Volume 19, Issue 11

Search all Journal of Molecular Modeling articles

November 2013

International conference on “Modeling interaction in biomolecules 2011”, in Kutná Hora, September 4th–9th, 2011

Issue Editors:

Jaroslav V. Burda,
W. Andrzej Sokalski

49 articles in this issue

International conference on “Modeling interaction in biomolecules 2011”, in Kutná Hora, September 4th–9th, 2011
Jaroslav V. Burda
Andrzej W. Sokalski
Introduction 13 September 2013 Pages: 4627 - 4627
Congratulations to Professor Pavel Mach on the occasion of his 60th birthday
Ondrej Kysel
Editorial 22 May 2012 Pages: 4629 - 4630
Computational and experimental studies of the electronic excitation spectra of EDTA and DTPA substituted tetraphenylporphyrins and their Lu complexes
Rashid R. Valiev
Elena G. Ermolina
Dage Sundholm
Original Paper 25 March 2012 Pages: 4631 - 4637
Theoretical study of electronic absorptions in aminopyridines – TCNE CT complexes by quantum chemical methods, including solvent
Pavel Mach
György Juhász
Ondrej Kyseľ
Original Paper 08 May 2012 Pages: 4639 - 4650
Halogen bond tunability II: the varying roles of electrostatic and dispersion contributions to attraction in halogen bonds
Kevin E. Riley
Jane S. Murray
Peter Politzer
Original Paper 29 May 2012 Pages: 4651 - 4659
Ligation of water to magnesium chelates of biological importance
Dorota Rutkowska-Zbik
Małgorzata Witko
Leszek Fiedor
Original Paper Open access 29 May 2012 Pages: 4661 - 4667
Can Satraplatin be hydrated before the reduction process occurs? The DFT computational study
Ondřej Bradáč
Tomáš Zimmermann
Jaroslav V. Burda
Original Paper 30 May 2012 Pages: 4669 - 4680
Theoretical description of halogen bonding – an insight based on the natural orbitals for chemical valence combined with the extended-transition-state method (ETS-NOCV)
Mariusz P. Mitoraj
Artur Michalak
Original Paper Open access 06 June 2012 Pages: 4681 - 4688
Regulation of the transient receptor potential channel TRPA1 by its N-terminal ankyrin repeat domain
Vasilina Zayats
Abdul Samad
Rudiger Ettrich
Original Paper 03 July 2012 Pages: 4689 - 4700
Interaction of organic solvents with protein structures at protein-solvent interface
Morteza Khabiri
Babak Minofar
Rudiger Ettrich
Original Paper 04 July 2012 Pages: 4701 - 4711
Non-covalent interactions – QTAIM and NBO analysis
Sławomir J. Grabowski
Original Paper 08 July 2012 Pages: 4713 - 4721
Effect of the aminoacid composition of model α-helical peptides on the physical properties of lipid bilayers and peptide conformation: a molecular dynamics simulation
Milan Melicherčík
Alžbeta Holúbeková
Ján Urban
Original Paper 15 August 2012 Pages: 4723 - 4730
The use of supramolecular structures as protein ligands
Barbara Stopa
Anna Jagusiak
Irena Roterman
Original Paper Open access 08 January 2013 Pages: 4731 - 4740
Theoretical studies on the structure, thermochemical and detonation properties of amino and nitroso substituted 1,2,4-triazol-5-one-N-oxides
P. Ravi
V. Venkatesan
Surya P. Tewari
Original Paper 28 August 2013 Pages: 4741 - 4751
Stereoselectivity of chalcone isomerase with chalcone derivatives: a computational study
Yuan Yao
Hui Zhang
Ze-Sheng Li
Original Paper 30 August 2013 Pages: 4753 - 4761
Do coinage metal anions interact with substituted benzene derivatives?
Zahra Aliakbar Tehrani
Zahra Jamshidi
Hossein Farhangian
Original Paper 30 August 2013 Pages: 4763 - 4772
