Thermodynamics of helix formation in small peptides of varying length in vacuo, in implicit solvent, and in explicit solvent

Enhanced configurational sampling with hybrid non-equilibrium molecular dynamics–Monte Carlo propagator

(2018) Donghyuk Suh et al.   JOURNAL OF CHEMICAL PHYSICS

Statistical Model To Decipher Protein Folding/Unfolding at a Local Scale

(2018) Paul Grassein et al.   JOURNAL OF PHYSICAL CHEMISTRY B

BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation: the nonequilibrium stratification

(2018) Xiaohui Wang et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Interaction entropy for protein-protein binding

(2017) Zhaoxi Sun et al.   JOURNAL OF CHEMICAL PHYSICS

Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino Acid Side Chains in Water. VII. Charged–Hydrophobic/Polar and Polar–Hydrophobic/Polar Side Chains

(2017) Mariusz Makowski et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Backbone Hydrogen Bond Strengths Can Vary Widely in Transmembrane Helices

(2017) Zheng Cao et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Helix Propensities of Amino Acid Residues via Thioester Exchange

(2017) Brian F. Fisher et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation

(2017) Zhao X. Sun et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Speed of Conformational Change: Comparing Explicit and Implicit Solvent Molecular Dynamics Simulations

(2015) Ramu Anandakrishnan et al.   BIOPHYSICAL JOURNAL

Guidelines for the analysis of free energy calculations

(2015) Pavel V. Klimovich et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Static and dynamic headspace analysis of instant coffee blends by proton-transfer-reaction mass spectrometry

(2015) Andrea Romano et al.   JOURNAL OF MASS SPECTROMETRY

Sequence- and Temperature-Dependent Properties of Unfolded and Disordered Proteins from Atomistic Simulations

(2015) Gül H. Zerze et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Diffusion of Hydration Water around Intrinsically Disordered Proteins

(2015) Pooja Rani et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Conformational effects in protein electrospray-ionization mass spectrometry

(2015) Jinyu Li et al.   MASS SPECTROMETRY REVIEWS

Multiple branched adaptive steered molecular dynamics

(2014) Gungor Ozer et al.   JOURNAL OF CHEMICAL PHYSICS

Thermodynamics of Deca-alanine Folding in Water

(2014) Anthony Hazel et al.   Journal of Chemical Theory and Computation

Building Water Models: A Different Approach

(2014) Saeed Izadi et al.   Journal of Physical Chemistry Letters

Biological insights from hydrogen exchange mass spectrometry

(2012) Sheila S. Jaswal   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Residue-Specific α-Helix Propensities from Molecular Simulation

(2012) Robert B. Best et al.   BIOPHYSICAL JOURNAL

Adaptive steered molecular dynamics: Validation of the selection criterion and benchmarking energetics in vacuum

(2012) Gungor Ozer et al.   JOURNAL OF CHEMICAL PHYSICS

A New Maximum Likelihood Approach for Free Energy Profile Construction from Molecular Simulations

(2012) Tai-Sung Lee et al.   Journal of Chemical Theory and Computation

Thermodynamics of Decaalanine Stretching in Water Obtained by Adaptive Steered Molecular Dynamics Simulations

(2012) Gungor Ozer et al.   Journal of Chemical Theory and Computation

Routine Access to Millisecond Time Scale Events with Accelerated Molecular Dynamics

(2012) Levi C.T. Pierce et al.   Journal of Chemical Theory and Computation

Structural propensities and entropy effects in peptide helix-coil transitions

(2012) Ilan E. Chemmama et al.   PHYSICAL REVIEW E

Helix formation and capping energetics of arginine analogs with varying side chain length

(2011) Richard P. Cheng et al.   AMINO ACIDS

Effects of solvents on the intrinsic propensity of peptide backbone conformations

(2011) Wenfei Li et al.   PHYSICAL REVIEW E

Umbrella sampling

(2011) Johannes Kästner   Wiley Interdisciplinary Reviews-Computational Molecular Science

Adaptive Steered Molecular Dynamics of the Long-Distance Unfolding of Neuropeptide Y

(2010) Gungor Ozer et al.   Journal of Chemical Theory and Computation

Helix propensities of the amino acids measured in alanine-based peptides without helix-stabilizing side-chain interactions

(2010) Avijit Chakrabartty et al.   PROTEIN SCIENCE

Molecular Dynamics Simulations of the Dynamic and Energetic Properties of Alkali and Halide Ions Using Water-Model-Specific Ion Parameters

(2009) In Suk Joung et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Characterizing Loop Dynamics and Ligand Recognition in Human- and Avian-Type Influenza Neuraminidases via Generalized Born Molecular Dynamics and End-Point Free Energy Calculations

(2009) Rommie E. Amaro et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The impact of monovalent ion force field model in nucleic acids simulations

(2009) Agnes Noy et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Helix propensities calculations for amino acids in alanine based peptides using Jarzynski's equality

(2009) Ignacia Echeverria et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

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