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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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TLDR
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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Identification of a putative binding site for [2',5'-bis-O-(tert-butyldimethylsilyl)-beta-D-ribofuranosyl]-3'-spiro-5''-(4''-amino-1'',2''-oxathiole-2'',2''-dioxide)thymine (TSAO) derivatives at the p51-p66 interface of HIV-1 reverse transcriptase.
Fátima Rodríguez-Barrios,Carlos Perez,Esther Lobatón,Sonsoles Velázquez,Cristina Chamorro,Ana San-Félix,María-Jesús Pérez-Pérez,María-José Camarasa,Heidi Pelemans,Jan Balzarini,Federico Gago +10 more
TL;DR: The molecular model is in agreement with a previous proposal, with known structure-activity and mutagenesis data for this unique class of inhibitors, and also with recent biochemical evidence indicating that TSAO analogues can affect enzyme dimerization.
Journal ArticleDOI
Early stage intercalation of doxorubicin to DNA fragments observed in molecular dynamics binding simulations.
TL;DR: This study conducted molecular dynamics binding simulations of doxorubicin and two 6-base-pair DNA model fragments using AMBER DNA and drug force fields and observed that the minor groove binding is the dominant pre-intercalation step.
Journal ArticleDOI
Novel huprine derivatives with inhibitory activity toward β-amyloid aggregation and formation as disease-modifying anti-Alzheimer drug candidates.
Elisabet Viayna,Tània Gómez,Carles Galdeano,Lorena Ramírez,Miriam Ratia,Albert Badia,M. Victòria Clos,Ester Verdaguer,Felix Junyent,Antoni Camins,Mercè Pallàs,Manuela Bartolini,Francesca Mancini,Vincenza Andrisano,Mariana P. Arce,María Isabel Rodríguez-Franco,Axel Bidon-Chanal,F. Javier Luque,Pelayo Camps,Diego Muñoz-Torrero +19 more
TL;DR: The new heterodimers are potent inhibitors of human AChE and moderately potent inhibitors that are predicted to be able to enter the central nervous system (CNS), thus constituting promising multitarget anti‐Alzheimer drug candidates with the potential to modify the natural course of this disease.
Journal ArticleDOI
Molecular dynamics simulations of the structural and thermodynamic properties of imidazolium-based ionic liquid mixtures.
TL;DR: In this work, extensive molecular dynamics simulations of mixtures of alcohols of several chain lengths (methanol and ethanol) with the ionic liquids (ILs) composed of the cation 1-hexyl-3-methylimidazolium and several anions of different hydrophobicity degrees are reported and analyzed.
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Binding free energy calculations of N -sulphonyl-glutamic acid inhibitors of MurD ligase
TL;DR: Calculations of binding free energies for selected moieties of compounds in this structural class substantiated even deeper insight into the source of inhibitory activity and constitute new valuable information to further assist the lead optimization process.
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.