Volume 18; Issue 6

Journal of Molecular Modeling

Volume 18; Issue 6

1

Effect of the thermostat in the molecular dynamics simulation on the folding of the model protein chignolin

Carlos A. Fuzo, Léo Degrève

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 803 KB

english, 2012

2

Quantum mechanical studies of lincosamides

Katarzyna Kulczycka-Mierzejewska, Joanna Trylska, Joanna Sadlej

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 793 KB

english, 2012

3

Structural determinants of imidacloprid-based nicotinic acetylcholine receptor inhibitors identified using 3D-QSAR, docking and molecular dynamics

Qinfan Li, Xiangya Kong, Zhengtao Xiao, Lihui Zhang, Fangfang Wang, Hong Zhang, Yan Li, Yonghua Wang

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 834 KB

english, 2012

4

Computational investigation of a new ion-pair receptor for calix[4]pyrrole

Yong Xia, Xueye Wang, Yu Zhang, Benhua Luo, Yi Liu

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 432 KB

english, 2012

5

Theoretical studies on the structures and detonation properties of nitramine explosives containing benzene ring

GuoZheng Zhao, Ming Lu

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 350 KB

english, 2012

6

Dimensionality reduction in computational demarcation of protein tertiary structures

Rajani R. Joshi, Priyabrata R. Panigrahi, Reshma N. Patil

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 230 KB

english, 2012

7

How to simulate affinities for host–guest systems lacking binding mode information: application to the liquid chromatographic separation of hexabromocyclododecane stereoisomers

Vedat Durmaz, Marcus Weber, Roland Becker

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 428 KB

english, 2012

8

Exploration of the valproic acid binding site on histone deacetylase 8 using docking and molecular dynamic simulations

Jorge Antonio Bermúdez-Lugo, Oscar Perez-Gonzalez, Martha Cecilia Rosales-Hernández, Ian Ilizaliturri-Flores, José Trujillo-Ferrara, Jose Correa-Basurto

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 891 KB

english, 2012

9

Methane storage in homogeneous armchair open-ended single-walled boron nitride nanotube triangular arrays: a grand canonical Monte Carlo simulation study

Sayyed Jalil Mahdizadeh, Sayyed Faramarz Tayyari

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 1021 KB

english, 2012

10

Molecular modeling of temperature dependence of solubility parameters for amorphous polymers

Xianping Chen, Cadmus Yuan, Cell K. Y. Wong, Guoqi Zhang

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 564 KB

english, 2012

11

Hydrogen storage in C3Ti complex using quantum chemical methods and molecular dynamics simulations

Vijayanand Kalamse, Nitin Wadnerkar, Ajay Chaudhari

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 451 KB

english, 2012

12

Are formal oxidation states above one viable in cyclopentadienylcopper cyanides?

Congzhi Wang, Xiuhui Zhang, Qian-shu Li, Yaoming Xie, R. Bruce King, Henry F. Schaefer III

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 521 KB

english, 2012

13

The structure, properties, and nature of unconventional π halogen bond in the complexes of Al42-and halohydrocarbons

Ran Li, Qingzhong Li, Jianbo Cheng, Wenzuo Li

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 335 KB

english, 2012

14

Molecular simulation of water removal from simple gases with zeolite NaA

Éva Csányi, Zoltán Ható, Tamás Kristóf

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 391 KB

english, 2012

15

Size and chain length effects on structural behaviors of biphenylcyclohexane-based liquid crystal nanoclusters by a coarse-grained model

Ming-Liang Liao, Shin-Pon Ju, Chun-Yi Chang, Wei-Lin Huang

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 718 KB

english, 2012

16

Mapping multiple potential ATP binding sites on the matrix side of the bovine ADP/ATP carrier by the combined use of MD simulation and docking

Daniele Di Marino, Francesco Oteri, Blasco Morozzo della Rocca, Ilda D’Annessa, Mattia Falconi

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 566 KB

english, 2012

17

The H2dissociation on the BN, AlN, BP and AlP nanotubes: a comparative study

Javad Beheshtian, Hamed Soleymanabadi, Mohammad Kamfiroozi, Ali Ahmadi

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 449 KB

english, 2012

18

DFT modeling, UV-Vis and IR spectroscopic study of acetylacetone-modified zirconia sol-gel materials

Ivelina Georgieva, Nina Danchova, Stoyan Gutzov, Natasha Trendafilova

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 1.48 MB

english, 2012

19

Theoretical investigation of the two-photon absorption properties of 3,6-bis(4-vinylpyridinium) carbazole derivatives—new biological fluorescent probes

