons
Itay Koren et al.
CELL (2018)
Phase Separation of FUS Is Suppressed by Its Nuclear Import Receptor and Arginine Methylation
Mario Hofweber et al.
CELL (2018)
A Molecular Grammar Governing the Driving Forces for Phase Separation of Prion-like RNA Binding Proteins
Jie Wang et al.
CELL (2018)
Force field development and simulations of intrinsically disordered proteins
Jing Huang et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2018)
Interpreting solution X-ray scattering data using molecular simulations
Jochen S. Hub
CURRENT OPINION IN STRUCTURAL BIOLOGY (2018)
Learning Effective Molecular Models from Experimental Observables
Justin Chen et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2018)
An Extended Guinier Analysis for Intrinsically Disordered Proteins
Wenwei Zheng et al.
JOURNAL OF MOLECULAR BIOLOGY (2018)
On the Calculation of SAXS Profiles of Folded and Intrinsically Disordered Proteins from Computer Simulations
Joao Henriques et al.
JOURNAL OF MOLECULAR BIOLOGY (2018)
High-throughput discovery of functional disordered regions: investigation of transactivation domains
Charles N. J. Ravarani et al.
MOLECULAR SYSTEMS BIOLOGY (2018)
Multiplex assessment of protein variant abundance by massively parallel sequencing
Kenneth A. Matreyek et al.
NATURE GENETICS (2018)
Developing a molecular dynamics force field for both folded and disordered protein states
Paul Robustelli et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)
Short linear motif core and flanking regions modulate retinoblastoma protein binding affinity and specificity
Nicolas Palopoli et al.
PROTEIN ENGINEERING DESIGN & SELECTION (2018)
Structure of Radical-Induced Cell Death1 Hub Domain Reveals a Common αα-Scaffold for Disorder in Transcriptional Networks
Katrine Bugge et al.
STRUCTURE (2018)
Enhancing coevolution-based contact prediction by imposing structural self-consistency of the contacts
Maher M. Kassem et al.
SCIENTIFIC REPORTS (2018)
Sequence determinants of protein phase behavior from a coarse-grained model
Gregory L. Dignon et al.
PLOS COMPUTATIONAL BIOLOGY (2018)
A High-Throughput Mutational Scan of an Intrinsically Disordered Acidic Transcriptional Activation Domain
Max V. Staller et al.
CELL SYSTEMS (2018)
Mutations in Disordered Regions Can Cause Disease by Creating Dileucine Motifs
Katrina Meyer et al.
CELL (2018)
Cancer Mutations of the Tumor Suppressor SPOP Disrupt the Formation of Active, Phase-Separated Compartments
Jill J. Bouchard et al.
MOLECULAR CELL (2018)
Proteome-wide analysis of phospho-regulated PDZ domain interactions
Gustav N. Sundell et al.
MOLECULAR SYSTEMS BIOLOGY (2018)
Phase-separation mechanism for C-terminal hyperphosphorylation of RNA polymerase II
Huasong Lu et al.
NATURE (2018)
Extreme disorder in an ultrahigh-affinity protein complex
Alessandro Borgia et al.
NATURE (2018)
Deep generative models of genetic variation capture the effects of mutations
Adam J. Riesselman et al.
NATURE METHODS (2018)
Relation between single-molecule properties and phase behavior of intrinsically disordered proteins
Gregory L. Dignon et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)
Deep neural network processing of DEER data
Steven G. Worswick et al.
SCIENCE ADVANCES (2018)
Evolution of weak cooperative interactions for biological specificity
Ang Gao et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)
Nonproteinogenic deep mutational scanning of linear and cyclic peptides
Joseph M. Rogers et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2018)
'Nonlinear' Biochemistry of Nucleosome Detergents
Alexandre M. Erkine
TRENDS IN BIOCHEMICAL SCIENCES (2018)
Structures and Short Linear Motif of Disordered Transcription Factor Regions Provide Clues to the Interactome of the Cellular Hub Protein Radical-induced Cell Death1
Charlotte O'Shea et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2017)
Disentangling polydispersity in the PCNA-p15PAF complex, a disordered, transient and multivalent macromolecular assembly
Tiago N. Cordeiro et al.
NUCLEIC ACIDS RESEARCH (2017)
Biomolecular condensates: organizers of cellular biochemistry
Salman F. Banani et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2017)
Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements
Gustavo Fuertes et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)
Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water
Joshua A. Riback et al.
