Journal ArticleDOI
A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model
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In this paper, the authors present an approach to generate electrostatic potential (ESP) derived charges for molecules, which optimally reproduce the intermolecular interaction properties of molecules with a simple two-body additive potential, provided that a suitably accurate level of quantum mechanical calculation is used to derive the ESP around the molecule.Abstract:
We present a new approach to generating electrostatic potential (ESP) derived charges for molecules. The major strength of electrostatic potential derived charges is that they optimally reproduce the intermolecular interaction properties of molecules with a simple two-body additive potential, provided, of course, that a suitably accurate level of quantum mechanical calculation is used to derive the ESP around the molecule. Previously, the major weaknesses of these charges have been that they were not easily transferable between common functional groups in related molecules, they have often been conformationally dependent, and the large charges that frequently occur can be problematic for simulating intramolecular interactionsread more
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Book ChapterDOI
Thermodynamics of Ligand-Protein Interactions: Implications for Molecular Design
TL;DR: This chapter addresses several practical aspects of assessing the thermodynamic parameters in molecular design, and provides the reader several examples of ligand-protein interactions and focus on the forces driving the associations, which can be very different from case to case.
Journal ArticleDOI
On the Origin of the Stronger Binding of PIB over Thioflavin T to Protofibrils of the Alzheimer Amyloid-β Peptide: A Molecular Dynamics Study
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Computer simulation of polypropylene/organoclay nanocomposites: characterization of atomic scale structure and prediction of the binding energy
Emo Chiellini,A. Coslanich,Maurizio Fermeglia,Marco Ferrone,S Meriani,Stanislav Miertus,Sabrina Pricl,Radovan Toth +7 more
TL;DR: In this paper, molecular simulation techniques are used to explore and characterize the atomic scale structure, and to predict binding energies and basal spacing of polymer/clay nanocomposites based on polypropylene (PP) and maleated polypropylon (PPMA), montmorillonite (MMT), and different alkylammonium ions (quats) as surfactants.
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ATP Hydrolysis in the βTP and βDP Catalytic Sites of F1-ATPase
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References
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Journal ArticleDOI
The MIDAS display system
TL;DR: At the core of MIDAS is a hierarchical database system, designed specifically for macromolecules, that is both compact in its storage requirements and fast in its data access.