𝔖 Bobbio Scriptorium
✦   LIBER   ✦

Theoretical study of the prion protein based on the fragment molecular orbital method

✍ Scribed by Takeshi Ishikawa; Takakazu Ishikura; Kazuo Kuwata

Publisher
John Wiley and Sons
Year
2009
Tongue
English
Weight
552 KB
Volume
30
Category
Article
ISSN
0192-8651

No coin nor oath required. For personal study only.

✦ Synopsis

Abstract

We performed fragment molecular orbital (FMO) calculations to examine the molecular interactions between the prion protein (PrP) and GN8, which is a potential curative agent for prion diseases. This study has the following novel aspects: we introduced the counterpoise method into the FMO scheme to eliminate the basis set superposition error and examined the influence of geometrical fluctuation on the interaction energies, thereby enabling rigorous analysis of the molecular interaction between PrP and GN8. This analysis could provide information on key amino acid residues of PrP as well as key units of GN8 involved in the molecular interaction between the two molecules. The present FMO calculations were performed using an original program developed in our laboratory, called “Parallelized ab initio calculation system based on FMO (PAICS)”. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009

📜 SIMILAR VOLUMES

QM/QM docking method based on the variat
QM/QM docking method based on the variational finite localized molecular orbital approximation
✍ Victor M. Anisimov; Vladislav L. Bugaenko 📂 Article 📅 2009 🏛 John Wiley and Sons 🌐 English ⚖ 236 KB

## Abstract We present a derivation of the semiempirical variational finite localized molecular orbital (VFL) approximation, which was introduced by Anikin et al. (J Chem Phys 2004, 121, 1266). On the basis of VFL approximation, we developed the novel semiempirical (quantum mechanical) QM/QM method

Fragment molecular orbital study of the
Fragment molecular orbital study of the electronic excitations in the photosynthetic reaction center of Blastochloris viridis
✍ Tsutomu Ikegami; Toyokazu Ishida; Dmitri G. Fedorov; Kazuo Kitaura; Yuichi Inado 📂 Article 📅 2009 🏛 John Wiley and Sons 🌐 English ⚖ 345 KB

## Abstract All electron calculations were performed on the photosynthetic reaction center of __Blastochloris viridis__, using the fragment molecular orbital (FMO) method. The protein complex of 20,581 atoms and 77,754 electrons was divided into 1398 fragments, and the two‐body expansion of FMO/6‐3

Accuracy of the three-body fragment mole
Accuracy of the three-body fragment molecular orbital method applied to Møller–Plesset perturbation theory
✍ Dmitri G. Fedorov; Kazuya Ishimura; Toyokazu Ishida; Kazuo Kitaura; Peter Pulay; 📂 Article 📅 2007 🏛 John Wiley and Sons 🌐 English ⚖ 833 KB

## Abstract The three‐body energy expansion in the fragment molecular orbital method (FMO) was applied to the 2nd order Møller–Plesset theory (MP2). The accuracy of both the two and three‐body expansions was determined for water clusters, alanine __n__‐mers (α‐helices and β‐strands) and one synthet

On the justifiability of neglect of diff
On the justifiability of neglect of differential overlap molecular orbital methods
✍ K.R. Roby 📂 Article 📅 1971 🏛 Elsevier Science 🌐 English ⚖ 618 KB

A theorem found recentIy is used to justify dirktly the NDDO approximate MoIecuhr hrbitai method. A simifar ,' justikation of CNDO-type methods cannot be obtained. The theorem also suggests how previous treatments based '\_ .' on a power series expansion may be generaiiscd so that divergence difficu