SCIENCE (2017)
Liquid phase condensation in cell physiology and disease
Yongdae Shin et al.
SCIENCE (2017)
Genetically tunable frustration controls allostery in an intrinsically disordered transcription factor
Jing Li et al.
ELIFE (2017)
An introduction to deep learning on biological sequence data: examples and solutions
Vanessa Isabell Jurtz et al.
BIOINFORMATICS (2017)
Phosphorylation of the FUS low-complexity domain disrupts phase separation, aggregation, and toxicity
Zachary Monahan et al.
EMBO JOURNAL (2017)
Variant Interpretation: Functional Assays to the Rescue
Lea M. Starita et al.
AMERICAN JOURNAL OF HUMAN GENETICS (2017)
Behaviour of intrinsically disordered proteins in protein-protein complexes with an emphasis on fuzziness
Johan G. Olsen et al.
CELLULAR AND MOLECULAR LIFE SCIENCES (2017)
Phase Separation and Single-Chain Compactness of Charged Disordered Proteins Are Strongly Correlated
Yi-Hsuan Lin et al.
BIOPHYSICAL JOURNAL (2017)
Principles of protein structural ensemble determination
Massimiliano Bonomi et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2017)
Computational and theoretical advances in studies of intrinsically disordered proteins
Robert B. Best
CURRENT OPINION IN STRUCTURAL BIOLOGY (2017)
The human Na+/H+ exchanger 1 is a membrane scaffold protein for extracellular signal-regulated kinase 2
Ruth Hendus-Altenburger et al.
BMC BIOLOGY (2016)
Structured States of Disordered Proteins from Genomic Sequences
Agnes Toth-Petroczy et al.
CELL (2016)
Multi-Timescale Dynamics in Intrinsically Disordered Proteins from NMR Relaxation and Molecular Simulation
Nicola Salvi et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2016)
Experimental Inferential Structure Determination of Ensembles for Intrinsically Disordered Proteins
David H. Brookes et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2016)
Mapping the Landscape of a Eukaryotic Degronome
Yifat Geffen et al.
MOLECULAR CELL (2016)
Phase Separation: Linking Cellular Compartmentalization to Disease
Adriano Aguzzi et al.
TRENDS IN CELL BIOLOGY (2016)
14-3-3-Pred: improved methods to predict 14-3-3-binding phosphopeptides
Fabio Madeira et al.
BIOINFORMATICS (2015)
Widespread Macromolecular Interaction Perturbations in Human Genetic Disorders
Nidhi Sahni et al.
CELL (2015)
Short linear motifs - ex nihilo evolution of protein regulation
Norman E. Davey et al.
CELL COMMUNICATION AND SIGNALING (2015)
Functional advantages of dynamic protein disorder
Rebecca B. Berlow et al.
FEBS LETTERS (2015)
CAMELOT: A machine learning approach for coarse-grained simulations of aggregation of block-copolymeric protein sequences
Kiersten M. Ruff et al.
JOURNAL OF CHEMICAL PHYSICS (2015)
A theoretical method to compute sequence dependent configurational properties in charged polymers and proteins
Lucas Sawle et al.
JOURNAL OF CHEMICAL PHYSICS (2015)
Phase Transition of a Disordered Nuage Protein Generates Environmentally Responsive Membraneless Organelles
Timothy J. Nott et al.
MOLECULAR CELL (2015)
Systematic discovery of linear binding motifs targeting an ancient protein interaction surface on MAP kinases
Andras Zeke et al.
MOLECULAR SYSTEMS BIOLOGY (2015)
Conformational propensities of intrinsically disordered proteins influence the mechanism of binding and folding
Munehito Arai et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)
CSNAP Is a Stoichiometric Subunit of the COP9 Signalosome
Shelly Rozen et al.
CELL REPORTS (2015)
Intrinsically disordered proteins and their (disordered) proteomes in neurodegenerative disorders
Vladimir N. Uversky
FRONTIERS IN AGING NEUROSCIENCE (2015)
ENCORE: Software for Quantitative Ensemble Comparison
Matteo Tiberti et al.
PLOS COMPUTATIONAL BIOLOGY (2015)
Structure of a Functional Amyloid Protein Subunit Computed Using Sequence Variation
Pengfei Tian et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2015)
Globular and disordered-the non-identical twins in protein-protein interactions
Kaare Teilum et al.
