CAMELOT: A machine learning approach for coarse-grained simulations of aggregation of block-copolymeric protein sequences

A Liquid-to-Solid Phase Transition of the ALS Protein FUS Accelerated by Disease Mutation

(2015) Avinash Patel et al.   CELL

Inverse Size Scaling of the Nucleolus by a Concentration-Dependent Phase Transition

(2015) Stephanie C. Weber et al.   CURRENT BIOLOGY

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

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

PolyQ-dependent RNA–protein assemblies control symmetry breaking

(2015) ChangHwan Lee et al.   JOURNAL OF CELL BIOLOGY

Dynamic force matching: A method for constructing dynamical coarse-grained models with realistic time dependence

(2015) Aram Davtyan et al.   JOURNAL OF CHEMICAL PHYSICS

Parametrization of Backbone Flexibility in a Coarse-Grained Force Field for Proteins (COFFDROP) Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of All Possible Two-Residue Peptides

(2015) Tamara Frembgen-Kesner et al.   Journal of Chemical Theory and Computation

Multiscale enhanced sampling of intrinsically disordered protein conformations

(2015) Kuo Hao Lee et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Quantitative Assessments of the Distinct Contributions of Polypeptide Backbone Amides versus Side Chain Groups to Chain Expansion via Chemical Denaturation

(2015) Alex S. Holehouse et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Dictyostelium discoideumhas a highly Q/N-rich proteome and shows an unusual resilience to protein aggregation

(2015) Liliana Malinovska et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The disordered P granule protein LAF-1 drives phase separation into droplets with tunable viscosity and dynamics

(2015) Shana Elbaum-Garfinkle et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nup98 FG domains from diverse species spontaneously phase-separate into particles with nuclear pore-like permselectivity

(2015) Hermann Broder Schmidt et al.   eLife

Aggregation Behavior of Chemically Synthesized, Full-Length Huntingtin Exon1

(2014) Bankanidhi Sahoo et al.   BIOCHEMISTRY

Role of the Coiled-Coil Structural Motif in Polyglutamine Aggregation

(2014) Bashkim Kokona et al.   BIOCHEMISTRY

From Micelles to Fibers: Balancing Self-Assembling and Random Coiling Domains in pH-Responsive Silk-Collagen-Like Protein-Based Polymers

(2014) Lennart H. Beun et al.   BIOMACROMOLECULES

Molecular Description of the LCST Behavior of an Elastin-Like Polypeptide

(2014) Nan K. Li et al.   BIOMACROMOLECULES

A Coarse-Grained Model for Polyglutamine Aggregation Modulated by Amphipathic Flanking Sequences

(2014) Kiersten M. Ruff et al.   BIOPHYSICAL JOURNAL

Nuclear Pore Complex Protein Sequences Determine Overall Copolymer Brush Structure and Function

(2014) David Ando et al.   BIOPHYSICAL JOURNAL

Proteins without unique 3D structures: Biotechnological applications of intrinsically unstable/disordered proteins

(2014) Vladimir N. Uversky   Biotechnology Journal

Classification of Intrinsically Disordered Regions and Proteins

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

Silk-elastin-like protein biomaterials for the controlled delivery of therapeutics

(2014) Wenwen Huang et al.   Expert Opinion on Drug Delivery

Intrinsically disordered proteins as crucial constituents of cellular aqueous two phase systems and coacervates

(2014) Vladimir N. Uversky et al.   FEBS LETTERS

Biophysical Underpinnings of the Repeat Length Dependence of Polyglutamine Amyloid Formation

(2014) Elizabeth Landrum et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Assemblages: Functional units formed by cellular phase separation

(2014) Jeffrey A. Toretsky et al.   JOURNAL OF CELL BIOLOGY

Cooperative polymerization of one-patch colloids

(2014) Teun Vissers et al.   JOURNAL OF CHEMICAL PHYSICS

Derivation of coarse-grained potentials via multistate iterative Boltzmann inversion

(2014) Timothy C. Moore et al.   JOURNAL OF CHEMICAL PHYSICS

COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids

(2014) Casey T. Andrews et al.   Journal of Chemical Theory and Computation

Accelerate Sampling in Atomistic Energy Landscapes Using Topology-Based Coarse-Grained Models

(2014) Weihong Zhang et al.   Journal of Chemical Theory and Computation

Investigation of Coarse-Grained Mappings via an Iterative Generalized Yvon–Born–Green Method

(2014) Joseph F. Rudzinski et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Building Force Fields: An Automatic, Systematic, and Reproducible Approach

(2014) Lee-Ping Wang et al.   Journal of Physical Chemistry Letters

Influence of repeat numbers on self-assembly rates of repetitive recombinant spider silk proteins

(2014) Martin Humenik et al.   JOURNAL OF STRUCTURAL BIOLOGY

Solution conditions determine the relative importance of nucleation and growth processes in  -synuclein aggregation

(2014) A. K. Buell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Poly-dipeptides encoded by the C9orf72 repeats bind nucleoli, impede RNA biogenesis, and kill cells

(2014) I. Kwon et al.   SCIENCE

Equilibrium phases of one-patch colloids with short-range attractions

(2014) Zdeněk Preisler et al.   Soft Matter

Stimuli-sensitive intrinsically disordered protein brushes

(2014) Nithya Srinivasan et al.   Nature Communications

Structure–function–property–design interplay in biopolymers: Spider silk

(2013) Olena Tokareva et al.   Acta Biomaterialia

Functional block copolymer assemblies responsive to tumor and intracellular microenvironments for site-specific drug delivery and enhanced imaging performance

(2013) Zhishen Ge et al.   CHEMICAL SOCIETY REVIEWS

Representation Learning: A Review and New Perspectives

(2013) Y. Bengio et al.   IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE

Phase transitions and size scaling of membrane-less organelles

(2013) Clifford P. Brangwynne   JOURNAL OF CELL BIOLOGY

Fitting coarse-grained distribution functions through an iterative force-matching method

(2013) Lanyuan Lu et al.   JOURNAL OF CHEMICAL PHYSICS

Perspective: Coarse-grained models for biomolecular systems

(2013) W. G. Noid   JOURNAL OF CHEMICAL PHYSICS

PRIMO: A Transferable Coarse-Grained Force Field for Proteins

(2013) Parimal Kar et al.   Journal of Chemical Theory and Computation

The Theory of Ultra-Coarse-Graining. 1. General Principles

(2013) James F. Dama et al.   Journal of Chemical Theory and Computation

Phase Diagram of One-Patch Colloids Forming Tubes and Lamellae

(2013) Zdenek Preisler et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Spatial Organization of the Cell Cytoplasm by Position-Dependent Phase Separation

(2013) Chiu Fan Lee et al.   PHYSICAL REVIEW LETTERS

Unmasking the roles of N- and C-terminal flanking sequences from exon 1 of huntingtin as modulators of polyglutamine aggregation

(2013) S. L. Crick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Challenges in Multiscale Modeling of Polymer Dynamics

(2013) Ying Li et al.   Polymers

Multifunctional Materials through Modular Protein Engineering

(2012) Rebecca L. DiMarco et al.   ADVANCED MATERIALS

Kinetically Competing Huntingtin Aggregation Pathways Control Amyloid Polymorphism and Properties

(2012) Murali Jayaraman et al.   BIOCHEMISTRY

Identification of Minimally Interacting Modules in an Intrinsically Disordered Protein

(2012) Anurag Sethi et al.   BIOPHYSICAL JOURNAL

Cell-free Formation of RNA Granules: Low Complexity Sequence Domains Form Dynamic Fibers within Hydrogels

(2012) Masato Kato et al.   CELL

Cell-free Formation of RNA Granules: Bound RNAs Identify Features and Components of Cellular Assemblies

(2012) Tina W. Han et al.   CELL

An intrinsically disordered yeast prion arrests the cell cycle by sequestering a spindle pole body component

(2012) Sebastian Treusch et al.   JOURNAL OF CELL BIOLOGY

Serine Phosphorylation Suppresses Huntingtin Amyloid Accumulation by Altering Protein Aggregation Properties

(2012) Rakesh Mishra et al.   JOURNAL OF MOLECULAR BIOLOGY

Physical Chemistry of Polyglutamine: Intriguing Tales of a Monotonous Sequence

(2012) Ronald Wetzel   JOURNAL OF MOLECULAR BIOLOGY

Improved Atomistic Monte Carlo Simulations Demonstrate That Poly-l-Proline Adopts Heterogeneous Ensembles of Conformations of Semi-Rigid Segments Interrupted by Kinks

(2012) Aditya Radhakrishnan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Phase transitions in the assembly of multivalent signalling proteins

(2012) Pilong Li et al.   NATURE

An Efficient Learning Procedure for Deep Boltzmann Machines

(2012) Ruslan Salakhutdinov et al.   NEURAL COMPUTATION

Intrinsically disordered proteins aggregate at fungal cell-to-cell channels and regulate intercellular connectivity

(2012) J. Lai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Resilin-like polypeptide hydrogels engineered for versatile biological function

(2012) Linqing Li et al.   Soft Matter

Systematic coarse-graining methods for soft matter simulations – a review

(2012) Emiliano Brini et al.   Soft Matter

Ordered and disordered proteins as nanomaterial building blocks

(2012) Nithya Srinivasan et al.   Wiley Interdisciplinary Reviews-Nanomedicine and Nanobiotechnology

