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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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Crystal Structure and Molecular Modeling of 17-DMAG in Complex with Human Hsp90
TL;DR: Targeted molecular dynamics simulations and energetic analysis indicate that geldanamycin undergoes two major conformational changes when it binds Hsp90, with the key step of the conversion being the trans to cis conformational change of the macrocycle amide bond.
Journal ArticleDOI
Mitochondrial Targeting of Vitamin E Succinate Enhances Its Pro-apoptotic and Anti-cancer Activity via Mitochondrial Complex II
Lan-Feng Dong,Victoria J.A. Jameson,David Tilly,Jiri Cerny,Elahe Mahdavian,Alvaro Marín-Hernández,Luz Hernández-Esquivel,Sara Rodríguez-Enríquez,Jan Stursa,Paul K. Witting,Bela Stantic,Jakub Rohlena,Jaroslav Truksa,Katarina Kluckova,Jeffrey Clifford Dyason,Miroslav Ledvina,Brian A. Salvatore,Rafael Moreno-Sánchez,Mark J. Coster,Stephen John Ralph,Robin A.J. Smith,Jiri Neuzil +21 more
TL;DR: It is proposed that mitochondrial targeting of VES with an 11-carbon chain localizes the agent into an ideal position across the interface of the mitochondrial inner membrane and matrix, optimizing its biological effects as an anti-cancer drug.
Journal ArticleDOI
Soft‐core potentials in thermodynamic integration: Comparing one‐ and two‐step transformations
TL;DR: This work provides recommended values for the two parameters αLJ and βC controlling the behavior of the soft‐core Lennard–Jones and Coulomb potentials and compares one‐ and two‐step transformations with regard to their suitability for numerical integration.
Journal ArticleDOI
Correlated ab initio study of nucleic acid bases and their tautomers in the gas phase, in a microhydrated environment and in aqueous solution. Part 4. Uracil and thymine
TL;DR: It is concluded that it is impossible to utilize the method used by Suwaiyan and Morsy for tautomer detection, even if a very sensitive fluorimeter is used, because gas phase destabilization of these enol forms is too high and canonical structure will also be dominant in this phase.
Journal ArticleDOI
Reentrant liquid condensate phase of proteins is stabilized by hydrophobic and non-ionic interactions
Georg Krainer,Timothy J. Welsh,Jerelle A. Joseph,Jorge R. Espinosa,Sina Wittmann,Sina Wittmann,Ella de Csillery,Akshay Sridhar,Zenon Toprakcioglu,Giedre Gudiškytė,Magdalena A. Czekalska,Magdalena A. Czekalska,William E. Arter,Jordina Guillén-Boixet,Titus M. Franzmann,Seema Qamar,Peter St George-Hyslop,Peter St George-Hyslop,Anthony A. Hyman,Rosana Collepardo-Guevara,Simon Alberti,Tuomas P. J. Knowles +21 more
TL;DR: In this paper, the authors show that a wide range of cellular proteins, including FUS, TDP-43, Brd4, Sox2, and Annexin A11, can reenter a phase-separated regime at high salt concentrations.
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.