The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems

A linker strategy fortrans-FRET assay to determine activation intermediate of NEDDylation cascade

(2014) Harbani Kaur Malik-Chaudhry et al.   BIOTECHNOLOGY AND BIOENGINEERING

Innovative interactive flexible docking method for multi-scale reconstruction elucidates dystrophin molecular assembly

(2014) A.-E. Molza et al.   FARADAY DISCUSSIONS

Conopeptide Vt3.1 Preferentially Inhibits BK Potassium Channels Containing β4 Subunits via Electrostatic Interactions

(2014) Min Li et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A Kinetic Approach to the Sequence–Aggregation Relationship in Disease-Related Protein Assembly

(2014) Bogdan Barz et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular Structures of Amyloid and Prion Fibrils: Consensus versus Controversy

(2013) Robert Tycko et al.   ACCOUNTS OF CHEMICAL RESEARCH

Understanding Amyloid Fibril Nucleation and Aβ Oligomer/Drug Interactions from Computer Simulations

(2013) Phuong Nguyen et al.   ACCOUNTS OF CHEMICAL RESEARCH

Effect of the Tottori Familial Disease Mutation (D7N) on the Monomers and Dimers of Aβ40 and Aβ42

(2013) Man Hoang Viet et al.   ACS Chemical Neuroscience

Atomic and Dynamic Insights into the Beneficial Effect of the 1,4-Naphthoquinon-2-yl-l-tryptophan Inhibitor on Alzheimer’s Aβ1–42 Dimer in Terms of Aggregation and Toxicity

(2013) Tong Zhang et al.   ACS Chemical Neuroscience

Cell Membranes Open “Doors” for Cationic Nanoparticles/Biomolecules: Insights into Uptake Kinetics

(2013) Jiaqi Lin et al.   ACS Nano

Coarse-Graining Methods for Computational Biology

(2013) Marissa G. Saunders et al.   Annual Review of Biophysics

ATR-FTIR: A “rejuvenated” tool to investigate amyloid proteins

(2013) Rabia Sarroukh et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Fast protein fragment similarity scoring using a Binet–Cauchy kernel

(2013) Frédéric Guyon et al.   BIOINFORMATICS

Differences in β-strand Populations of Monomeric Aβ40 and Aβ42

(2013) K. Aurelia Ball et al.   BIOPHYSICAL JOURNAL

On the Importance of Hydrodynamic Interactions in Lipid Membrane Formation

(2013) Tadashi Ando et al.   BIOPHYSICAL JOURNAL

Stepwise identification of potent antimicrobial peptides from human genome

(2013) Li Yan et al.   BIOSYSTEMS

The non-coding transcriptome as a dynamic regulator of cancer metastasis

(2013) Francesco Crea et al.   CANCER AND METASTASIS REVIEWS

Long noncoding RNAs: Novel insights into hepatocelluar carcinoma

(2013) Yong He et al.   CANCER LETTERS

Molecular Structure of β-Amyloid Fibrils in Alzheimer’s Disease Brain Tissue

(2013) Jun-Xia Lu et al.   CELL

Perspective on the Martini model

(2013) Siewert J. Marrink et al.   CHEMICAL SOCIETY REVIEWS

Coarse-grain modelling of protein–protein interactions

(2013) Marc Baaden et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

 -Aminobutyric Acid Regulates Both the Survival and Replication of Human  -Cells

(2013) J. Tian et al.   DIABETES

Ask the Experts: Past, present and future of the rule of five

(2013) Jonathan Baell et al.   Future Medicinal Chemistry

Communication: Simulated tempering with fast on-the-fly weight determination

(2013) Phuong H. Nguyen et al.   JOURNAL OF CHEMICAL PHYSICS

Perspective: Coarse-grained models for biomolecular systems

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

Importance of the Ion-Pair Interactions in the OPEP Coarse-Grained Force Field: Parametrization and Validation

(2013) Fabio Sterpone et al.   Journal of Chemical Theory and Computation

PRIMO: A Transferable Coarse-Grained Force Field for Proteins

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

Aβ Monomers Transiently Sample Oligomer and Fibril-Like Configurations: Ensemble Characterization Using a Combined MD/NMR Approach

(2013) David J. Rosenman et al.   JOURNAL OF MOLECULAR BIOLOGY

The Alzheimer's Amyloid-β(1–42) Peptide Forms Off-Pathway Oligomers and Fibrils That Are Distinguished Structurally by Intermolecular Organization

