Journal of Biomolecular Structure and Dynamics, Volume 33, Issue 10 (2015)

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Journal of Biomolecular Structure and Dynamics, Volume 33, Issue 10 (2015)

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Articles

Article
Role of DNA conformation & energetic insights in Msx-1-DNA recognition as revealed by molecular dynamics studies on specific and nonspecific complexes
Sangita Kachhap & Balvinder Singh
Pages: 2069-2082
Published online: 12 Jan 2015
AbstractforRole of DNA conformation & energetic insights in Msx-1-DNA recognition as revealed by molecular dynamics studies on specific and nonspecific complexes | Full Text | References | PDF (777.6 KB) | Supplemental
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Article
Investigation of arc repressor DNA-binding specificity by comparative molecular dynamics simulations
Wei Song & Jun-Tao Guo
Pages: 2083-2093
Published online: 14 Jan 2015
AbstractforInvestigation of arc repressor DNA-binding specificity by comparative molecular dynamics simulations | Full Text | References | PDF (566.5 KB) | Supplemental
  • 269 Views
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Article
Mutations in exons 3 and 7 resulting in truncated expression of human ATP6V1B1 gene showing structural variations contributing to poor substrate binding-causative reason for distal renal tubular acidosis with sensorineural deafness
Pasupuleti Santhosh Kumar, Katari Venkatesh, Gopal Sowjenya, Lokanathan Srikanth, Manne Mudhu Sunitha, Uppu Venkateswara Prasad, Vimjam Swarupa, Sthanikam Yeswanth, P. Sri Ram Naveen, A. Sridhar, V. Siva Kumar & P.V.G.K. Sarma
Pages: 2094-2103
Published online: 23 Jan 2015
AbstractforMutations in exons 3 and 7 resulting in truncated expression of human ATP6V1B1 gene showing structural variations contributing to poor substrate binding-causative reason for distal renal tubular acidosis with sensorineural deafness | Full Text | References | PDF (864.6 KB)
  • 138 Views
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Article
Eukaryotic tRNAs fingerprint invertebrates vis-à-vis vertebrates
Sanga Mitra, Pijush Das, Arpa Samadder, Smarajit Das, Rupal Betai & Jayprokas Chakrabarti
Pages: 2104-2120
Published online: 12 Jan 2015
AbstractforEukaryotic tRNAs fingerprint invertebrates vis-à-vis vertebrates | Full Text | References | PDF (996.5 KB)
  • 211 Views
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Article
Electronic structure of alloxan and its dimers: QM/QD simulations and quantum chemical topology analysis
Basmah H. Allehyani, Shaaban A. Elroby, Saadalluh G. Aziz & Rifaat H. Hilal
Pages: 2121-2132
Published online: 12 Jan 2015
AbstractforElectronic structure of alloxan and its dimers: QM/QD simulations and quantum chemical topology analysis | Full Text | References | PDF (484.7 KB)
  • 147 Views
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Article
Sequence and structural difference favors a distinct preference of Wnt3a binding with co-receptor LRP6
Itishri Sahu, Seema Mishra, R. Undi, Ravinder Kandi, Usha Gutti & R. K. Gutti
Pages: 2133-2144
Published online: 06 Jan 2015
AbstractforSequence and structural difference favors a distinct preference of Wnt3a binding with co-receptor LRP6 | Full Text | References | PDF (2.1 MB)
  • 227 Views
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Article
pH-induced structural change of a multi-tryptophan protein MPT63 with immunoglobulin-like fold: identification of perturbed tryptophan residue/residues
Manini Mukherjee, Ranendu Ghosh, Krishnananda Chattopadhyay & Sanjib Ghosh
Pages: 2145-2160
Published online: 19 Jan 2015
AbstractforpH-induced structural change of a multi-tryptophan protein MPT63 with immunoglobulin-like fold: identification of perturbed tryptophan residue/residues | Full Text | References | PDF (730.4 KB) | Supplemental
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Article
Deciphering the GPER/GPR30-agonist and antagonists interactions using molecular modeling studies, molecular dynamics, and docking simulations
D. Méndez-Luna, M. Martínez-Archundia, Rachid C. Maroun, G. Ceballos-Reyes, M.J. Fragoso-Vázquez, D.E. González-Juárez & J. Correa-Basurto
Pages: 2161-2172
Published online: 14 Jan 2015
AbstractforDeciphering the GPER/GPR30-agonist and antagonists interactions using molecular modeling studies, molecular dynamics, and docking simulations | Full Text | References | PDF (913.7 KB) | Supplemental
  • 1025 Views