Ying Sun, Yang Zhao, Xiao-Ting Liu, Ai-Min Ren, Ji-Kang Feng, Xiao-Qiang Yu

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 635 KB

english, 2012

20

Crystal structure, detonation performance, and thermal stability of a new polynitro cage compound: 2, 4, 6, 8, 10, 12, 13, 14, 15-nonanitro-2, 4, 6, 8, 10, 12, 13, 14, 15-nonaazaheptacyclo [5.5.1.13, 11. 15, 9] pentadecane

Jian-ying Zhang, Hong-chen Du, Fang Wang, Xue-dong Gong, San-jiu Ying

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 429 KB

english, 2012

21

First-principles molecular dynamics simulations of the H2O / Cu(111) interface

Roger Nadler, Javier Fernandez Sanz

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 403 KB

english, 2012

22

Ab initioand DFT study of luminescent cyclometalated N-heterocyclic carbene organogold(III) complexes

Baozhu Yang, Qi Zhang, Jing Zhong, Shuang Huang, Hong-Xing Zhang

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 372 KB

english, 2012

23

Estimating the carbonyl anharmonic vibrational frequency from affordable harmonic frequency calculations

Aneta Buczek, Teobald Kupka, Stephan P. A. Sauer, Małgorzata A. Broda

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 460 KB

english, 2012

24

Polarization-induced σ-holes and hydrogen bonding

Matthias Hennemann, Jane S. Murray, Peter Politzer, Kevin E. Riley, Timothy Clark

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 718 KB

english, 2012

25

Aromatic character of heptafulvene and its complexes with halogen atoms

Tadeusz M. Krygowski, Wojciech P. Oziminski, Michał K. Cyrański

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 398 KB

english, 2012

26

Pharmacophore modeling, molecular docking, QSAR, and in silico ADMET studies of gallic acid derivatives for immunomodulatory activity

Dharmendra Kumar Yadav, Feroz Khan, Arvind Singh Negi

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 577 KB

english, 2012

27

Metastable region of phase diagram: optimum parameter range for processing ultrahigh molecular weight polyethylene blends

Jing-Gang Gai, Yuan Zuo

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 832 KB

english, 2012

28

Role of cationic size in the optical properties of the LiCl crystal surface: theoretical study

Wael Salah Abdel Halim, Noha Abdullah, Safaa Abdel-Aal, A. S. Shalabi

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 286 KB

english, 2012

29

Molecular mechanics modeling of azobenzene-based photoswitches

Patrick Duchstein, Christian Neiss, Andreas Görling, Dirk Zahn

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 173 KB

english, 2012

30

Conformational and stereoelectronic investigation of tryptamine. An AIM/NBO study

Rosana M. Lobayan, María C. Pérez Schmit, Alicia H. Jubert, Arturo Vitale

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 698 KB

english, 2012

31

Harmonic force field for nitro compounds

Edson P. Bellido, Jorge M. Seminario

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 363 KB

english, 2012

32

A QSAR study of radical scavenging antioxidant activity of a series of flavonoids using DFT based quantum chemical descriptors – the importance of group frontier electron density

Ananda Sarkar, Tapas Ranjan Middya, Atish Dipnakar Jana

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 342 KB

english, 2012

33

Exploration of the binding of curcumin analogues to human P450 2C9 based on docking and molecular dynamics simulation

Rongwei Shi, Yin Wang, Xiaolei Zhu, Xiaohua Lu

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 1.15 MB

english, 2012

34

The importance of secondary structure in determining CO2-protein binding patterns

Michael L. Drummond, Angela K. Wilson, Thomas R. Cundari

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 665 KB

english, 2012

35

Conserved water-mediated H-bonding dynamics of catalytic His159 and Asp158: insight into a possible acid–base coupled mechanism in plant thiol protease

Tapas K. Nandi, Hridoy R. Bairagya, Bishnu P. Mukhopadhyay, Payel Mallik, Dipankar Sukul, Asim K. Bera

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 320 KB

english, 2012

36

Structure and stability of kaolinite/TiO2nanocomposite: DFT and MM computations

Jonáš Tokarský, Pavla Čapková, Jaroslav V. Burda

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 870 KB

english, 2012

37

Substituent effects on geometric and electronic properties of iron tetraphenylporphyrin: a DFT investigation

Lu Wei, Yuanbin She, Yanmin Yu, Xiaoqian Yao, Suojiang Zhang

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 228 KB

english, 2012

38

Hit clustering can improve virtual fragment screening: CDK2 and PARP1 case studies

Alexey A. Zeifman, Victor S. Stroylov, Fedor N. Novikov, Oleg V. Stroganov, Alexandra L. Zakharenko, Svetlana N. Khodyreva, Olga I. Lavrik, Ghermes G. Chilov

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 1.53 MB

english, 2012

39

Comparative homology modeling of pyruvate dehydrogenase kinase isozymes fromXenopus tropicalisreveals structural basis for their subfunctionalization

Alexander A. Tokmakov

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 1.23 MB

english, 2012

40

Oxygenation of the phenylhalocarbenes. Are they spin-allowed or spin-forbidden reactions?