(2013) William M. Tay et al.   JOURNAL OF MOLECULAR BIOLOGY

Stepwise design of non-covalent wrapping of large diameter carbon nanotubes by peptides

(2013) Xin Chen et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Transferable Mixing of Atomistic and Coarse-Grained Water Models

(2013) Humberto C. Gonzalez et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Conformational Ensemble and Polymorphism of the All-Atom Alzheimer’s Aβ37–42 Amyloid Peptide Oligomers

(2013) Phuong H. Nguyen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

How Conformational Flexibility Stabilizes the Hyperthermophilic Elongation Factor G-Domain

(2013) Maria Kalimeri et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular Mechanism of the Inhibition of EGCG on the Alzheimer Aβ1–42 Dimer

(2013) Tong Zhang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Coarse-Grained Simulations of RNA and DNA Duplexes

(2013) Tristan Cragnolini et al.   JOURNAL OF PHYSICAL CHEMISTRY B

RNA 3D Structure Prediction by Using a Coarse-Grained Model and Experimental Data

(2013) Zhen Xia et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Coarse-Grained Model for Predicting RNA Folding Thermodynamics

(2013) Natalia A. Denesyuk et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Familial Alzheimer A2 V Mutation Reduces the Intrinsic Disorder and Completely Changes the Free Energy Landscape of the Aβ1–28 Monomer

(2013) Phuong H. Nguyen et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Reduced Native State Stability in Crowded Cellular Environment Due to Protein–Protein Interactions

(2013) Ryuhei Harada et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Dynamics of an Intrinsically Disordered Protein Reveal Metastable Conformations That Potentially Seed Aggregation

(2013) Qin Qiao et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Polymorph-Specific Kinetics and Thermodynamics of β-Amyloid Fibril Growth

(2013) Wei Qiang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

In silico design of small peptide-based Hsp90 inhibitor: A novel anticancer agent

(2013) Uday Kumar Gupta et al.   MEDICAL HYPOTHESES

Characterization of an antimicrobial peptide produced by Bacillus subtilis subsp. spizezinii showing inhibitory activity towards Haemophilus parasuis

(2013) M. L. Teixeira et al.   MICROBIOLOGY-SGM

Recent Approaches in Design of Peptidomimetics for Antimicrobial Drug Discovery Research

(2013) Sandeep Lohan et al.   MINI-REVIEWS IN MEDICINAL CHEMISTRY

Designing immunogenic peptides

(2013) Darren R Flower   Nature Chemical Biology

Tumor adaptation and resistance to RAF inhibitors

(2013) Piro Lito et al.   NATURE MEDICINE

Moving towards early clinical trials for amyloid-targeted therapy in Alzheimer's disease

(2013) Paul S. Aisen et al.   NATURE REVIEWS DRUG DISCOVERY

AVPdb: a database of experimentally validated antiviral peptides targeting medically important viruses

(2013) Abid Qureshi et al.   NUCLEIC ACIDS RESEARCH

Nucleation Process of a Fibril Precursor in the C-Terminal Segment of Amyloid-β

(2013) Fahimeh Baftizadeh et al.   PHYSICAL REVIEW LETTERS

Mean-Field Interactions between Nucleic-Acid-Base Dipoles can Drive the Formation of a Double Helix

(2013) Yi He et al.   PHYSICAL REVIEW LETTERS

Game On, Science - How Video Game Technology May Help Biologists Tackle Visualization Challenges

(2013) Zhihan Lv et al.   PLoS One

Predicting Helical Topologies in RNA Junctions as Tree Graphs

(2013) Christian Laing et al.   PLoS One

Detecting Protein Candidate Fragments Using a Structural Alphabet Profile Comparison Approach

(2013) Yimin Shen et al.   PLoS One

Inhibition of Influenza A Virus Infection In Vitro by Peptides Designed In Silico

(2013) Rogelio López-Martínez et al.   PLoS One

High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations

(2013) A. A. Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stabilization of a protein conferred by an increase in folded state entropy

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

The allosteric communication pathways in KIX domain of CBP

(2013) F. Palazzesi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pulsed hydrogen–deuterium exchange mass spectrometry probes conformational changes in amyloid beta (Aβ) peptide aggregation

