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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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Discovery of Rho-kinase inhibitors by docking-based virtual screening
Mingyun Shen,Huidong Yu,Youyong Li,Pixu Li,Peichen Pan,Shunye Zhou,Liling Zhang,Shang Li,Simon Ming-Yuen Lee,Tingjun Hou,Tingjun Hou +10 more
TL;DR: The structural analysis shows that two active compounds present novel scaffolds and are potential leads for the development of novel anti-cancer drugs and the pharmacological effect of the two ROCK1 inhibitors with novel scaffolding on atorvastatin-induced cerebral hemorrhage was evaluated by using zebrafish model.
Journal ArticleDOI
Prediction of the binding free energies of new TIBO-like HIV-1 reverse transcriptase inhibitors using a combination of PROFEC, PB/SA, CMC/MD, and free energy calculations.
TL;DR: It was found that one of the new derivatives was predicted to bind 1-2 kcal/mol better than R86183, which is the hitherto most tightly binding derivative, and this result was subsequently supported by the most rigorous free energy computational methods: free energy perturbation (FEP) and thermodynamic integration (TI).
Journal ArticleDOI
Cellulose Crystal Dissolution in Imidazolium-Based Ionic Liquids: A Theoretical Study.
TL;DR: This work adopts a molecular dynamics approach to study the dissolution of model cellulose crystal structures in imidazolium-based ILs and gains deep mechanistic insights, demonstrating that dissolution involves IL penetration-induced cleavage of hydrogen bonds between cellulose molecular chains.
Journal ArticleDOI
Modeling of Bulk Kerogen Porosity: Methods for Control and Characterization
TL;DR: In this paper, molecular dynamics simulations are used to study the porosity of model kerogen, which is controlled effectively with systematic variations of the number and the size of dummy LJ particles that are used during the constru...
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Energetics of short hydrogen bonds in photoactive yellow protein
Keisuke Saito,Hiroshi Ishikita +1 more
TL;DR: The short H bond between Glu46 and ionized pCA in the PYP ground state could be simply explained by electrostatic stabilization without invoking LBHB.
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.