Volume 18; Issue 3

Journal of Molecular Modeling

Volume 18; Issue 3

1

Unique example of amyloid aggregates stabilized by main chain H-bond instead of the steric zipper: molecular dynamics study of the amyloidogenic segment of amylin wild-type and mutants

Workalemahu Mikre Berhanu, Artëm E. Masunov

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 1.08 MB

english, 2012

2

Probing the structural requirements of A-type Aurora kinase inhibitors using 3D-QSAR and molecular docking analysis

Hui-xiao Zhang, Yan Li, Xia Wang, Yong-hua Wang

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 1.01 MB

english, 2012

3

Transformation of the θ-phase in Mg-Li-Al alloys: a density functional theory study

Caili Zhang, Peide Han, Zhuxia Zhang, Minghui Dong, Lili Zhang, Xiangyang Gu, Yanqing Yang, Bingshe Xu

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 226 KB

english, 2012

4

Interactions of uranyl ion with cytochromeb5and its His39Ser variant as revealed by molecular simulation in combination with experimental methods

Dun Wan, Li-Fu Liao, Min-Min Zhao, Min-Long Wu, Yi-Mou Wu, Ying-Wu Lin

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 328 KB

english, 2012

5

Analysis of surface cavity in serpin family reveals potential binding sites for chemical chaperone to reduce polymerization

Poonam Singh, Mohammad Sazzad Khan, Asma Naseem, Mohamad Aman Jairajpuri

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 509 KB

english, 2012

6

Ab initioDFT study of bisphosphonate derivatives as a drug for inhibition of cancer: NMR and NQR parameters

Hussein Aghabozorg, Beheshteh Sohrabi, Sara Mashkouri, Hamid Reza Aghabozorg

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 245 KB

english, 2012

7

Influence of stereochemistry on proton transfer in protonated tripeptide models

Namat Ali Soliman, Petr Kulhánek, Jaroslav Koča

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 311 KB

english, 2012

8

Problems with molecular mechanics implementations on the example of 4-benzoyl-1-(4-methyl-imidazol-5-yl)-carbonylthiosemicarbazide

Agata Siwek, Katarzyna Świderek, Stefan Jankowski

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 322 KB

english, 2012

9

Density functional theory studies on the inclusion complexes of cyclic decapeptide with 1-phenyl-1-propanol enantiomers

Hongge Zhao, Yanyan Zhu, Mingqiong Tong, Juan He, Chunmei Liu, Mingsheng Tang

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 474 KB

english, 2012

10

Computational characterization of the molecular structure and properties of Dye 7 for organic photovoltaics

Jesús Baldenebro-López, José Castorena-González, Norma Flores-Holguin, Joel Calderón-Guillén, Daniel Glossman-Mitnik

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 447 KB

english, 2012

11

Insights into the permeability of drugs and drug-likemolecules from MI-QSAR and HQSAR studies

Ranajit N. Shinde, K. Srikanth, M. Elizabeth Sobhia

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 538 KB

english, 2012

12

Controlling the aggregation and rate of release in order to improve insulin formulation: molecular dynamics study of full-length insulin amyloid oligomer models

Workalemahu Mikre Berhanu, Artëm E. Masunov

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 833 KB

english, 2012

13

Determination of best-fit potential parameters for a reactive force field using a genetic algorithm

Poonam Pahari, Shashank Chaturvedi

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 332 KB

english, 2012

14

Ab initio simulation of the effect of the potential of water on the electronic structure of arginine

Xingrong Wang, Haoping Zheng

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 319 KB

english, 2012

15

Theoretical study on the structural, vibrational, and thermodynamic properties of the (Br2GaN3)n(n = 1–4) clusters

Qi-Ying Xia, Qing-Fu Lin, Wen-Wei Zhao

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 175 KB

english, 2012

16

Topological properties of some PhSeX compounds

Nora Beatriz Okulik, Alicia H. Jubert, Eduardo A. Castro

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 278 KB

english, 2012

17

The role of CS2in CS2/NMP mixed solvent in weakening the hydrogen bond of OH–N in coal: a DFT investigation

Baojun Wang, Liping Wang, Riguang Zhang, Lixia Ling

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 367 KB

english, 2012

18

The insertion reactions of the p-complex silylenoid H2SiLiF with Si-X (X=F, Cl, Br, O, N) bonds

Yuhua Qi, Bing Geng, Zhonghe Chen

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 348 KB

english, 2012

19

NMR and NQR parameters of the SiC-doped on the (4,4)armchairsingle-walled BPNT: a computational study

Mohammad T. Baei, S. Zahra Sayyad-Alangi, Ali Varasteh Moradi, Parviz Torabi

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 338 KB

english, 2012

20

Time-dependent density functional theory study on the electronic excited-state hydrogen bonding of the chromophore coumarin 153 in a room-temperature ionic liquid