Molecular basis of lateral force spectroscopy nano-diagnostics: computational unbinding of autism related chemokine MCP-1 from IgG antibody
Anna Gogolinska
Wieslaw Nowak
Original Paper Open access 06 September 2013 Pages: 4773 - 4780
Influence of doped nitrogen and vacancy defects on the thermal conductivity of graphene nanoribbons
Haiying Yang
Yunqing Tang
Shuting Wang
Original Paper 07 September 2013 Pages: 4781 - 4788
Thiophenic compounds adsorption on Na(I)Y and rare earth exchanged Y zeolites: a density functional theory study
Xionghou Gao
Wei Geng
Xiaojun Yao
Original Paper 08 September 2013 Pages: 4789 - 4795
Theoretical study on cooperative effects between X⋯N and X⋯Carbene halogen bonds (X = F,Cl,Br and I)
Mehdi D. Esrafili
Fariba Mohammdain-Sabet
Parvin Esmailpour
Original Paper 08 September 2013 Pages: 4797 - 4804
Design of Lewis acid–base complex: enhancing the stability and first hyperpolarizability of large excess electron compound
Fang Ma
Tifang Miao
Dengming Sun
Original Paper 11 September 2013 Pages: 4805 - 4813
Theoretical investigation on the kinetics and branching ratio of the gas phase reaction of sevoflurane with Cl atom
Hari Ji Singh
Nand Kishor Gour
Laxmi Tiwari
Original Paper 11 September 2013 Pages: 4815 - 4822
DFT and docking studies of rhodostreptomycins A and B and their interactions with solvated/nonsolvated Mg²⁺ and Ca²⁺ ions
Christiaan Jardínez
Ines Nicolás-Vázquez
Rene Miranda
Original Paper 13 September 2013 Pages: 4823 - 4836
Conformational analysis and intramolecular hydrogen bonding of cis-3-aminoindan-1-ol: a quantum chemical study
Djaffar Kheffache
Hind Guemmour
Ourida Ouamerali
Original Paper 13 September 2013 Pages: 4837 - 4847
A comparative DFT study on aquation and nucleobase binding of ruthenium (II) and osmium (II) arene complexes
Hanlu Wang
Xingye Zeng
Cunyuan Zhao
Original Paper 15 September 2013 Pages: 4849 - 4856
Redox and Lewis acid–base activities through an electronegativity-hardness landscape diagram
Ranjita Das
Jean-Louis Vigneresse
Pratim Kumar Chattaraj
Original Paper 17 September 2013 Pages: 4857 - 4864
Insight into the structural stability of wild type and mutants of the tobacco etch virus protease with molecular dynamics simulations
Yu Wang
Guo-Fei Zhu
Lin-Fang Du
Original Paper 17 September 2013 Pages: 4865 - 4875
Exploring surface reactivity of phosphorous-doped (6,0) and (4,4) BC3 nanotubes: a DFT study
Mohammad Alizadeh
Mehdi D. Esrafili
Esmail Vessally
Original Paper 17 September 2013 Pages: 4877 - 4886
Discovery of σ-hole interactions involving ylides
Jiannan Ji
Yanli Zeng
Lingpeng Meng
Original Paper 17 September 2013 Pages: 4887 - 4895
The intrinsic helical propensities of the helical fragments in prion protein under neutral and low pH conditions: a replica exchange molecular dynamics study
Xiaoliang Lu
Juan Zeng
Ye Mei
Original Paper 17 September 2013 Pages: 4897 - 4908
Easy methods to study the smart energetic TNT/CL-20 co-crystal
Huarong Li
Yuanjie Shu
Xuehai Ju
Original Paper 17 September 2013 Pages: 4909 - 4917
Molecular interactions between fenoterol stereoisomers and derivatives and the β₂-adrenergic receptor binding site studied by docking and molecular dynamics simulations
Anita Plazinska
Michal Kolinski
Krzysztof Jozwiak
Original Paper Open access 17 September 2013 Pages: 4919 - 4930
Conformational flexibility of the leucine binding protein examined by protein domain coarse-grained molecular dynamics
Iwona Siuda