(2013) Ying Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rational modification of protein stability by targeting surface sites leads to complicated results

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

Atomic-level description of ubiquitin folding

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

Role of loops connecting secondary structure elements in the stabilization of proteins isolated from thermophilic organisms

(2013) Nicole Balasco et al.   PROTEIN SCIENCE

Combining coarse-grained nonbonded and atomistic bonded interactions for protein modeling

(2013) Martin Zacharias   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Folding 19 proteins to their native state and stability of large proteins from a coarse-grained model

(2013) Abhijeet Kapoor et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The stability ofTaqDNA polymerase results from a reduced entropic folding penalty; identification of other thermophilic proteins with similar folding thermodynamics

(2013) Chin-Chi Liu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The four ingredients of single-sequence RNA secondary structure prediction. A unifying perspective

(2013) Elena Rivas   RNA Biology

A Coarse-Grained Protein Model in a Water-like Solvent

(2013) Sumit Sharma et al.   Scientific Reports

Mechanism of amyloid β−protein dimerization determined using single−molecule AFM force spectroscopy

(2013) Zhengjian Lv et al.   Scientific Reports

Widespread Aggregation and Neurodegenerative Diseases Are Associated with Supersaturated Proteins

(2013) Prajwal Ciryam et al.   Cell Reports

Biochemistry of Amyloid  -Protein and Amyloid Deposits in Alzheimer Disease

(2013) C. L. Masters et al.   Cold Spring Harbor Perspectives in Medicine

Formation of Raft-Like Assemblies within Clusters of Influenza Hemagglutinin Observed by MD Simulations

(2013) Daniel L. Parton et al.   PLoS Computational Biology

Probing the Self-Assembly Mechanism of Diphenylalanine-Based Peptide Nanovesicles and Nanotubes

(2012) Cong Guo et al.   ACS Nano

The N-Methylated Peptide SEN304 Powerfully Inhibits Aβ(1–42) Toxicity by Perturbing Oligomer Formation

(2012) Hozefa Amijee et al.   BIOCHEMISTRY

Unexpected Effects of Macromolecular Crowding on Protein Stability

(2012) Laura A. Benton et al.   BIOCHEMISTRY

Effects of Familial Mutations on the Monomer Structure of Aβ42

(2012) Yu-Shan Lin et al.   BIOPHYSICAL JOURNAL

Peptide Scanning for Studying Structure-Activity Relationships in Drug Discovery

(2012) Andrew G. Jamieson et al.   Chemical Biology & Drug Design

Petaflop hydrokinetic simulations of complex flows on massive GPU clusters

(2012) M. Bernaschi et al.   COMPUTER PHYSICS COMMUNICATIONS

Effect of Gold Nanoparticle Conjugation on Peptide Dynamics and Structure

(2012) Kuo Hao Lee et al.   Entropy

Haptic-driven applications to molecular modeling: state-of-the-art and perspectives

(2012) Antonio Ricci et al.   Future Medicinal Chemistry

Real-time quantum chemistry

(2012) Moritz P. Haag et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

Degradation of an Old Human Protein

(2012) Michael G. Friedrich et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Combined Effects of Agitation, Macromolecular Crowding, and Interfaces on Amyloidogenesis

(2012) Chiu Fan Lee et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Structural, thermodynamical, and dynamical properties of oligomers formed by the amyloid NNQQ peptide: Insights from coarse-grained simulations

(2012) Yan Lu et al.   JOURNAL OF CHEMICAL PHYSICS

Understanding the EF-hand closing pathway using non-biased interatomic potentials

(2012) L. Dupuis et al.   JOURNAL OF CHEMICAL PHYSICS

Ab initio determination of coarse-grained interactions in double-stranded DNA

(2012) Chia Wei Hsu et al.   JOURNAL OF CHEMICAL PHYSICS

Modeling Protein–Protein Recognition in Solution Using the Coarse-Grained Force Field SCORPION

(2012) Nathalie Basdevant et al.   Journal of Chemical Theory and Computation

PaLaCe: A Coarse-Grain Protein Model for Studying Mechanical Properties

(2012) Marco Pasi et al.   Journal of Chemical Theory and Computation

Further Optimization of a Hybrid United-Atom and Coarse-Grained Force Field for Folding Simulations: Improved Backbone Hydration and Interactions between Charged Side Chains