Dandan Wang, Ce Hao, Se Wang, Hong Dong, Jieshan Qiu

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 285 KB

english, 2012

21

Theoretical study of crown ethers with incorporated azobenzene moiety

Yuan Miao, Xueye Wang, Dan Ouyang

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 471 KB

english, 2012

22

Substrate binding and translocation of the serotonin transporter studied by docking and molecular dynamics simulations

Mari Gabrielsen, Aina Westrheim Ravna, Kurt Kristiansen, Ingebrigt Sylte

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 758 KB

english, 2012

23

Molecular modeling studies on phosphonic acid-containing thiazole derivatives: design for fructose-1,6-bisphosphatase inhibitors

Ping Lan, Zhi-Wei Wu, Wan-Na Chen, Ping-Hua Sun, Wei-Min Chen

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 870 KB

english, 2012

24

In silico screening of epidermal growth factor receptor (EGFR) in the tyrosine kinase domain through a medicinal plant compound database

Orathai Sawatdichaikul, Supa Hannongbua, Chak Sangma, Peter Wolschann, Kiattawee Choowongkomon

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 887 KB

english, 2012

25

Predicting the potency of hERG K+channel inhibition by combining 3D-QSAR pharmacophore and 2D-QSAR models

Yayu Tan, Yadong Chen, Qidong You, Haopeng Sun, Manhua Li

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 320 KB

english, 2012

26

Studies of H4R antagonists using 3D-QSAR, molecular docking and molecular dynamics

Jing Liu, Yan Li, Hui-Xiao Zhang, Shu-Wei Zhang, Ling Yang

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 756 KB

english, 2012

27

Ab initio study of MKrn2+(M = Cu, Ag, and Au, n = 1-6) clusters

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 338 KB

english, 2012

28

Virtual screening for potential inhibitors of bacterial MurC and MurD ligases

Tihomir Tomašić, Andreja Kovač, Gerhard Klebe, Didier Blanot, Stanislav Gobec, Danijel Kikelj, Lucija Peterlin Mašič

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 802 KB

english, 2012

29

Molecular docking and structural analysis of cofactor-protein interaction between NAD+and 11β-hydroxysteroid dehydrogenase type 2

Hideaki Yamaguchi, Tatsuo Akitaya, Tao Yu, Yumi Kidachi, Katsuyoshi Kamiie, Toshiro Noshita, Hironori Umetsu, Kazuo Ryoyama

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 1.24 MB

english, 2012

30

Improving the desolvation penalty in empirical protein pKamodeling

Mats H. M. Olsson

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 363 KB

english, 2012

31

Homology modeling of the structure of acyl coA:isopenicillin N-acyltransferase (IAT) fromPenicillium chrysogenum. IAT interaction studies with isopenicillin-N, combining molecular dynamics simulations and docking

Liliana Moreno-Vargas, Jose Correa-Basurto, Rachid C. Maroun, Francisco J. Fernández

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 964 KB

english, 2012

32

Insight into the binding interactions of CYP450 aromatase inhibitors with their target enzyme: a combined molecular docking and molecular dynamics study

Roberta Galeazzi, Luca Massaccesi

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 1.18 MB

english, 2012

33

Homology modeling, molecular dynamics and QM/MM study of the regulatory protein PhoP fromCorynebacterium pseudotuberculosis

Gleiciane Moraes, Vasco Azevedo, Marcília Costa, Anderson Miyoshi, Artur Silva, Vivian da Silva, Diana de Oliveira, Maria Fátima Teixeira, Jerônimo Lameira, Cláudio Nahum Alves

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 478 KB

english, 2012

34

Molecular docking and 3D-QSAR study on 4-(1H-indazol-4-yl) phenylamino and aminopyrazolopyridine urea derivatives as kinase insert domain receptor (KDR) inhibitors

Xiaoyun Wu, Shuguang Wu, Wen-Hua Chen

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 776 KB

english, 2012

35

Replica exchange molecular dynamics simulation of structure variation from α/4β-fold to 3α-fold protein

Raudah Lazim, Ye Mei, Dawei Zhang

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 695 KB

english, 2012

36

Quantitative structure activity relationships of some pyridine derivatives as corrosion inhibitors of steel in acidic medium

El Sayed H. El Ashry, Ahmed El Nemr, Safaa Ragab

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 681 KB

english, 2012

37

Pressure-induced phase transition in wurtzite ZnTe: an ab initio study

Sebahaddin Alptekin

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 334 KB

english, 2012

38

Mechanism of intermolecular hydroacylation of vinylsilanes catalyzed by a rhodium(I) olefin complex: a DFT study

Qingxi Meng, Wei Shen, Ming Li

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 605 KB

english, 2012

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