Lea Thøgersen
Original Paper 19 September 2013 Pages: 4931 - 4945
A DFT study of the Al₂Cl₆-catalyzed Friedel–Crafts acylation of phenyl aromatic compounds
Sigismund T. A. G. Melissen
Vincent Tognetti
Laurent Joubert
Original Paper 20 September 2013 Pages: 4947 - 4958
Effect of surface hydroxyls on dimethyl ether synthesis over the γ-Al₂O₃ in liquid paraffin: a computational study
Zhi-jun Zuo
Le Wang
Wei Huang
Original Paper 22 September 2013 Pages: 4959 - 4967
Destabilization of the MutSα’s protein-protein interface due to binding to the DNA adduct induced by anticancer agent carboplatin via molecular dynamics simulations
Lacramioara Negureanu
Freddie R. Salsbury Jr
Original Paper 24 September 2013 Pages: 4969 - 4989
Armchair BN nanotubes—levothyroxine interactions: a molecular study
E. Chigo Anota
Gregorio H. Cocoletzi
J. F. Sánchez Ramírez
Original Paper 26 September 2013 Pages: 4991 - 4996
The study of interactions between DNA and PcrA DNA helicase by using targeted molecular dynamic simulations
Hao Wang
Jiajia Cui
Charles A. Laughton
Original Paper 26 September 2013 Pages: 4997 - 5006
The competition of C-X⋯O=P halogen bond and π-hole⋯O=P bond between halopentafluorobenzenes C₆F₅X (X=F, Cl, Br, I) and triethylphosphine oxide
Xiao Ran Zhao
Hui Wang
Wei Jun Jin
Original Paper 26 September 2013 Pages: 5007 - 5014
A knowledge-based halogen bonding scoring function for predicting protein-ligand interactions
Yingtao Liu
Zhijian Xu
Weiliang Zhu
Original Paper 27 September 2013 Pages: 5015 - 5030
Competition and interplay between the lithium bonding and hydrogen bonding: R₃C···HY···LiY and R₃C···LiY···HY triads as a working model (R=H, CH₃; Y=CN, NC)
Mohammad Solimannejad
Zahra Rezaei
Mehdi D. Esrafili
Original Paper 28 September 2013 Pages: 5031 - 5035
Theoretical investigations on the synthesis mechanism of cyanuric acid from NH₃ and CO₂
Xueli Cheng
Yanyun Zhao
Yongjun Liu
Original Paper 29 September 2013 Pages: 5037 - 5043
A theoretical investigation on the conformation and the interaction of CHF₂OCF₂CHF₂ (desflurane II) with one water molecule
Dipankar Sutradhar
Therese Zeegers-Huyskens
Asit K. Chandra
Original Paper 29 September 2013 Pages: 5045 - 5052
Molecular dynamics simulation of cross-linked urea-formaldehyde polymers for self-healing nanocomposites: prediction of mechanical properties and glass transition temperature
Behrouz Arab
Ali Shokuhfar
Original Paper 01 October 2013 Pages: 5053 - 5062
DFT model cluster studies of O2 adsorption on hydrogenated titania sub-nanoparticles
Alexey S. Andreev
Vyacheslav N. Kuznetsov
Yuri V. Chizhov
Original Paper 02 October 2013 Pages: 5063 - 5073
Optimized CGenFF force-field parameters for acylphosphate and N-phosphonosulfonimidoyl functional groups
Lamees Hegazy
Nigel G. J. Richards
Original Paper 02 October 2013 Pages: 5075 - 5087
Gas phase acidities of N-substituted amine-boranes
Aiko Adamson
Jean-Claude Guillemin
Peeter Burk
Original Paper 02 October 2013 Pages: 5089 - 5095
Binding selectivity studies of PKBα using molecular dynamics simulation and free energy calculations
Shi-Feng Chen
Yang Cao
Jian-Zhong Chen
Original Paper 02 October 2013 Pages: 5097 - 5112
Structure and spectral characteristics of diquat-cucurbituril complexes from density functional theory
Swarada R. Peerannawar
Shridhar P. Gejji
Original Paper 03 October 2013 Pages: 5113 - 5127

Volume 19, Issue 11

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