(2012) Wei Han et al.   Journal of Chemical Theory and Computation

Improved Parameters for the Martini Coarse-Grained Protein Force Field

(2012) Djurre H. de Jong et al.   Journal of Chemical Theory and Computation

Dual role of Cu2+ ions on the aggregation and degradation of soluble Aβ oligomers and protofibrils investigated by fluorescence spectroscopy and AFM

(2012) Silvia García et al.   JOURNAL OF INORGANIC BIOCHEMISTRY

Driving Forces and Structural Determinants of Steric Zipper Peptide Oligomer Formation Elucidated by Atomistic Simulations

(2012) Dirk Matthes et al.   JOURNAL OF MOLECULAR BIOLOGY

The Coarse-Grained OPEP Force Field for Non-Amyloid and Amyloid Proteins

(2012) Yassmine Chebaro et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Distinct Dimerization for Various Alloforms of the Amyloid-Beta Protein: Aβ1–40, Aβ1–42, and Aβ1–40(D23N)

(2012) Sébastien Côté et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structures of Aβ17–42 Trimers in Isolation and with Five Small-Molecule Drugs Using a Hierarchical Computational Procedure

(2012) Yassmine Chebaro et al.   JOURNAL OF PHYSICAL CHEMISTRY B

AWSEM-MD: Protein Structure Prediction Using Coarse-Grained Physical Potentials and Bioinformatically Based Local Structure Biasing

(2012) Aram Davtyan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structural Characterization of λ-Repressor Folding from All-Atom Molecular Dynamics Simulations

(2012) Yanxin Liu et al.   Journal of Physical Chemistry Letters

Crowding Alters the Folding Kinetics of a β-Hairpin by Modulating the Stability of Intermediates

(2012) Nicholas A. Kurniawan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Intrinsic Contribution of the 2′-Hydroxyl to RNA Conformational Heterogeneity

(2012) Elizabeth J. Denning et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Multidimensional View of Amyloid Fibril Nucleation in Atomistic Detail

(2012) Fahimeh Baftizadeh et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Protein Crowding Affects Hydration Structure and Dynamics

(2012) Ryuhei Harada et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Use of fast conformational sampling to improve the characterization of VEGF A–peptide interactions

(2012) Gang Wu et al.   JOURNAL OF THEORETICAL BIOLOGY

Intersubtype Differences in the Effect of a Rare p24 Gag Mutation on HIV-1 Replicative Fitness

(2012) D. R. Chopera et al.   JOURNAL OF VIROLOGY

Principles for designing ideal protein structures

(2012) Nobuyasu Koga et al.   NATURE

Two-dimensional infrared spectroscopy reveals the complex behaviour of an amyloid fibril inhibitor

(2012) Chris T. Middleton et al.   Nature Chemistry

Cancer treatment according to BRCA1 and BRCA2 mutations

(2012) Kara N. Maxwell et al.   Nature Reviews Clinical Oncology

PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides

(2012) P. Thevenet et al.   NUCLEIC ACIDS RESEARCH

Systematic Validation of Protein Force Fields against Experimental Data

(2012) Kresten Lindorff-Larsen et al.   PLoS One

In Silico Prediction and Analysis of Caenorhabditis EF-hand Containing Proteins

(2012) Manish Kumar et al.   PLoS One

Structure-Function Analysis of the Glioma Targeting NFL-TBS.40-63 Peptide Corresponding to the Tubulin-Binding Site on the Light Neurofilament Subunit

(2012) Raphael Berges et al.   PLoS One

Human mitochondrial holocytochromecsynthase’s heme binding, maturation determinants, and complex formation with cytochromec

(2012) Brian San Francisco et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sampling protein motion and solvent effect during ligand binding

(2012) V. Limongelli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular crowding creates traffic jams of kinesin motors on microtubules

(2012) C. Leduc et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Intrinsic disorder modulates protein self-assembly and aggregation

(2012) A. De Simone et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epitope-specificity of recombinant antibodies reveals promiscuous peptide-binding properties

(2012) Niclas Olsson et al.   PROTEIN SCIENCE

RNA-Puzzles: A CASP-like evaluation of RNA three-dimensional structure prediction

