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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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The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme.
TL;DR: The relaxed complex method recognizes that ligand may bind to conformations that occur only rarely in the dynamics of the receptor, and is capable of finding the best ligand enzyme complexes.
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Effective Charges for Macromolecules in Solvent
TL;DR: In this article, the authors derived the effective charges by fitting them to reproduce the molecular electrostatic potential calculated by numerical solution of the finite-difference linearized Poisson−Boltzmann equation.
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Modeling structure and flexibility of Candida antarctica lipase B in organic solvents
Peter Trodler,Jürgen Pleiss +1 more
TL;DR: The reduced flexibility of Candida antarctica lipase B in organic solvent is caused by a spanning water network resulting from less mobile and slowly exchanging water molecules at the protein-surface, caused by the interactions between solvent-protein.
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GROMACS molecule & liquid database
TL;DR: A web-based database, containing 145 organic molecules, is provided, containing pre-calculated physical properties along with experimental values for the same, which are simulated using two different force fields, OPLS all atom and Generalized Amber Force Field.
Journal ArticleDOI
Pyrano[3,2-c]quinoline−6-Chlorotacrine Hybrids as a Novel Family of Acetylcholinesterase- and β-Amyloid-Directed Anti-Alzheimer Compounds
Pelayo Camps,Xavier Formosa,Carles Galdeano,Diego Muñoz-Torrero,Lorena Ramírez,Elena Gómez,Nicolas Isambert,Rodolfo Lavilla,Albert Badia,M. Victòria Clos,Manuela Bartolini,Francesca Mancini,Vincenza Andrisano,Mariana P. Arce,M. Isabel Rodríguez-Franco,Oscar Huertas,Thomai Dafni,F. Javier Luque +17 more
TL;DR: Two isomeric series of dual binding site acetylcholinesterase (AChE) inhibitors that retain the potent and selective human AChE inhibitory activity of the parent 6-chlorotacrine while exhibiting a significant in vitro inhibitoryActivity toward the AChe-induced and self-induced Abeta aggregation and toward BACE-1, as well as ability to enter the central nervous system, which makes them promising anti-Alzheimer lead compounds.
References
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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.