Molecular modelling: Principles and applications

By J. Crabbe. 1997

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Citations in the corpus

Directional Message Passing for Molecular Graphs (2020, background): “Classically, these functions have been modeled as the sum of four parts: (Leach, 2001) E = Ebonds + Eangle + Etorsion + Enon-bonded, (1) where Ebonds models the dependency on bond lengths, Eangle on the angles between bonds, Etorsion on bond rotations, i.”
REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for its use. (2004, background): “period equal to zero or one as they can only have a single value. (vii) Plane category. This category contains the list of planes and of all atoms belonging to them. (viii) Chirality category. This category contains the list of all chiral centres. For each chiral centre it also lists the central ato”
Fluctuating charge force fields: recent developments and applications from small molecules to macromolecular biological systems (2006, unknown): “observations and guiding further experiment [1].”
Recent advances in ligand-based drug design: relevance and utility of the conformationally sampled pharmacophore approach. (2011, background): “In order to achieve a complete sampling of conformational space rigorous molecular dynamics (MD) simulations [95] are an essential part of CSP.”
A machine learning approach to predicting protein-ligand binding affinity with applications to molecular docking (2010, unknown): “…the r−6 attractive term can be shown to arise as a result of dispersion interactions between two isolated atoms, this does not include the significant higher order contributions to the dispersion energy, as well as the many-body effects that are present in protein–ligand interactions (Leach, 2001).”
Exploring potential energy surfaces for chemical reactions: An overview of some practical methods (2003, methodology): “Similar to the RFO and trust radius methods, the step is controlled by adding an offset to the Hessian, as in eq. ( 7 ).”
Shadow hybrid Monte Carlo: an efficient propagator in phase space of macromolecules (2004, background): “Examples of observables A are potential energy, pressure, free energy, and distribution of solvent molecules in vacancies [3,9].”
Bridging Molecular Docking to Molecular Dynamics in Exploring Ligand-Protein Recognition Process: An Overview (2018, methodology): “Molecular dynamics compute the movements of atoms along time by the integration of Newton’s equations of motions (classical mechanics), reported in the following equation (Leach, 2001; Adcock and McCammon, 2006).”
Docking and scoring in virtual screening for drug discovery: methods and applications (2004, background): “These algorithms try to explore all the degrees of freedom in a molecule, but ultimately face the problem of combinatorial explosio”
Predicting Molecular Conformation via Dynamic Graph Score Matching (2021, background): “While in molecular mechanics, the potential energy of a molecule that alters conformations can be modeled as a sum of four parts [22]: E = Ebond + Eangle + Etorsion + Enon-bonded, (1) where Ebond, Eangle, and Etorsion model local interactions between bonded atoms, which are modeled in previous metho”
Thermal conductivity of metal-organic framework 5 (MOF-5): Part I. Molecular dynamics simulations (2007, background): “The C3-H group is taken to be a rigid entity (by adding the hydrogen mass to the carbon mass), a common treatment for hydrogen atoms in MD [16].”
GROMACS: Fast, flexible, and free (2005, background): “72), such questions can be reduced to the difference in Gibbs free energy between two systems with different Hamil-tonians.”
Multiwfn: A multifunctional wavefunction analyzer (2012, background): “[63] It denotes the number of states in unit energy interval.”