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Article
Structural conversion of the transformer protein RfaH: new insights derived from protein structure prediction and molecular dynamics simulations
Nicole Balasco, Daniela Barone & Luigi Vitagliano
Pages: 2173-2179
Published online: 12 Jan 2015
AbstractforStructural conversion of the transformer protein RfaH: new insights derived from protein structure prediction and molecular dynamics simulations | Full Text | References | PDF (541.3 KB) | Supplemental
  • 310 Views
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Article
Evidence of salicylic acid pathway with EDS1 and PAD4 proteins by molecular dynamics simulation for grape improvement
Gitanjali Tandon, Sarika Jaiswal, M.A. Iquebal, Sunil Kumar, Sukhdeep Kaur, Anil Rai & Dinesh Kumar
Pages: 2180-2191
Published online: 12 Jan 2015
AbstractforEvidence of salicylic acid pathway with EDS1 and PAD4 proteins by molecular dynamics simulation for grape improvement | Full Text | References | PDF (1,004.4 KB)
  • 575 Views
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Article
Conformational changes and allosteric communications in human serum albumin due to ligand binding
Navjeet Ahalawat & Rajesh K. Murarka
Pages: 2192-2204
Published online: 12 Jan 2015
AbstractforConformational changes and allosteric communications in human serum albumin due to ligand binding | Full Text | References | PDF (748.7 KB) | Supplemental
  • 507 Views
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Article
Amino acid composition analysis of secondary transport proteins from Escherichia coli with relation to functional classification, ligand specificity and structure
Massoud Saidijam & Simon G. Patching
Pages: 2205-2220
Published online: 14 Jan 2015
AbstractforAmino acid composition analysis of secondary transport proteins from Escherichia coli with relation to functional classification, ligand specificity and structure | Full Text | References | PDF (4.2 MB) | Supplemental
  • 358 Views
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Article
iDrug-Target: predicting the interactions between drug compounds and target proteins in cellular networking via benchmark dataset optimization approach
Xuan Xiao, Jian-Liang Min, Wei-Zhong Lin, Zi Liu, Xiang Cheng & Kuo-Chen Chou
Pages: 2221-2233
Published online: 14 Jan 2015
AbstractforiDrug-Target: predicting the interactions between drug compounds and target proteins in cellular networking via benchmark dataset optimization approach | Full Text | References | PDF (703.4 KB) | Supplemental
  • 1121 Views
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Article
Theoretical insight into the structural mechanism for the binding of vinblastine with tubulin
Shaoming Chi, Wei Xie, Jiwei Zhang & Sichuan Xu
Pages: 2234-2254
Published online: 14 Jan 2015
AbstractforTheoretical insight into the structural mechanism for the binding of vinblastine with tubulin | Full Text | References | PDF (1.3 MB)
  • 517 Views
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Article
Inhibitory effects of deferasirox on the structure and function of bovine liver catalase: a spectroscopic and theoretical study
M. Moradi, A. Divsalar, A.A. Saboury, B. Ghalandari & A.R. Harifi
Pages: 2255-2266
Published online: 14 Jan 2015
AbstractforInhibitory effects of deferasirox on the structure and function of bovine liver catalase: a spectroscopic and theoretical study | Full Text | References | PDF (1,015.6 KB)
  • 411 Views
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Review Article
Structural characterization of MG and pre-MG states of proteins by MD simulations, NMR, and other techniques
Abdullah Naiyer, Md. Imtaiyaz Hassan, Asimul Islam, Monica Sundd & Faizan Ahmad
Pages: 2267-2284
Published online: 14 Jan 2015
AbstractforStructural characterization of MG and pre-MG states of proteins by MD simulations, NMR, and other techniques | Full Text | References | PDF (791.4 KB)
  • 439 Views
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Article
Integrating docking and molecular dynamics approaches for a series of proline-based 2,5-diketopiperazines as novel αβ-tubulin inhibitors
Najmeh Fani, Abdol-Khalegh Bordbar, Yousef Ghayeb & Saghi Sepehri
Pages: 2285-2295
Published online: 23 Jan 2015
AbstractforIntegrating docking and molecular dynamics approaches for a series of proline-based 2,5-diketopiperazines as novel αβ-tubulin inhibitors | Full Text | References | PDF (1.2 MB)
  • 270 Views
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