Sensitivity of local hydration behaviour and conformational preferences of peptides to choice of water model

Molecular dynamics simulation of a single-stranded DNA with heterogeneous distribution of nucleobases in aqueous medium

(2013) Kaushik Chakraborty et al.   JOURNAL OF CHEMICAL PHYSICS

Molecular Dynamics Study of β-Cyclodextrin–Phenylalanine (1:1) Inclusion Complex in Aqueous Medium

(2013) Madhurima Jana et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Water and water-like liquids: relationships between structure, entropy and mobility

(2013) Divya Nayar et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

A computational investigation of the phase behavior and capillary sublimation of water confined between nanoscale hydrophobic plates

(2012) Andrew L. Ferguson et al.   JOURNAL OF CHEMICAL PHYSICS

Are Protein Force Fields Getting Better? A Systematic Benchmark on 524 Diverse NMR Measurements

(2012) Kyle A. Beauchamp et al.   Journal of Chemical Theory and Computation

Water–protein dynamic coupling and new opportunities for probing it at low to physiological temperatures in aqueous solutions

(2012) Eugene Mamontov et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Conformational flexibility of a protein–carbohydrate complex and the structure and ordering of surrounding water

(2012) Madhurima Jana et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

The interfacial dynamics of water sandwiched between graphene sheets are governed by the slit width

(2012) Sanket A. Deshmukh et al.   SURFACE SCIENCE

Structure of hydration water in proteins: A comparison of molecular dynamics simulations and database analysis

(2011) Nicholus Bhattacharjee et al.   BIOPHYSICAL CHEMISTRY

Conformational fluctuations of a protein–DNA complex and the structure and ordering of water around it

(2011) Sudipta Kumar Sinha et al.   JOURNAL OF CHEMICAL PHYSICS

Differential flexibility of the secondary structures of lysozyme and the structure and ordering of surrounding water molecules

(2011) Sudipta Kumar Sinha et al.   JOURNAL OF CHEMICAL PHYSICS

Comparison of Tetrahedral Order, Liquid State Anomalies, and Hydration Behavior of mTIP3P and TIP4P Water Models

(2011) Divya Nayar et al.   Journal of Chemical Theory and Computation

Optimizing Protein−Solvent Force Fields to Reproduce Intrinsic Conformational Preferences of Model Peptides

(2011) Paul S. Nerenberg et al.   Journal of Chemical Theory and Computation

A Possible Role of Water in the Protein Folding Process

(2011) Francesco Mallamace et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Dissecting the Energetics of Hydrophobic Hydration of Polypeptides

(2011) Silvina Matysiak et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Local Order and Mobility of Water Molecules around Ambivalent Helices

(2011) Nicholus Bhattacharjee et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Thermodynamic, Diffusional, and Structural Anomalies in Rigid-Body Water Models

(2011) Manish Agarwal et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Influence of water–protein hydrogen bonding on the stability of Trp-cage miniprotein. A comparison between the TIP3P and TIP4P-Ew water models

(2011) Dietmar Paschek et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Increase of both Order and Disorder in the First Hydration Shell with Increasing Solute Polarity

(2011) Aljaž Godec et al.   PHYSICAL REVIEW LETTERS

Microscopic events in  -hairpin folding from alternative unfolded ensembles

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

Explicit Water Models Affect the Specific Solvation and Dynamics of Unfolded Peptides While the Conformational Behavior and Flexibility of Folded Peptides Remain Intact

(2010) Petra Florová et al.   Journal of Chemical Theory and Computation

Temperature Dependence of Protein Dynamics Simulated with Three Different Water Models

(2010) Dennis C. Glass et al.   Journal of Chemical Theory and Computation

Relationship between Structure, Entropy, and Diffusivity in Water and Water-Like Liquids

(2010) Manish Agarwal et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Protein Simulations with an Optimized Water Model: Cooperative Helix Formation and Temperature-Induced Unfolded State Collapse

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

Hydrogen bond strength and network structure effects on hydration of non-polar molecules

(2010) R. M. Lynden-Bell et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Free-energy landscape of the GB1 hairpin in all-atom explicit solvent simulations with different force fields: Similarities and differences

(2010) Robert B. Best et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Local Order, Energy, and Mobility of Water Molecules in the Hydration Shell of Small Peptides

(2009) Manish Agarwal et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Unraveling Water’s Entropic Mysteries: A Unified View of Nonpolar, Polar, and Ionic Hydration

(2008) Dor Ben-Amotz et al.   ACCOUNTS OF CHEMICAL RESEARCH

Are Current Molecular Dynamics Force Fields too Helical?

(2008) Robert B. Best et al.   BIOPHYSICAL JOURNAL

What ice can teach us about water interactions: a critical comparison of the performance of different water models

(2008) C. Vega et al.   FARADAY DISCUSSIONS