Titratable Martini model for constant pH simulations

Molecular Dynamics Simulations of PAMAM and PPI Dendrimers Using the GROMOS-Compatible 2016H66 Force Field

(2019) Mayk C. Ramos et al.   Journal of Chemical Information and Modeling

Intrinsic Membrane Permeability to Small Molecules

(2019) Christof Hannesschlaeger et al.   CHEMICAL REVIEWS

Dynamic Protonation Dramatically Affects the Membrane Permeability of Drug-like Molecules

(2019) Zhi Yue et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Histidine-Mediated Intramolecular Electrostatic Repulsion for Controlling pH-Dependent Protein–Protein Interaction

(2019) Hideki Watanabe et al.   ACS Chemical Biology

Drivers of α-Sheet Formation in Transthyretin under Amyloidogenic Conditions

(2019) Matthew Carter Childers et al.   BIOCHEMISTRY

Bioinspired pH- and Temperature-Responsive Injectable Adhesive Hydrogels with Polyplexes Promotes Skin Wound Healing

(2018) Thai Minh Duy Le et al.   BIOMACROMOLECULES

Mechanism of Long-Chain Free Fatty Acid Protonation at the Membrane-Water Interface

(2018) Alina A. Pashkovskaya et al.   BIOPHYSICAL JOURNAL

Transferable MARTINI Model of Poly(ethylene Oxide)

(2018) Fabian Grunewald et al.   JOURNAL OF PHYSICAL CHEMISTRY B

PubChem 2019 update: improved access to chemical data

(2018) Sunghwan Kim et al.   NUCLEIC ACIDS RESEARCH

A refined polarizable water model for the coarse-grained MARTINI force field with long-range electrostatic interactions

(2017) Julian Michalowsky et al.   JOURNAL OF CHEMICAL PHYSICS

Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems

(2017) Brian K. Radak et al.   Journal of Chemical Theory and Computation

Second-Generation ReaxFF Water Force Field: Improvements in the Description of Water Density and OH-Anion Diffusion

(2017) Weiwei Zhang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Bulk Heterojunction Morphologies with Atomistic Resolution from Coarse-Grain Solvent Evaporation Simulations

(2017) Riccardo Alessandri et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Exchange pathways of plastoquinone and plastoquinol in the photosystem II complex

(2017) Floris J. Van Eerden et al.   Nature Communications

Martini straight: Boosting performance using a shorter cutoff and GPUs

(2016) Djurre H. de Jong et al.   COMPUTER PHYSICS COMMUNICATIONS

Charge-Neutral Constant pH Molecular Dynamics Simulations Using a Parsimonious Proton Buffer

(2016) Serena Donnini et al.   Journal of Chemical Theory and Computation

Accurate Three States Model for Amino Acids with Two Chemically Coupled Titrating Sites in Explicit Solvent Atomistic Constant pH Simulations and pKa Calculations

(2016) Plamen Dobrev et al.   Journal of Chemical Theory and Computation

All-Atom Continuous Constant pH Molecular Dynamics With Particle Mesh Ewald and Titratable Water

(2016) Yandong Huang et al.   Journal of Chemical Theory and Computation

Blind prediction of cyclohexane–water distribution coefficients from the SAMPL5 challenge

(2016) Caitlin C. Bannan et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Phospholipophilicity of CxHyN+ amines: chromatographic descriptors and molecular simulations for understanding partitioning into membranes

(2016) S. T. J. Droge et al.   Environmental Science-Processes & Impacts

Guidelines for the analysis of free energy calculations

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

Accelerated weight histogram method for exploring free energy landscapes

(2014) V. Lindahl et al.   JOURNAL OF CHEMICAL PHYSICS

Prediction of Phospholipid–Water Partition Coefficients of Ionic Organic Chemicals Using the Mechanistic Model COSMOmic

(2014) Kai Bittermann et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Lipid Organization of the Plasma Membrane

(2014) Helgi I. Ingólfsson et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Exploring the sequence space for (tri-)peptide self-assembly to design and discover new hydrogels

(2014) Pim W. J. M. Frederix et al.   Nature Chemistry

Introducing Titratable Water to All-Atom Molecular Dynamics at Constant pH

(2013) Wei Chen et al.   BIOPHYSICAL JOURNAL

Constant pH simulations with the coarse-grained MARTINI model — Application to oleic acid aggregates

(2013) W.F. Drew Bennett et al.   CANADIAN JOURNAL OF CHEMISTRY

Structural Determinants of Drug Partitioning in n-Hexadecane/Water System

(2013) Senthil Natesan et al.   Journal of Chemical Information and Modeling

Atomistic simulations of pH-dependent self-assembly of micelle and bilayer from fatty acids

(2012) Brian H. Morrow et al.   JOURNAL OF CHEMICAL PHYSICS

Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH

(2012) Jason A. Wallace et al.   JOURNAL OF CHEMICAL PHYSICS

Efficient Algorithms for Langevin and DPD Dynamics

(2012) N. Goga et al.   Journal of Chemical Theory and Computation

Constant pH Molecular Dynamics in Explicit Solvent with λ-Dynamics

(2011) Serena Donnini et al.   Journal of Chemical Theory and Computation

A New Coarse-Grained Force Field for Membrane–Peptide Simulations

(2011) Zhe Wu et al.   Journal of Chemical Theory and Computation

Umbrella sampling

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

Polarizable Water Model for the Coarse-Grained MARTINI Force Field

(2010) Semen O. Yesylevskyy et al.   PLoS Computational Biology

Location, Tilt, and Binding: A Molecular Dynamics Study of Voltage-Sensitive Dyes in Biomembranes

(2009) Marlon J. Hinner et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Toward a Class-Independent Quantitative Structure−Activity Relationship Model for Uncouplers of Oxidative Phosphorylation

(2008) Simon Spycher et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Statistically optimal analysis of samples from multiple equilibrium states

(2008) Michael R. Shirts et al.   JOURNAL OF CHEMICAL PHYSICS

The MARTINI Coarse-Grained Force Field: Extension to Proteins

(2008) Luca Monticelli et al.   Journal of Chemical Theory and Computation