Microscopic picture of water-ethylene glycol interaction near a model DNA by computer simulation: Concentration dependence, structure, and localized thermodynamics

DNA’s Chiral Spine of Hydration

(2017) M. Luke McDermott et al.   ACS Central Science

How Mg2+ ion and water network affect the stability and structure of non-Watson–Crick base pairs in E. coli loop E of 5S rRNA: a molecular dynamics and reference interaction site model (RISM) study

(2016) Sudhanshu Shanker et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST

(2016) Steven Ramsey et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Long-timescale dynamics of the Drew–Dickerson dodecamer

(2016) Pablo D. Dans et al.   NUCLEIC ACIDS RESEARCH

Can A Denaturant Stabilize DNA? Pyridine Reverses DNA Denaturation in Acidic pH

(2015) Guillem Portella et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Distribution of Residence Time of Water around DNA Base Pairs: Governing Factors and the Origin of Heterogeneity

(2015) Debasis Saha et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Crowding-Induced Hybridization of Single DNA Hairpins

(2015) Laura E. Baltierra-Jasso et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Unexpected Swelling of Stiff DNA in a Polydisperse Crowded Environment

(2015) Hongsuk Kang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Parmbsc1: a refined force field for DNA simulations

(2015) Ivan Ivani et al.   NATURE METHODS

Analyzing ion distributions around DNA: sequence-dependence of potassium ion distributions from microsecond molecular dynamics

(2015) Marco Pasi et al.   NUCLEIC ACIDS RESEARCH

What Macromolecular Crowding Can Do to a Protein

(2014) Irina Kuznetsova et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Conformational Preferences of DNA in Reduced Dielectric Environments

(2014) Asli Yildirim et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structure and Properties of DNA in Apolar Solvents

(2014) Annalisa Arcella et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Analyzing ion distributions around DNA

(2014) Richard Lavery et al.   NUCLEIC ACIDS RESEARCH

Unraveling the sequence-dependent polymorphic behavior of d(CpG) steps in B-DNA

(2014) Pablo Daniel Dans et al.   NUCLEIC ACIDS RESEARCH

A New Coarse-Grained Model for E. coli Cytoplasm: Accurate Calculation of the Diffusion Coefficient of Proteins and Observation of Anomalous Diffusion

(2014) Sabeeha Hasnain et al.   PLoS One

Effects of Molecular Crowding on the Structures, Interactions, and Functions of Nucleic Acids

(2013) Shu-ichi Nakano et al.   CHEMICAL REVIEWS

Ethylene glycol revisited: Molecular dynamics simulations and visualization of the liquid and its hydrogen-bond network

(2013) Alexander Kaiser et al.   JOURNAL OF MOLECULAR LIQUIDS

Control of stability and structure of nucleic acids using cosolutes

(2013) Hisae Tateishi-Karimta et al.   METHODS

Molecular structure and hydrogen bonding in pure liquid ethylene glycol and ethylene glycol–water mixtures studied using NIR spectroscopy

(2013) Yujing Chen et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Grid inhomogeneous solvation theory: Hydration structure and thermodynamics of the miniature receptor cucurbit[7]uril

(2012) Crystal N. Nguyen et al.   JOURNAL OF CHEMICAL PHYSICS

Crowding effect on DNA melting: a molecular thermodynamic model with explicit solvent

(2012) Yu Liu et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

Molecular Dynamics Study of Effects of Temperature and Concentration on Hydrogen-Bond Abilities of Ethylene Glycol and Glycerol: Implications for Cryopreservation

(2011) Lindong Weng et al.   JOURNAL OF PHYSICAL CHEMISTRY A

R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments

(2011) Enguerran Vanquelef et al.   NUCLEIC ACIDS RESEARCH

Separation of preferential interaction and excluded volume effects on DNA duplex and hairpin stability

(2011) D. B. Knowles et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Models of macromolecular crowding effects and the need for quantitative comparisons with experiment

(2010) Adrian H Elcock   CURRENT OPINION IN STRUCTURAL BIOLOGY

Three-Dimensional Molecular Theory of Solvation Coupled with Molecular Dynamics in Amber

(2010) Tyler Luchko et al.   Journal of Chemical Theory and Computation

The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building

(2010) François-Yves Dupradeau et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

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

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

PACKMOL: A package for building initial configurations for molecular dynamics simulations

(2009) L. Martínez et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Understanding how the crowded interior of cells stabilizes DNA/DNA and DNA/RNA hybrids–in silico predictions and in vitro evidence

(2009) Karthik S. Harve et al.   NUCLEIC ACIDS RESEARCH

Macromolecular Crowding and Confinement: Biochemical, Biophysical, and Potential Physiological Consequences

(2008) Huan-Xiang Zhou et al.   Annual Review of Biophysics

Coarse-Grained Molecular Simulation of Diffusion and Reaction Kinetics in a Crowded Virtual Cytoplasm

(2008) Douglas Ridgway et al.   BIOPHYSICAL JOURNAL

Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations

(2008) In Suk Joung et al.   JOURNAL OF PHYSICAL CHEMISTRY B