Volume 19; Issue 8

Journal of Molecular Modeling

Volume 19; Issue 8

1

Proteasomal cleavage site prediction of protein antigen using BP neural network based on a new set of amino acid descriptor

Wang, Yuanqiang, Lin, Yong, Shu, Mao, Wang, Rui, Hu, Yong, Lin, Zhihua

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 246 KB

english, 2013

2

Thermodynamic computational approach to capture molecular recognition in the binding of different inhibitors to the DNA gyrase B subunit fromEscherichia coli

SaÃz-Urra, Liane, PÃ©rez, Miguel Ãngel Cabrera, Froeyen, Matheus

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 487 KB

english, 2013

3

Synthesis and biological evaluation of cationic fullerene quinazolinone conjugates and their binding mode with modeledMycobacterium tuberculosishypoxanthine-guanine phosphoribosyltransferase enzyme

Patel, Manishkumar B., Kumar, Sivakumar Prasanth, Valand, Nikunj N., Jasrai, Yogesh T., Menon, Shobhana K.

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 996 KB

english, 2013

4

A theoretical investigation on the proton transfer tautomerization mechanisms of 2-thioxanthine within microsolvent and long range solvent

Ren, Hong-Jiang, Su, Ke-He, Liu, Yan, Li, Xiao-Jun, Xiao, Jun, Wang, Yan-Li

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 2.03 MB

english, 2013

5

Understanding the antioxidant behavior of some vitamin molecules: a first-principles density functional approach

Kumar, Vipin, Kishor, Shyam, Ramaniah, Lavanya M.

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 665 KB

english, 2013

6

Comparison of gas phase intrinsic properties of cytosine and thymine nucleobases with their O-alkyl adducts: different hydrogen bonding preferences for thymine versus O-alkyl thymine

Aliakbar Tehrani, Zahra, Fattahi, Alireza

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 475 KB

english, 2013

7

A large gap opening of graphene induced by the adsorption of CO on the Al-doped site

Peyghan, Ali Ahmadi, Noei, Maziar, Tabar, Mohammad Bigdeli

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 698 KB

english, 2013

8

Gene identification and comparative molecular modeling of aTrypanosoma rangelimajor surface protease

Calixto, Paulo H. M., Bitar, MainÃ¡, Ferreira, Keila A. M., AbrahÃ£o, OdonÃrio, Lages-Silva, Eliane, Franco, GlÃ³ria R., RamÃrez, Luis E., Pedrosa, AndrÃ© L.

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 1.06 MB

english, 2013

9

Insight into the 3D structure of ADP-glucose pyrophosphorylase from rice (Oryza sativaL.)

Dawar, Chhavi, Jain, Sunita, Kumar, Sudhir

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 1.64 MB

english, 2013

10

Quantum-chemical studies on thermodynamic feasibility of 1-methyl-2,4,5-trinitroimidazole processes

Jadhav, Pandurang M., Sarangapani, Radhakrishnan, Ghule, Vikas D., Prasanth, Hima, Pandey, Raj Kishore

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 356 KB

english, 2013

11

Retrospective molecular docking study of WY-25105 ligand to β-secretase and bias of the three-dimensional structure flexibility

Ghemtio, Leo, Muzet, Nicolas

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 797 KB

english, 2013

12

Insight into the binding model of new antagonists of kappa receptor using docking and molecular dynamics simulation

Hu, Shiyuan, Yu, Haijing, Liu, Yongjuan, Xue, Tian, Zhang, Huabei

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 688 KB

english, 2013

13

Relation between topology and stability of bent titanocenes

Lima dos Santos, Hugo Felix, L. Pontes, Daniel, Firme, Caio L.