FRONTIERS IN MOLECULAR BIOSCIENCES (2015)
Helical Propensity in an Intrinsically Disordered Protein Accelerates Ligand Binding
Vytautas Iesmantavicius et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2014)
Short Linear Motifs: Ubiquitous and Functionally Diverse Protein Interaction Modules Directing Cell Regulation
Kim Van Roey et al.
CHEMICAL REVIEWS (2014)
Building Force Fields: An Automatic, Systematic, and Reproducible Approach
Lee-Ping Wang et al.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2014)
Coupled Folding and Binding of the Disordered Protein PUMA Does Not Require Particular Residual Structure
Joseph M. Rogers et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2014)
A Million Peptide Motifs for the Molecular Biologist
Peter Tompa et al.
MOLECULAR CELL (2014)
Deep mutational scanning: a new style of protein science
Douglas M. Fowler et al.
NATURE METHODS (2014)
Transcriptional enhancers: from properties to genome-wide predictions
Daria Shlyueva et al.
NATURE REVIEWS GENETICS (2014)
Structural basis of recognition of interferon-α receptor by tyrosine kinase 2
Heidi J. A. Wallweber et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2014)
The binding mechanisms of intrinsically disordered proteins
Jakob Dogan et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2014)
Large-scale interaction profiling of PDZ domains through proteomic peptide-phage display using human and viral phage peptidomes
Ylva Ivarsson et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
Intrinsically Disordered Segments Affect Protein Half-Life in the Cell and during Evolution
Robin van der Lee et al.
CELL REPORTS (2014)
Describing intrinsically disordered proteins at atomic resolution by NMR
Malene Ringkjobing Jensen et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2013)
The most important thing is the tail: Multitudinous functionalities of intrinsically disordered protein termini
Vladimir N. Uversky
FEBS LETTERS (2013)
Automated Optimization of Potential Parameters
Michele Di Pierro et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Molecular Mechanisms of Disease-Causing Missense Mutations
Shannon Stefl et al.
JOURNAL OF MOLECULAR BIOLOGY (2013)
Protein Expansion Is Primarily due to Indels in Intrinsically Disordered Regions
Sara Light et al.
MOLECULAR BIOLOGY AND EVOLUTION (2013)
Predicting Binding within Disordered Protein Regions to Structurally Characterised Peptide-Binding Domains
Waqasuddin Khan et al.
PLOS ONE (2013)
Protein Structure Validation and Refinement Using Amide Proton Chemical Shifts Derived from Quantum Mechanics
Anders S. Christensen et al.
PLOS ONE (2013)
Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues
Rahul K. Das et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
Fast Association and Slow Transitions in the Interaction between Two Intrinsically Disordered Protein Domains
Jakob Dogan et al.
JOURNAL OF BIOLOGICAL CHEMISTRY (2012)
PPM: a side-chain and backbone chemical shift predictor for the assessment of protein conformational ensembles
Da-Wei Li et al.
JOURNAL OF BIOMOLECULAR NMR (2012)
Characterization of the Conformational Equilibrium between the Two Major Substates of RNase A Using NMR Chemical Shifts
Carlo Camilloni et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2012)
Phase transitions in the assembly of multivalent signalling proteins
Pilong Li et al.
NATURE (2012)
ELM-the database of eukaryotic linear motifs
Holger Dinkel et al.
NUCLEIC ACIDS RESEARCH (2012)
Polymer scaling laws of unfolded and intrinsically disordered proteins quantified with single-molecule spectroscopy
Hagen Hofmann et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)
Disease-Associated Mutations Disrupt Functionally Important Regions of Intrinsic Protein Disorder
Vladimir Vacic et al.
PLOS COMPUTATIONAL BIOLOGY (2012)
How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization?
Stefano Piana et al.
BIOPHYSICAL JOURNAL (2011)
Intrinsically disordered proteins: regulation and disease
M. Madan Babu et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2011)
Correlating Disease-Related Mutations to Their Effect on Protein Stability: A Large-Scale Analysis of the Human Proteome
Rita Casadio et al.
HUMAN MUTATION (2011)
SHIFTX2: significantly improved protein chemical shift prediction
Beomsoo Han et al.
JOURNAL OF BIOMOLECULAR NMR (2011)
The Acidic Transcription Activator Gcn4 Binds the Mediator Subunit Gal11/Med15 Using a Simple Protein Interface Forming a Fuzzy Complex
Peter S. Brzovic et al.
MOLECULAR CELL (2011)
Protein 3D Structure Computed from Evolutionary Sequence Variation
Debora S. Marks et al.