(2012) J. A. Cruz et al.   RNA

Atomic View of a Toxic Amyloid Small Oligomer

(2012) Arthur Laganowsky et al.   SCIENCE

Human pIgR mimetic peptidic ligand for affinity purification of IgM

(2012) Satyen Gautam et al.   SEPARATION AND PURIFICATION TECHNOLOGY

The Crystal Structure of the MAP Kinase LmaMPK10 from Leishmania Major Reveals Parasite-Specific Features and Regulatory Mechanisms

(2012) Sofía Horjales et al.   STRUCTURE

Effect of Enamel Matrix Derivative and of Proline-Rich Synthetic Peptides on the Differentiation of Human Mesenchymal Stem Cells Toward the Osteogenic Lineage

(2012) Joana Maria Ramis et al.   TISSUE ENGINEERING PART A

Overlapping profiles of Abeta peptides in the Alzheimer's disease and pathological aging brains

(2012) Brenda D Moore et al.   Alzheimers Research & Therapy

Kinetics of Amyloid Aggregation: A Study of the GNNQQNY Prion Sequence

(2012) Jessica Nasica-Labouze et al.   PLoS Computational Biology

Toward a Molecular Theory of Early and Late Events in Monomer to Amyloid Fibril Formation

(2011) John E. Straub et al.   Annual Review of Physical Chemistry

Thermophilic proteins: insight and perspective from in silico experiments

(2011) Fabio Sterpone et al.   CHEMICAL SOCIETY REVIEWS

How to remain nonfolded and pliable: the linkers in modular α-amylases as a case study

(2011) Georges Feller et al.   FEBS Journal

Highly Conserved Structural Properties of the C-terminal Tail of HIV-1 gp41 Protein Despite Substantial Sequence Variation among Diverse Clades

(2011) Jonathan D. Steckbeck et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model

(2011) Thomas E. Ouldridge et al.   JOURNAL OF CHEMICAL PHYSICS

Simulations of the confinement of ubiquitin in self-assembled reverse micelles

(2011) Jianhui Tian et al.   JOURNAL OF CHEMICAL PHYSICS

Assessing the Quality of the OPEP Coarse-Grained Force Field

(2011) Alessandro Barducci et al.   Journal of Chemical Theory and Computation

Distinct Morphologies for Amyloid Beta Protein Monomer: Aβ1–40, Aβ1–42, and Aβ1–40(D23N)

(2011) Sébastien Côté et al.   Journal of Chemical Theory and Computation

Impact of Thermostats on Folding and Aggregation Properties of Peptides Using the Optimized Potential for Efficient Structure Prediction Coarse-Grained Model

(2011) Yannick G. Spill et al.   Journal of Chemical Theory and Computation

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

(2011) Marie Zgarbová et al.   Journal of Chemical Theory and Computation

Modeling of the structure and interactions of the B. anthracis antitoxin, MoxX: deletion mutant studies highlight its modular structure and repressor function

(2011) Nikita Chopra et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

RNA and protein 3D structure modeling: similarities and differences

(2011) Kristian Rother et al.   JOURNAL OF MOLECULAR MODELING

Energy Landscape and Global Optimization for a Frustrated Model Protein

(2011) Mark T. Oakley et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Physics-Based De Novo Prediction of RNA 3D Structures

(2011) Song Cao et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino-Acid Side Chains in Water. VI. Oppositely Charged Side Chains

(2011) Mariusz Makowski et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Simulation Studies of Protein Folding/Unfolding Equilibrium under Polar and Nonpolar Confinement

(2011) Jianhui Tian et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Characteristics of Amyloid-Related Oligomers Revealed by Crystal Structures of Macrocyclic β-Sheet Mimics

(2011) Cong Liu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

ModeRNA: a tool for comparative modeling of RNA 3D structure

(2011) Magdalena Rother et al.   NUCLEIC ACIDS RESEARCH

Effects of all-atom force fields on amyloid oligomerization: replica exchange molecular dynamics simulations of the Aβ16–22 dimer and trimer

(2011) Phuong H. Nguyen et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Coarse-grained force field: general folding theory

(2011) Adam Liwo et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Intrinsic Determinants of Aβ12–24 pH-Dependent Self-Assembly Revealed by Combined Computational and Experimental Studies

(2011) Weixin Xu et al.   PLoS One

Protein self-diffusion in crowded solutions

(2011) F. Roosen-Runge et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fully differentiable coarse-grained and all-atom knowledge-based potentials for RNA structure evaluation