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 724 KB

english, 2013

14

Density functional theory study of epoxy polymer chains adsorbing onto single-walled carbon nanotubes: electronic and mechanical properties

Ahangari, Morteza Ghorbanzadeh, Fereidoon, Abdolhosein, Ganji, Masoud Darvish

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 613 KB

english, 2013

15

Density functional theory investigation of cocaine water complexes

Senthilkumar, Lakshmipathi, Umadevi, Palanivel, Nithya, Kumaranathapuram Natarajan Sweety, Kolandaivel, Ponmalai

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 816 KB

english, 2013

16

Degradation of polyvinyl alcohol under mechanothermal stretching

Cristancho, Dahiyana, Zhou, Yan, Cooper, Rodrigo, Huitink, David, Aksoy, Funda, Liu, Zhi, Liang, Hong, Seminario, Jorge M.

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 570 KB

english, 2013

17

Density functional theory studies of the adsorption of hydrogen sulfide on aluminum doped silicane

Francisco Sánchez-Ochoa, Jonathan Guerrero-Sánchez…

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 547 KB

english, 2013

18

Computational comparison of the kinetic stabilities of diamino- and diamidocarbenes in the 1,2-H shift reaction

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 810 KB

english, 2013

19

Theoretical design of energetic nitrogen-rich derivatives of 1,7-diamino-1,7-dinitrimino-2,4,6-trinitro-2,4,6-triazaheptane

Qiong Wu, Weihua Zhu, Heming Xiao

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 409 KB

english, 2013

20

Tunable differential conductance of single wall C/BN nanotube heterostructure

Huaping Xiao, Chuanxiao Zhang, Kaiwang Zhang, Lizhong Sun…

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 465 KB

english, 2013

21

Zwitterionic conformers of pyrrolysine and their interactions with metal ions—a theoretical study

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 449 KB

english, 2013

22

DFT studies of the conversion of four mesylate esters during reaction with ammonia

Andrzej Nowacki, Karol Sikora, Barbara Dmochowska…

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 658 KB

english, 2013

23

Mechanisms on inhibition of polyethylene electrical tree aging: a theoretical study

Hui Zhang, Yan Shang, Hong Zhao, Baozhong Han, Zesheng Li

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 616 KB

english, 2013

24

Density functional study of structural and electronic properties of small binary BenCum(n + m = 2∼7) clusters

Si-Cheng Li, Ying Li, Di Wu, Zhi-Ru Li

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 536 KB

english, 2013

25

High-spin binuclear cyclopentadienyliron chlorides: a density functional theory study

Congzhi Wang, Xiuhui Zhang, Yang Bai, Fengxin Gao…

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 533 KB

english, 2013

26

Electron correlation effects and density analysis of the first-order hyperpolarizability of neutral guanine tautomers

Andrea Alparone

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 356 KB

english, 2013

27

Theoretical studies of energetic nitrogen-rich ionic salts composed of substituted 5-nitroiminotetrazolate anions and various cations

Fang Xiang, Weihua Zhu, Heming Xiao

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 610 KB

english, 2013

28

Theoretical evaluation of flotation performance of carboxyl hydroxamic acids with different number of polar groups on the surfaces of diaspore (010) and kaolinite (001)

Fang-ping Wang, Guo-ping Zhan, Yu-ren Jiang, Jing-nan Guo…

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 614 KB

english, 2013

29

Computational insights into the binding modes of Sr-Rex with cofactor NADH/NAD+and operator DNA

Yanyan Chu, Weihua Li, Jianfeng Wang, Guixia Liu, Yun Tang

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 946 KB

english, 2013

30

A B3LYP and MP2(full) theoretical investigation into the cooperativity effect between dihydrogen-bonding and H–M∙∙∙π (M = Li, Na, K) interactions among HF, MH with the π-electron donor C2H2, C2H4or C6H6

Jian-feng Guo, Wen-jing Shi, Fu-de Ren, Duan-lin Cao…

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 597 KB

english, 2013

31

Key role of hydrazine to the interaction between oxaloacetic against phosphoenolpyruvic carboxykinase (PEPCK): ONIOM calculations

