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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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Reaction Pathway and Free Energy Profile for Papain-Catalyzed Hydrolysis of N-Acetyl-Phe-Gly 4-Nitroanilide
TL;DR: Possible reaction pathways for papain-catalyzed hydrolysis of N-acetyl-Phe-Gly 4-nitroanilide (APGNA) have been studied by performing pseudobond first-principles quantum mechanical/molecular mechanical-free energy calculations and it has been demonstrated that the most favorable reaction path in this stage is path B.
Journal ArticleDOI
Influence of doxorubicin on model cell membrane properties: insights from in vitro and in silico studies.
Ana Catarina Alves,Aniket Magarkar,Aniket Magarkar,Miguel Horta,José L. F. C. Lima,Alex Bunker,Cláudia Nunes,Salette Reis +7 more
TL;DR: This work represents a successful approach, combining experimental and computational studies of membrane based systems to unveil the behavior of drugs and candidate drug molecules.
Journal ArticleDOI
Crosslinked Aspartic Acids as Helix-Nucleating Templates
Hui Zhao,Qisong Liu,Hao Geng,Yuan Tian,Min Cheng,Yanhong Jiang,Mingsheng Xie,Xiaogang Niu,Fan Jiang,Yaou Zhang,Yuanzhi Lao,Yun-Dong Wu,Naihan Xu,Zigang Li +13 more
TL;DR: Peptidomimetic estrogen receptor modulators (PERMs) constructed using this strategy show improved therapeutic properties and can be regarded as a good complement to existing helix-stabilizing methods.
Journal ArticleDOI
DNA repair mechanism by photolyase: electron transfer path from the photolyase catalytic cofactor FADH(-) to DNA thymine dimer.
TL;DR: Analysis of the electronic coupling and electron transfer pathway between the catalytic cofactor FADH(-) and the pyrimidine dimer by the method of interatomic tunneling currents shows explicitly that despite of the close proximity between the donor and acceptor complexes, the electron transfer mechanism is not direct, but indirect, with the adenine acting as an intermediate.
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Synthesis, Activity, and Molecular Modeling Studies of Novel Human Aldose Reductase Inhibitors Based on a Marine Natural Product
Jesús Ángel de la Fuente,Sonia Manzanaro,María Jesús Martín,Teresa García De Quesada,Isabel Reymundo,Santos Luengo,Federico Gago +6 more
TL;DR: A polybrominated diphenyl ether naturally occurring in a marine sponge was found to inhibit recombinant human ALR2 with an IC(50) of 6.4 microM, and a crucial bromine atom is assessed that distinguishes the active lead compound from a much less active close natural analogue.
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.