Coarse-Grained and Atomistic MD Simulations of RNA and DNA Folding

A flexible algorithm for calculating pair interactions on SIMD architectures

(2013) Szilárd Páll et al.   COMPUTER PHYSICS COMMUNICATIONS

Perspective: Reaches of chemical physics in biology

(2013) Martin Gruebele et al.   JOURNAL OF CHEMICAL PHYSICS

Sequence-Dependent Base-Stacking Stabilities Guide tRNA Folding Energy Landscapes

(2013) Rongzhong Li 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

Computational and Experimental Characterizations of Silver Nanoparticle–Apolipoprotein Biocorona

(2013) Rongzhong Li et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Kinetics of Allosteric Transitions in S-adenosylmethionine Riboswitch Are Accurately Predicted from the Folding Landscape

(2013) Jong-Chin Lin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Mechanical unfolding of human telomere G-quadruplex DNA probed by integrated fluorescence and magnetic tweezers spectroscopy

(2013) Xi Long et al.   NUCLEIC ACIDS RESEARCH

RNA does the folding dance of twist, turn, stack

(2013) K. B. Hall   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Biomolecular Simulation: A Computational Microscope for Molecular Biology

(2012) Ron O. Dror et al.   Annual Review of Biophysics

SPFP: Speed without compromise—A mixed precision model for GPU accelerated molecular dynamics simulations

(2012) Scott Le Grand et al.   COMPUTER PHYSICS COMMUNICATIONS

Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

(2012) Andreas W. Götz et al.   Journal of Chemical Theory and Computation

The Kinetics and Folding Pathways of Intramolecular G-Quadruplex Nucleic Acids

(2012) Amy Y. Q. Zhang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Single-Molecule Study ofG-Quadruplex Disruption Using Dynamic Force Spectroscopy

(2012) Michel de Messieres et al.   PHYSICAL REVIEW LETTERS

Chemical physics of protein folding

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

The Protein-Folding Problem, 50 Years On

(2012) K. A. Dill et al.   SCIENCE

Topological constraints: using RNA secondary structure to model 3D conformation, folding pathways, and dynamic adaptation

(2011) Maximillian H Bailor et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Interactions of a Platinum-Modified Perylene Derivative with the Human Telomeric G-Quadruplex

(2011) Lu Rao et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Fast Folding of RNA Pseudoknots Initiated by Laser Temperature-Jump

(2011) Ranjani Narayanan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Folding of Human Telomerase RNA Pseudoknot Using Ion-Jump and Temperature-Quench Simulations

(2011) Shi Biyun et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Cooperative and Directional Folding of the preQ1Riboswitch Aptamer Domain

(2011) Jun Feng et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Insight into G-DNA Structural Polymorphism and Folding from Sequence and Loop Connectivity through Free Energy Analysis

(2011) Xiaohui Cang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Frustration in protein-DNA binding influences conformational switching and target search kinetics

(2011) A. Marcovitz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular dynamics simulations of aqueous ions at the liquid-vapor interface accelerated using graphics processors

(2010) Brad A. Bauer et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Topological Frustration in βα-Repeat Proteins: Sequence Diversity Modulates the Conserved Folding Mechanisms of α/β/α Sandwich Proteins

(2010) Ronald D. Hills et al.   JOURNAL OF MOLECULAR BIOLOGY

GPU-accelerated molecular modeling coming of age

(2010) John E. Stone et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

Development of CHARMM Polarizable Force Field for Nucleic Acid Bases Based on the Classical Drude Oscillator Model

(2010) Christopher M. Baker et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Molecular Simulation ofab InitioProtein Folding for a Millisecond Folder NTL9(1−39)

(2010) Vincent A. Voelz et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Promoter melting triggered by bacterial RNA polymerase occurs in three steps

(2010) Jie Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Principles of protein folding - A perspective from simple exact models

(2010) Ken A. Dill et al.   PROTEIN SCIENCE

Sop-GPU: Accelerating biomolecular simulations in the centisecond timescale using graphics processors

(2010) A. Zhmurov et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Nonlocal Helix Formation Is Key to Understanding S-Adenosylmethionine-1 Riboswitch Function

(2009) Paul C. Whitford et al.   BIOPHYSICAL JOURNAL

The Dynamic Landscapes of RNA Architecture

(2009) José Almeida Cruz et al.   CELL

Assembly mechanisms of RNA pseudoknots are determined by the stabilities of constituent secondary structures

(2009) S. S. Cho et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Protein Folding Problem

(2008) Ken A. Dill et al.   Annual Review of Biophysics

Molecular dynamics simulations of nucleic acid–protein complexes

(2008) Alexander D MacKerell et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

General purpose molecular dynamics simulations fully implemented on graphics processing units

(2008) Joshua A. Anderson et al.   JOURNAL OF COMPUTATIONAL PHYSICS

Subdomain Competition, Cooperativity, and Topological Frustration in the Folding of CheY

(2008) Ronald D. Hills et al.   JOURNAL OF MOLECULAR BIOLOGY

Multiple Probes are Required to Explore and Control the Rugged Energy Landscape of RNA Hairpins

(2008) Changbong Hyeon et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Relative Stability of Helices Determines the Folding Landscape of Adenine Riboswitch Aptamers

(2008) Jong-Chin Lin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Kinetics and mechanism of K+- and Na+-induced folding of models of human telomeric DNA into G-quadruplex structures

(2008) Robert D. Gray et al.   NUCLEIC ACIDS RESEARCH

Quantitative criteria for native energetic heterogeneity influences in the prediction of protein folding kinetics

(2008) S. S. Cho et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-molecule nonequilibrium periodic Mg2+-concentration jump experiments reveal details of the early folding pathways of a large RNA

(2008) X. Qu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An all-atom structure-based potential for proteins: Bridging minimal models with all-atom empirical forcefields

(2008) Paul C. Whitford et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The origins of asymmetry in the folding transition states of protein L and protein G

(2002) John Karanicolas et al.   PROTEIN SCIENCE