Pongthep Prajongtat, Darinee Sae-Tang Phromyothin…

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 561 KB

english, 2013

32

[(B3O3H3)nM]+(n = 1, 2;M = Cu, Ag, Au): a new class of metal-cation complexes

Da-Zhi Li, Chen-Chu Dong, Shi-Guo Zhang

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 342 KB

english, 2013

33

A Gaussian-3 theoretical study of the alkylthio radicals and their anions: structures, thermochemistry, and electron affinities

Aifang Gao, Xuli Liang, Luhua Li, Jinghua Cui

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 388 KB

english, 2013

34

Study on the role of SBA-15 in the oxidative dehydrogenation of n-butane over vanadia catalyst using density functional theory

Nguyen Ngoc Ha, Ngo Duc Huyen, Le Minh Cam

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 441 KB

english, 2013

35

Structures and stabilities of ScBn(n = 1–12) clusters: anab initioinvestigation

Jianfeng Jia, Lijuan Ma, Jian-Feng Wang, Hai-Shun Wu

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 511 KB

english, 2013

36

Theoretical investigation of the gas-phase reactions of CF2ClC(O)OCH3with the hydroxyl radical and the chlorine atom at 298 K

Bhupesh Kumar Mishra, Arup Kumar Chakrabartty…

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 307 KB

english, 2013

37

Metal ions in sugar binding, sugar specificity and structural stability ofSpatholobus parviflorusseed lectin

Joseph Abhilash, Kalarickal Vijayan Dileep…

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 439 KB

english, 2013

38

Effects of local protein environment on the binding of diatomic molecules to heme in myoglobins. DFT and dispersion-corrected DFT studies

Meng-Sheng Liao, Ming-Ju Huang, John D. Watts

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 474 KB

english, 2013

39

Relativistic theoretical studies on hydrogen bonds and the electronic structure of aqueous solvatedbis(uranyl) complex: an insight into explicit and/or implicit solvent effects

Yuan-Ru Guo, Xin Zhou, Qing-Jiang Pan

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 464 KB

english, 2013

40

Electron-induced reductive debromination of 2,3,4-tribromodiphenyl ether: a computational study

Jin Luo, Jiwei Hu, Yuan Zhuang, Xionghui Wei…

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 277 KB

english, 2013

41

Sequence and structural investigation of a novel psychrophilic α-amylase fromGlaciozyma antarcticaPI12 for cold-adaptation analysis

Aizi Nor Mazila Ramli, Mohd Akmal Azhar…

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 1.01 MB

english, 2013

42

Rational synthesis of pindolol imprinted polymer by non-covalent protocol based on computational approach

Kiran Kumar Tadi, Ramani V. Motghare

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 774 KB

english, 2013

43

Effect of benzoannulation on tautomeric preferences of 4,6-di(pyridin-2-yl)cyclohexane-1,3-dione

Robert Dobosz, Ryszard Gawinecki

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 182 KB

english, 2013

44

Comparative theoretical studies of energetic pyrazole-pyridine derivatives

Guo-zheng Zhao, Ming Lu

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 452 KB

english, 2013

45

Incomplete mixing versus clathrate-like structures: A molecular view on hydrophobicity in methanol–water mixtures

Sven P. Benson, Jürgen Pleiss

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 313 KB

english, 2013

46

Density functional studies on photophysical properties and chemical reactivities of the triarylboranes: effect of the constraint of planarity

Jun-Ling Jin, Hai-Bin Li, Tian Lu, Yu-Ai Duan, Yun Geng…

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 604 KB

english, 2013

47

Stability and isomerization of complexes formed by metal ions and cytosine isomers in aqueous phase

Hongqi Ai, Jingjing Liu, Kwaichow Chan

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 1.12 MB

english, 2013

48

Structural and energetic properties of canonical and oxidized telomeric complexes studied by molecular dynamics simulations

Czeleń, Przemysław, Cysewski, Piotr

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 824 KB

english, 2013

49

Structural transitions in mixed ternary noble gas clusters

Xia Wu,Yan Sun,Yin-Chun Gao,Gen-Hua Wu

Journal:

Journal of Molecular Modeling

Year:

2013

Language:

english

File:

PDF, 966 KB

english, 2013