pdf #8 - ISLiM 次世代生命体統合シミュレーションソフトウェアの研究開発

生命基盤ソフトウェア開発・高度化チーム成果報告
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Conformational fluctuations of TTHA for in vivo (viv) and in vitro systems (vit1, vit2). The green, red,
and blue curves indicate the root mean square fluctuation (RMSF) of TTHA for in vivo and in vitro
systems. The abscissa axis is the residue number of TTHA and vertical axis is RMSF value (in
Angstrom). Red and white boxes indicate alpha-helices and beta-sheets, respectively.
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[1] Rivas, G., Ferrone, F. and Herzfeld, J. Life in a crowded world. EMBO reports, 5, 1 (Jan 2004), 23-27.
[2] Chebotareva, N. A., Kurganov, B. I. and Livanova, N. B. Biochemical effects of molecular crowding. Biochemistry. Biokhimiia, 69, 11 (Nov
2004), 1239-1251.
[3] Chebotareva, N. A., Andreeva, I. E., Makeeva, V. F., Livanova, N. B. and Kurganov, B. I. Effect of molecular crowding on self-association of
phosphorylase kinase and its interaction with phosphorylase b and glycogen. J. Mol. Recognit., 172004), 426-432.
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ISLiM
ISLiM
10
2011 2011 5
5
8 6 (ISLiM)
2011 (2011.12.21-­22)
42
58% 1500
164
ISLiM
+ ISLiM
2011 2011 11 J.R.Proudfoot, Bioorg. Med. Chem. Lett., 12, 1647(2002) + + 9 "Life Chemicals (Virtual)" subset (# 27) – 490709 entries 630
42
Chemical Library ISLiM
1500
Vietual Library Generator 2011 Rule of 5
Rule of 3
(
ISLiM
2011 ) 630
0.004 Virtual Library 10 12 [1] Lipinski, C., et. al., Adv. Drug. Deliv. Rev., 23, 3(1997) [2] Veber et al.,J. Med. Chem. 45, 2615-­2623 (2002) Lipinski’s rule of 5, rule of 3 (ISLiM)
2011 (2011.12.21-­22)
logP 165
A MW A ISLiM
64.8% 70.7% ISLiM
2011 2011 MW B 79.3% B 88.3% 15 13 "Life Chemicals (Virtual)" subset (# 27) 85.6% 75.3% A A A polar surface area ISLiM
89.9% B B 88.1% 98.5% 2011 10 B polar surface area B 16 91.0% 98.9% 14 "Life Chemicals" subset (# 124) -­ 412431 entries 2011 140 & rotatablebond
97.3% PSA A ISLiM
"Life Chemicals (Virtual)" subset (# 27) – 490709 entries Rotatable bonds Lipinski’s rule of 5
(ISLiM)
2011 (2011.12.21-­22)
logP ĺ
ISLiM
2011 17 ͗
͗
͗
ϭϬ
ϱ
Lipinski’s rule
DB
ISLiM
ϯ
2011 Ϭ͘ϬϬϰ
Transform
ї
ї
18 (ISLiM)
166
2011 (2011.12.21-­22)
(謝辞)
本資料集に記載されている「京」での計算は、2011 年 3 月の「京」の特別運用および
その後の試験利用によって行われたものです。
また、本資料集に記載されている「京」を使用した測定値は、開発整備中の「京」によ
る、測定時点での数値です。