(2011) J. Bernauer et al.   RNA

How Fast-Folding Proteins Fold

(2011) K. Lindorff-Larsen et al.   SCIENCE

A Multiscale Approach to Characterize the Early Aggregation Steps of the Amyloid-Forming Peptide GNNQQNY from the Yeast Prion Sup-35

(2011) Jessica Nasica-Labouze et al.   PLoS Computational Biology

Flow-Induced β-Hairpin Folding of the Glycoprotein Ibα β-Switch

(2010) Xueqing Zou et al.   BIOPHYSICAL JOURNAL

Macromolecule diffusion and confinement in prokaryotic cells

(2010) Jacek T Mika et al.   CURRENT OPINION IN BIOTECHNOLOGY

Spontaneous formation of polyglutamine nanotubes with molecular dynamics simulations

(2010) Rozita Laghaei et al.   JOURNAL OF CHEMICAL PHYSICS

A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality

(2010) Alex Morriss-Andrews et al.   JOURNAL OF CHEMICAL PHYSICS

Low molecular weight oligomers of amyloid peptides display β-barrel conformations: A replica exchange molecular dynamics study in explicit solvent

(2010) Alfonso De Simone et al.   JOURNAL OF CHEMICAL PHYSICS

Error and efficiency of simulated tempering simulations

(2010) Edina Rosta et al.   JOURNAL OF CHEMICAL PHYSICS

Disordered versus Fibril-like Amyloid β (25−35) Dimers in Water: Structure and Thermodynamics

(2010) Madeleine Kittner et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Coarse-Grained Model for Simulation of RNA Three-Dimensional Structures

(2010) Zhen Xia et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Effect of the Disulfide Bond on the Monomeric Structure of Human Amylin Studied by Combined Hamiltonian and Temperature Replica Exchange Molecular Dynamics Simulations

(2010) Rozita Laghaei et al.   JOURNAL OF PHYSICAL CHEMISTRY B

HiRE-RNA: A High Resolution Coarse-Grained Energy Model for RNA

(2010) Samuela Pasquali et al.   JOURNAL OF PHYSICAL CHEMISTRY B

A Coarse-Grained Model of DNA with Explicit Solvation by Water and Ions

(2010) Robert C. DeMille et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Using Sculptor and Situs for simultaneous assembly of atomic components into low-resolution shapes

(2010) Stefan Birmanns et al.   JOURNAL OF STRUCTURAL BIOLOGY

Elucidation of Amyloid β-Protein Oligomerization Mechanisms: Discrete Molecular Dynamics Study

(2010) B. Urbanc et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Amyloid Fibril Polymorphism Is under Kinetic Control

(2010) Riccardo Pellarin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Modeling the early stage of DNA sequence recognition within RecA nucleoprotein filaments

(2010) Adrien Saladin et al.   NUCLEIC ACIDS RESEARCH

The Crystal Structure of PPIL1 Bound to Cyclosporine A Suggests a Binding Mode for a Linear Epitope of the SKIP Protein

(2010) Christian M. Stegmann et al.   PLoS One

Complete Phenotypic Recovery of an Alzheimer's Disease Model by a Quinone-Tryptophan Hybrid Aggregation Inhibitor

(2010) Roni Scherzer-Attali et al.   PLoS One

Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion

(2010) T. Ando et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extending the PRIME model for protein aggregation to all 20 amino acids

(2010) Mookyung Cheon et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Turning limited experimental information into 3D models of RNA

(2010) S. C. Flores et al.   RNA

Multiscale Coarse-Graining of the Protein Energy Landscape

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

Effects of Macromolecular Crowding on Protein Conformational Changes

(2010) Hao Dong et al.   PLoS Computational Biology

Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm

(2010) Sean R. McGuffee et al.   PLoS Computational Biology

MUPHY: A parallel MUlti PHYsics/scale code for high performance bio-fluidic simulations

(2009) M. Bernaschi et al.   COMPUTER PHYSICS COMMUNICATIONS

Synthetic therapeutic peptides: science and market

(2009) Patrick Vlieghe et al.   DRUG DISCOVERY TODAY

Effect of β-sheet propensity on peptide aggregation

(2009) Giovanni Bellesia et al.   JOURNAL OF CHEMICAL PHYSICS

Structural diversity of the soluble trimers of the human amylin(20–29) peptide revealed by molecular dynamics simulations