PLOS ONE (2011)
Direct-coupling analysis of residue coevolution captures native contacts across many protein families
Faruck Morcos et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
Learning generative models for protein fold families
Sivaraman Balakrishnan et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2011)
NMR-Based Protein Potentials
Da-Wei Li et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2010)
Sequence Determinants of Compaction in Intrinsically Disordered Proteins
Joseph A. Marsh et al.
BIOPHYSICAL JOURNAL (2010)
Allostery and Intrinsic Disorder Mediate Transcription Regulation by Conditional Cooperativity
Abel Garcia-Pino et al.
CELL (2010)
SPARTA plus : a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network
Yang Shen et al.
JOURNAL OF BIOMOLECULAR NMR (2010)
Bidirectional binding of invariant chain peptides to an MHC class II molecule
Sebastian Guenther et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)
Fast and Accurate Predictions of Protein NMR Chemical Shifts from Interatomic Distances
Kai J. Kohlhoff et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2009)
Similarity Measures for Protein Ensembles
Kresten Lindorff-Larsen et al.
PLOS ONE (2009)
Identification of direct residue contacts in protein-protein interaction by message passing
Martin Weigt et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)
Experimental parameterization of an energy function for the simulation of unfolded proteins
Anders B. Norgaard et al.
BIOPHYSICAL JOURNAL (2008)
Flexible nets: disorder and induced fit in the associations of p53 and 14-3-3 with their partners
Christopher J. Oldfield et al.
BMC GENOMICS (2008)
Rewiring the specificity of two-component signal transduction systems
Jeffrey M. Skerker et al.
CELL (2008)
Dif1 Is a DNA-Damage-Regulated Facilitator of Nuclear Import for Ribonucleotide Reductase
Yang David Lee et al.
MOLECULAR CELL (2008)
Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method
Lukas Burger et al.
MOLECULAR SYSTEMS BIOLOGY (2008)
Contextual Specificity in Peptide-Mediated Protein Interactions
Amelie Stein et al.
PLOS ONE (2008)
A generative, probabilistic model of local protein structure
Wouter Boomsma et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)
Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology
Yang Shen et al.
JOURNAL OF BIOMOLECULAR NMR (2007)
Mechanism of coupled folding and binding of an intrinsically disordered protein
Kenji Sugase et al.
NATURE (2007)
Structural characterization of flexible proteins using small-angle X-ray scattering
Pau Bernado et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2007)
Atomic-level characterization of disordered protein ensembles
Tanja Mittag et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2007)
Systematic discovery of new recognition peptides mediating protein interaction networks
V Neduva et al.
PLOS BIOLOGY (2005)
A structural model for unfolded proteins from residual dipolar couplings and small-angle x-ray scattering
P Bernadó et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
Interpreting dynamically-averaged scalar couplings in proteins
K Lindorff-Larsen et al.
JOURNAL OF BIOMOLECULAR NMR (2005)
Prediction of aggregation-prone and aggregation-susceptible regions in proteins associated with neurodegenerative diseases
AP Pawar et al.
JOURNAL OF MOLECULAR BIOLOGY (2005)
Inferential structure determination
W Rieping et al.
SCIENCE (2005)
Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins
AM Fernandez-Escamilla et al.
NATURE BIOTECHNOLOGY (2004)
HBP1 and Mad1 repressors bind the Sin3 corepressor PAH2 domain with opposite helical orientations
KA Swanson et al.
NATURE STRUCTURAL & MOLECULAR BIOLOGY (2004)
Rationalization of the effects of mutations on peptide and protein aggregation rates
F Chiti et al.
NATURE (2003)
Inverse Monte Carlo procedure for conformation determination of macromolecules
M Bathe et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2003)
PROSHIFT: Protein chemical shift prediction using artificial neural networks
J Meiler
JOURNAL OF BIOMOLECULAR NMR (2003)
Intrinsic disorder in cell-signaling and cancer-associated proteins
LM Iakoucheva et al.
JOURNAL OF MOLECULAR BIOLOGY (2002)
Mutual synergistic folding in recruitment of CBP/p300 by p160 nuclear receptor coactivators
SJ Demarest et al.
NATURE (2002)
Automated prediction of 15N, 13Cα, 13Cβ and 13C′ chemical shifts in proteins using a density functional database
XP Xu et al.
JOURNAL OF BIOMOLECULAR NMR (2001)
HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins
C Bystroff et al.
JOURNAL OF MOLECULAR BIOLOGY (2000)
分享论文
