Literature DB >> 25796231

3D RISM theory with fast reciprocal-space electrostatics.

Jochen Heil1, Stefan M Kast1.   

Abstract

The calculation of electrostatic solute-solvent interactions in 3D RISM ("three-dimensional reference interaction site model") integral equation theory is recast in a form that allows for a computational treatment analogous to the "particle-mesh Ewald" formalism as used for molecular simulations. In addition, relations that connect 3D RISM correlation functions and interaction potentials with thermodynamic quantities such as the chemical potential and average solute-solvent interaction energy are reformulated in a way that calculations of expensive real-space electrostatic terms on the 3D grid are completely avoided. These methodical enhancements allow for both, a significant speedup particularly for large solute systems and a smoother convergence of predicted thermodynamic quantities with respect to box size, as illustrated for several benchmark systems.

Year:  2015        PMID: 25796231     DOI: 10.1063/1.4914321

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  8 in total

1.  Drugging the catalytically inactive state of RET kinase in RET-rearranged tumors.

Authors:  Dennis Plenker; Maximilian Riedel; Johannes Brägelmann; Marcel A Dammert; Rakhee Chauhan; Phillip P Knowles; Carina Lorenz; Marina Keul; Mike Bührmann; Oliver Pagel; Verena Tischler; Andreas H Scheel; Daniel Schütte; Yanrui Song; Justina Stark; Florian Mrugalla; Yannic Alber; André Richters; Julian Engel; Frauke Leenders; Johannes M Heuckmann; Jürgen Wolf; Joachim Diebold; Georg Pall; Martin Peifer; Maarten Aerts; Kris Gevaert; René P Zahedi; Reinhard Buettner; Kevan M Shokat; Neil Q McDonald; Stefan M Kast; Oliver Gautschi; Roman K Thomas; Martin L Sos
Journal:  Sci Transl Med       Date:  2017-06-14       Impact factor: 17.956

2.  Structure of a Therapeutic Full-Length Anti-NPRA IgG4 Antibody: Dissecting Conformational Diversity.

Authors:  Michaela Blech; Stefan Hörer; Alexander B Kuhn; Sebastian Kube; Hendrik Göddeke; Hans Kiefer; Yuguo Zang; Yannic Alber; Stefan M Kast; Martin Westermann; Mark D Tully; Lars V Schäfer; Patrick Garidel
Journal:  Biophys J       Date:  2019-04-05       Impact factor: 4.033

3.  The SAMPL6 challenge on predicting aqueous pKa values from EC-RISM theory.

Authors:  Nicolas Tielker; Lukas Eberlein; Stefan Güssregen; Stefan M Kast
Journal:  J Comput Aided Mol Des       Date:  2018-08-02       Impact factor: 3.686

4.  The SAMPL5 challenge for embedded-cluster integral equation theory: solvation free energies, aqueous pK a, and cyclohexane-water log D.

Authors:  Nicolas Tielker; Daniel Tomazic; Jochen Heil; Thomas Kloss; Sebastian Ehrhart; Stefan Güssregen; K Friedemann Schmidt; Stefan M Kast
Journal:  J Comput Aided Mol Des       Date:  2016-08-23       Impact factor: 3.686

5.  Signatures of Solvation Thermodynamics in Spectra of Intermolecular Vibrations.

Authors:  Rasmus A X Persson; Viren Pattni; Anurag Singh; Stefan M Kast; Matthias Heyden
Journal:  J Chem Theory Comput       Date:  2017-08-25       Impact factor: 6.006

6.  The SAMPL6 challenge on predicting octanol-water partition coefficients from EC-RISM theory.

Authors:  Nicolas Tielker; Daniel Tomazic; Lukas Eberlein; Stefan Güssregen; Stefan M Kast
Journal:  J Comput Aided Mol Des       Date:  2020-01-24       Impact factor: 3.686

7.  Integral equation models for solvent in macromolecular crystals.

Authors:  Jonathon G Gray; George M Giambaşu; David A Case; Tyler Luchko
Journal:  J Chem Phys       Date:  2022-01-07       Impact factor: 3.488

8.  Quantum-mechanical property prediction of solvated drug molecules: what have we learned from a decade of SAMPL blind prediction challenges?

Authors:  Nicolas Tielker; Lukas Eberlein; Gerhard Hessler; K Friedemann Schmidt; Stefan Güssregen; Stefan M Kast
Journal:  J Comput Aided Mol Des       Date:  2020-10-20       Impact factor: 3.686

  8 in total

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