Development of AMBER parameters for molecular dynamics simulations of boron compounds containing aromatic structure

AMBER Force Field Parameters for Cobalt-Containing Biological Systems: A Systematic Derivation Study

(2020) Hamed Haghshenas et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Parameterization of Boronates Using VFFDT and Paramfit for Molecular Dynamics Simulation

(2020) Barış Kurt et al.   MOLECULES

Synthesis, characterization, DNA interaction and docking studies of novel Schiff base ligand derived from 2,6-diaminopyridine and its complexes

(2020) Barış Kurt et al.   JOURNAL OF MOLECULAR STRUCTURE

Development of CHARMM-Compatible Force-Field Parameters for Cobalamin and Related Cofactors from Quantum Mechanical Calculations

(2018) Anna Pavlova et al.   Journal of Chemical Theory and Computation

Synthesis of biologically active boron-containing compounds

(2018) Fei Yang et al.   MedChemComm

VFFDT: A New Software for Preparing AMBER Force Field Parameters for Metal-Containing Molecular Systems

(2016) Suqing Zheng et al.   Journal of Chemical Information and Modeling

Paramfit: Automated optimization of force field parameters for molecular dynamics simulations

(2014) Robin M. Betz et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

(2013) Daniel R. Roe et al.   Journal of Chemical Theory and Computation

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

(2012) Marcus D Hanwell et al.   Journal of Cheminformatics

Comparison of Methods to Obtain Force-Field Parameters for Metal Sites

(2011) LiHong Hu et al.   Journal of Chemical Theory and Computation

AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility

(2009) Garrett M. Morris et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Evaluation of Amber force field parameters for copper(II) with pyridylmethyl-amine and benzimidazolylmethyl-amine ligands: A quantum chemical study

(2008) Yanyan Zhu et al.   CHEMICAL PHYSICS LETTERS