(2009) Yuxiang Mo et al.   JOURNAL OF CHEMICAL PHYSICS

Generic coarse-grained model for protein folding and aggregation

(2009) Tristan Bereau et al.   JOURNAL OF CHEMICAL PHYSICS

Transferable Coarse Grain Nonbonded Interaction Model for Amino Acids

(2009) Russell DeVane et al.   Journal of Chemical Theory and Computation

Striking Effects of Hydrodynamic Interactions on the Simulated Diffusion and Folding of Proteins

(2009) Tamara Frembgen-Kesner et al.   Journal of Chemical Theory and Computation

Complex molecular assemblies at hand via interactive simulations

(2009) Olivier Delalande et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

HIV-1 IN alternative molecular recognition of DNA induced by raltegravir resistance mutations

(2009) Jean-François Mouscadet et al.   JOURNAL OF MOLECULAR RECOGNITION

Structures and Thermodynamics of Alzheimer’s Amyloid-β Aβ(16−35) Monomer and Dimer by Replica Exchange Molecular Dynamics Simulations: Implication for Full-Length Aβ Fibrillation

(2009) Yassmine Chebaro et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Amyloid-β protein oligomerization and the importance of tetramers and dodecamers in the aetiology of Alzheimer's disease

(2009) Summer L. Bernstein et al.   Nature Chemistry

PEP-FOLD: an online resource for de novo peptide structure prediction

(2009) J. Maupetit et al.   NUCLEIC ACIDS RESEARCH

Hydrodynamic Selection of the Kinetic Pathway of a Polymer Coil-Globule Transition

(2009) Kumiko Kamata et al.   PHYSICAL REVIEW LETTERS

Rational stabilization of enzymes by computational redesign of surface charge–charge interactions

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

Shear flow promotes amyloid-  fibrilization

(2009) D. E. Dunstan et al.   PROTEIN ENGINEERING DESIGN & SELECTION

A coarse-grained potential for fold recognition and molecular dynamics simulations of proteins

(2009) Peter Májek et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Coarse-grained modeling of large RNA molecules with knowledge-based potentials and structural filters

(2009) M. A. Jonikas et al.   RNA

An Analytical Solution to the Kinetics of Breakable Filament Assembly

(2009) T. P. J. Knowles et al.   SCIENCE

In silico DNA vaccine designing against human papillomavirus (HPV) causing cervical cancer

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Multiscale Simulation of Nanobiological Flows

(2008) Maria Fyta et al.   COMPUTING IN SCIENCE & ENGINEERING

Self-assembly of amyloid-forming peptides by molecular dynamics simulations

(2008) Guanghong Wei   Frontiers in Bioscience-Landmark

Exploring energy landscapes of protein folding and aggregation

(2008) Normand Mousseau   Frontiers in Bioscience-Landmark

The complex folding pathways of protein A suggest a multiple-funnelled energy landscape

(2008) Jean-Francois St-Pierre et al.   JOURNAL OF CHEMICAL PHYSICS

Comparison of sampling efficiency between simulated tempering and replica exchange

(2008) Cheng Zhang et al.   JOURNAL OF CHEMICAL PHYSICS

Statistically optimal analysis of samples from multiple equilibrium states

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The MARTINI Coarse-Grained Force Field: Extension to Proteins

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How Does Shear Affect Aβ Fibrillogenesis?

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Self-Assembly of the β2-Microglobulin NHVTLSQ Peptide Using a Coarse-Grained Protein Model Reveals a β-Barrel Species

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Replica Exchange Molecular Dynamics Simulations of Coarse-grained Proteins in Implicit Solvent

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The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data

(2008) Marc Parisien et al.   NATURE

Peptoids that mimic the structure, function, and mechanism of helical antimicrobial peptides

(2008) N. P. Chongsiriwatana et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Thermodynamics and dynamics of amyloid peptide oligomerization are sequence dependent

(2008) Yan Lu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Targeting the early steps of Aβ16-22 protofibril disassembly by N-methylated inhibitors: A numerical study

(2008) Yassmine Chebaro et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Ab initio RNA folding by discrete molecular dynamics: From structure prediction to folding mechanisms

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Formation and Growth of Oligomers: A Monte Carlo Study of an Amyloid Tau Fragment

(2008) Da-Wei Li et al.   PLoS Computational Biology