Al Mokhtar Lamsabhi, Inés Corral, Patricia Pérez, Orlando Tapia, Manuel Yáñez

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 351 KB

english, 2012

41

An ONIOM investigation on anion recognition of alkali–metal complexes with diurea calix[4]arene receptor

Pornpan Chanapiwat, Vithaya Ruangpornvisuti

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 835 KB

english, 2012

42

Homology modeling and docking analyses ofM. lepraeMur ligases reveals the common binding residues for structure based drug designing to eradicate leprosy

Anusuya Shanmugam, Jeyakumar Natarajan

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 1.10 MB

english, 2012

43

A comparative study on the B12N12, Al12N12, B12P12and Al12P12fullerene-like cages

Javad Beheshtian, Zargham Bagheri, Mohammad Kamfiroozi, Ali Ahmadi

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 260 KB

english, 2012

44

Molecular dynamics simulation studies of betulinic acid with human serum albumin

Chandramouli Malleda, Navjeet Ahalawat, Mahesh Gokara, Rajagopal Subramanyam

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 475 KB

english, 2012

45

Accurate prediction of the binding free energy and analysis of the mechanism of the interaction of replication protein A (RPA) with ssDNA

Claudio Carra, Francis A. Cucinotta

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 2.03 MB

english, 2012

46

Aminoglycoside induced nephrotoxicity: molecular modeling studies of calreticulin-gentamicin complex

Gururao Hariprasad, Manoj Kumar, Komal Rani, Punit Kaur, Alagiri Srinivasan

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 444 KB

english, 2012

47

Predicting functional residues of theSolanum lycopersicumaspartic protease inhibitor (SLAPI) by combining sequence and structural analysis with molecular docking

Yasel Guerra, Pedro A. Valiente, Colin Berry, Tirso Pons

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 871 KB

english, 2012

48

Structural and electronic properties of 4H-cyclopenta[2,1-b,3;4-b′]dithiopheneS-oxide (BTO) derivatives with an S, S=O, O, SiH2, or BH2bridge: semi-empirical and DFT study

Semire Banjo, Odunola Olusegun Ayobami, Adejoro Isaiah Ajibade

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 135 KB

english, 2012

49

Quantum chemical modeling study of adsorption of benzoic acid on anatase TiO2nanoparticles

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 600 KB

english, 2012

50

Exploration of conformational transition in the aryl-binding site of human FXa using molecular dynamics simulations

Jing-Fang Wang, Pei Hao, Yi-Xue Li, Jian-Liang Dai, Xuan Li

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 520 KB

english, 2012

51

Computational investigation of the effect of thermal perturbation on the mechanical unfolding of titin I27

Navneet Bung, U. Deva Priyakumar

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 452 KB

english, 2012

52

Theoretical aspects of binary and ternary complexes of aziridine⋯ammonia ruled by hydrogen bond strength

Boaz G. Oliveira, Regiane C. M. U. Araújo

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 349 KB

english, 2012

53

First-principles study of energetic complexes (II): (5-cyanotetrazolato-N2) pentaammine cobalt (III) perchlorate (CP) and Ni, Fe and Zn analogues

Jing Shang, Jian-Guo Zhang, Tong-Lai Zhang, Hui-Sheng Huang, Shao-Wen Zhang, Zun-Ning Zhou

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 201 KB

english, 2012

54

A specific pharmacophore model of sodium-dependent glucose co-transporter 2 (SGLT2) inhibitors

Chunlei Tang, Xiaoyun Zhu, Dandan Huang, Xin Zan, Baowei Yang, Ying Li, Xiaoyong Du, Hai Qian, Wenlong Huang

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 563 KB

english, 2012

55

Molecular docking of 2-(benzimidazol-2-ylthio)-N-phenylacetamide-derived small-molecule agonists of human formyl peptide receptor 1

Andrei I. Khlebnikov, Igor A. Schepetkin, Liliya N. Kirpotina, Lars Brive, Claes Dahlgren, Mark A. Jutila, Mark T. Quinn

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 861 KB

english, 2012

56

Global and local molecular dynamics of a bacterial carboxylesterase provide insight into its catalytic mechanism

Xiaozhen Yu, Sara C. Sigler, Delwar Hossain, Monika Wierdl, Steven R. Gwaltney, Philip M. Potter, Randy M. Wadkins

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 1.12 MB

english, 2012

57

Chemical functionalization of graphene via aryne cycloaddition: a theoretical study

Jing-xiang Zhao, Hong-xia Wang, Bo Gao, Xiao-guang Wang, Qing-hai Cai, Xuan-zhang Wang

Journal:

Journal of Molecular Modeling

Year:

2012

Language:

english

File:

PDF, 636 KB

english, 2012

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