Protein-Based Block Copolymers

(2011) Olena S. Rabotyagova et al.   BIOMACROMOLECULES

Assessing the contribution of heterogeneous distributions of oligomers to aggregation mechanisms of polyglutamine peptides

(2011) Andreas Vitalis et al.   BIOPHYSICAL CHEMISTRY

A novel Method for Coarse Graining of Atomistic Simulations Using Boltzmann Inversion

(2011) Bram van Hoof et al.   BIOPHYSICAL JOURNAL

Location Trumps Length: Polyglutamine-Mediated Changes in Folding and Aggregation of a Host Protein

(2011) Matthew D. Tobelmann et al.   BIOPHYSICAL JOURNAL

Reversible gels of patchy particles

(2011) Francesco Sciortino et al.   CURRENT OPINION IN SOLID STATE & MATERIALS SCIENCE

Coarse-graining errors and numerical optimization using a relative entropy framework

(2011) Aviel Chaimovich et al.   JOURNAL OF CHEMICAL PHYSICS

Aggregation Kinetics of Interrupted Polyglutamine Peptides

(2011) Robert H. Walters et al.   JOURNAL OF MOLECULAR BIOLOGY

Inhibiting the Nucleation of Amyloid Structure in a Huntingtin Fragment by Targeting α-Helix-Rich Oligomeric Intermediates

(2011) Rakesh Mishra et al.   JOURNAL OF MOLECULAR BIOLOGY

Slow Amyloid Nucleation via α-Helix-Rich Oligomeric Intermediates in Short Polyglutamine-Containing Huntingtin Fragments

(2011) Murali Jayaraman et al.   JOURNAL OF MOLECULAR BIOLOGY

The Aggregation-Enhancing Huntingtin N-Terminus Is Helical in Amyloid Fibrils

(2011) V. N. Sivanandam et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Opposing Effects of Glutamine and Asparagine Govern Prion Formation by Intrinsically Disordered Proteins

(2011) Randal Halfmann et al.   MOLECULAR CELL

Effects of patch size and number within a simple model of patchy colloids

(2010) Achille Giacometti et al.   JOURNAL OF CHEMICAL PHYSICS

Molecular Dynamics Simulations of Polyglutamine Aggregation Using Solvent-Free Multiscale Coarse-Grained Models

(2010) Yanting Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Observation of empty liquids and equilibrium gels in a colloidal clay

(2010) Barbara Ruzicka et al.   NATURE MATERIALS

A numerical study of one-patch colloidal particles: from square-well to Janus

(2010) Francesco Sciortino et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Relative entropy as a universal metric for multiscale errors

(2010) Aviel Chaimovich et al.   PHYSICAL REVIEW E

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

Multiscale Coarse-Graining of the Protein Energy Landscape

(2010) Ronald D. Hills et al.   PLoS Computational Biology

A Systematic Survey Identifies Prions and Illuminates Sequence Features of Prionogenic Proteins

(2009) Simon Alberti et al.   CELL

Simulations of nucleation and elongation of amyloid fibrils

(2009) Jianing Zhang et al.   JOURNAL OF CHEMICAL PHYSICS

Modulation of Polyglutamine Conformations and Dimer Formation by the N-Terminus of Huntingtin

(2009) Tim E. Williamson et al.   JOURNAL OF MOLECULAR BIOLOGY

A Generalized-Yvon−Born−Green Theory for Determining Coarse-Grained Interaction Potentials

(2009) J. W. Mullinax et al.   Journal of Physical Chemistry C

The chaperonin TRiC blocks a huntingtin sequence element that promotes the conformational switch to aggregation

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

Polyglutamine disruption of the huntingtin exon 1 N terminus triggers a complex aggregation mechanism

(2009) Ashwani K Thakur et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Multiscale modeling of emergent materials: biological and soft matter

(2009) Teemu Murtola et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Generalized Yvon-Born-Green Theory for Molecular Systems

(2009) J. W. Mullinax et al.   PHYSICAL REVIEW LETTERS

A Bayesian statistics approach to multiscale coarse graining

(2008) Pu Liu et al.   JOURNAL OF CHEMICAL PHYSICS

Theoretical and numerical study of the phase diagram of patchy colloids: Ordered and disordered patch arrangements

(2008) Emanuela Bianchi et al.   JOURNAL OF CHEMICAL PHYSICS

The relative entropy is fundamental to multiscale and inverse thermodynamic problems

(2008) M. Scott Shell   JOURNAL OF CHEMICAL PHYSICS

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

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

Coarse-Graining in Interaction Space:  A Systematic Approach for Replacing Long-Range Electrostatics with Short-Range Potentials

(2008) Sergei Izvekov et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Community Structure in Directed Networks

(2008) E. A. Leicht et al.   PHYSICAL REVIEW LETTERS

A polymer physics perspective on driving forces and mechanisms for protein aggregation

(2007) Rohit V. Pappu et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS