Development of a multisite model for Ni(II) ion in solution from thermodynamic and kinetic data

Protein Tunnels: The Case of Urease Accessory Proteins

(2017) Francesco Musiani et al.   Journal of Chemical Theory and Computation

Rational Design of Methodology-Independent Metal Parameters Using a Nonbonded Dummy Model

(2016) Yang Jiang et al.   Journal of Chemical Theory and Computation

Role of Molecular Dynamics and Related Methods in Drug Discovery

(2016) Marco De Vivo et al.   JOURNAL OF MEDICINAL CHEMISTRY

Development and Application of a Nonbonded Cu2+ Model That Includes the Jahn–Teller Effect

(2015) Qinghua Liao et al.   Journal of Physical Chemistry Letters

The ligand binding mechanism to purine nucleoside phosphorylase elucidated via molecular dynamics and machine learning

(2015) Sergio Decherchi et al.   Nature Communications

Molecular mechanics and dynamics: numerical tools to sample the configuration space

(2014) Matteo Masetti   Frontiers in Bioscience-Landmark

Force Field Independent Metal Parameters Using a Nonbonded Dummy Model

(2014) Fernanda Duarte et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Nickel-dependent metalloenzymes

(2013) Jodi L. Boer et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Nonredox Nickel Enzymes

(2013) Michael J. Maroney et al.   CHEMICAL REVIEWS

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration

(2013) Cameron Abrams et al.   Entropy

Multisite Ion Models That Improve Coordination and Free Energy Calculations in Molecular Dynamics Simulations

(2013) Akansha Saxena et al.   Journal of Chemical Theory and Computation

Taking into Account the Ion-Induced Dipole Interaction in the Nonbonded Model of Ions

(2013) Pengfei Li et al.   Journal of Chemical Theory and Computation

Specific Metal Recognition in Nickel Trafficking

(2012) Khadine A. Higgins et al.   BIOCHEMISTRY

Magnesium Ion–Water Coordination and Exchange in Biomolecular Simulations

(2012) Olof Allnér et al.   Journal of Chemical Theory and Computation

Metadynamics with Adaptive Gaussians

(2012) Davide Branduardi et al.   Journal of Chemical Theory and Computation

Force Field for Monovalent, Divalent, and Trivalent Cations Developed under the Solvent Boundary Potential

(2012) Youngdo Won   JOURNAL OF PHYSICAL CHEMISTRY A

Cellular transport and homeostasis of essential and nonessential metals

(2012) Ebany J. Martinez-Finley et al.   Metallomics

Chemistry of Ni2+in Urease: Sensing, Trafficking, and Catalysis

(2011) Barbara Zambelli et al.   ACCOUNTS OF CHEMICAL RESEARCH

Crystal Structure Determination and Functional Characterization of the Metallochaperone SlyD from Thermus thermophilus

(2010) Christian Löw et al.   JOURNAL OF MOLECULAR BIOLOGY

Rate theories for biologists

(2010) Huan-Xiang Zhou   QUARTERLY REVIEWS OF BIOPHYSICS

Computing accurate potentials of mean force in electrolyte solutions with the generalized gradient-augmented harmonic Fourier beads method

(2008) Ilja V. Khavrutskii et al.   JOURNAL OF CHEMICAL PHYSICS

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

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS