Journal of Biomolecular Structure and Dynamics, Volume 34, Issue 6 (2016)

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Journal of Biomolecular Structure and Dynamics, Volume 34, Issue 6 (2016)

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Original Articles

Article
The effects of tautomerization and protonation on the adenine–cytosine mismatches: a density functional theory study
Hamid Reza Masoodi, Sotoodeh Bagheri & Mahsa Abareghi
Pages: 1143-1155
Published online: 17 Aug 2015
AbstractforThe effects of tautomerization and protonation on the adenine–cytosine mismatches: a density functional theory study | Full Text | References | PDF (366.4 KB) | Supplemental
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Article
Nucleosome repeat lengths and columnar chromatin structure
Edward N. Trifonov
Pages: 1156-1158
Published online: 12 Oct 2015
AbstractforNucleosome repeat lengths and columnar chromatin structure | Full Text | References | PDF (136.4 KB)
  • 233 Views
  • 3 CrossRef citations
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Article
Structural modeling and molecular simulation analysis of HvAP2/EREBP from barley
Bharati Pandey, Pradeep Sharma, Chetna Tyagi, Sukriti Goyal, Abhinav Grover & Indu Sharma
Pages: 1159-1175
Published online: 19 Oct 2015
AbstractforStructural modeling and molecular simulation analysis of HvAP2/EREBP from barley | Full Text | References | PDF (987.9 KB) | Supplemental
  • 423 Views
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Article
Structural and mechanistic analysis of engineered trichodiene synthase enzymes from Trichoderma harzianum: towards higher catalytic activities empowering sustainable agriculture
Indu Kumari, Nitika Chaudhary, Padmani Sandhu, Mushtaq Ahmed & Yusuf Akhter
Pages: 1176-1189
Published online: 18 Aug 2015
AbstractforStructural and mechanistic analysis of engineered trichodiene synthase enzymes from Trichoderma harzianum: towards higher catalytic activities empowering sustainable agriculture | Full Text | References | PDF (1.4 MB) | Supplemental
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Article
Streptomycin affinity depends on 13 amino acids forming a loop in homology modelled ribosomal S12 protein (rpsL gene) of Lysinibacillus sphaericus DSLS5 associated with marine sponge (Tedania anhelans)
Balasubramanian Suriyanarayanan, Praveena Pothuraju Lakshmi, Ramachandran Sarojini Santhosh, Kandasamy Dhevendaran, Balakrishnan Priya & Shivaani Krishna
Pages: 1190-1200
Published online: 14 Aug 2015
AbstractforStreptomycin affinity depends on 13 amino acids forming a loop in homology modelled ribosomal S12 protein (rpsL gene) of Lysinibacillus sphaericus DSLS5 associated with marine sponge (Tedania anhelans) | Full Text | References | PDF (770.4 KB)
  • 271 Views
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Article
Allosterism in human complement component 5a (hC5a): a damper of C5a receptor (C5aR) signaling
Soumendra Rana, Amita Rani Sahoo & Bharat Kumar Majhi
Pages: 1201-1213
Published online: 18 Aug 2015
AbstractforAllosterism in human complement component 5a (hC5a): a damper of C5a receptor (C5aR) signaling | Full Text | References | PDF (818.9 KB) | Supplemental
  • 278 Views
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Article
Investigation on critical structural motifs of ligands for triggering glucocorticoid receptor nuclear migration through molecular docking simulations
Ya-Lin Liu, Soonmin Jang, Shih-Min Wang, Chiu-Hao Chen & Feng-Yin Li
Pages: 1214-1231
Published online: 14 Aug 2015
AbstractforInvestigation on critical structural motifs of ligands for triggering glucocorticoid receptor nuclear migration through molecular docking simulations | Full Text | References | PDF (1.5 MB) | Supplemental
  • 250 Views
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Article
Structural investigations into the binding mode of novel neolignans Cmp10 and Cmp19 microtubule stabilizers by in silico molecular docking, molecular dynamics, and binding free energy calculations
Shubhandra Tripathi, Akhil Kumar, B. Sathish Kumar, Arvind S. Negi & Ashok Sharma
Pages: 1232-1240
Published online: 01 Sep 2015
AbstractforStructural investigations into the binding mode of novel neolignans Cmp10 and Cmp19 microtubule stabilizers by in silico molecular docking, molecular dynamics, and binding free energy calculations | Full Text | References | PDF (824.9 KB)
  • 321 Views
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Article
Human microtubule affinity-regulating kinase 4 is stable at extremes of pH
Farha Naz, Parvesh Singh, Asimul Islam, Faizan Ahmad & Md. Imtaiyaz Hassan
Pages: 1241-1251
Published online: 21 Aug 2015
AbstractforHuman microtubule affinity-regulating kinase 4 is stable at extremes of pH | Full Text | References | PDF (788.4 KB) | Supplemental
  • 163 Views
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Article
Molecular insight into amyloid oligomer destabilizing mechanism of flavonoid derivative 2-(4′ benzyloxyphenyl)-3-hydroxy-chromen-4-one through docking and molecular dynamics simulations
Akhil Kumar, Swati Srivastava, Shubhandra Tripathi, Sandeep Kumar Singh, Saripella Srikrishna & Ashok Sharma
Pages: 1252-1263
Published online: 19 Oct 2015
AbstractforMolecular insight into amyloid oligomer destabilizing mechanism of flavonoid derivative 2-(4′ benzyloxyphenyl)-3-hydroxy-chromen-4-one through docking and molecular dynamics simulations | Full Text | References | PDF (900.3 KB) | Supplemental
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Article
Insights into the binding of thiosemicarbazone derivatives with human serum albumin: spectroscopy and molecular modelling studies
Subramani Karthikeyan, Ganesan Bharanidharan, Manish Kesherwani, Karthik Ananth Mani, Narasimhan Srinivasan, Devadasan Velmurugan, Prakasarao Aruna & Singaravelu Ganesan
Pages: 1264-1281
Published online: 03 Nov 2015
AbstractforInsights into the binding of thiosemicarbazone derivatives with human serum albumin: spectroscopy and molecular modelling studies | Full Text | References | PDF (1.4 MB)
  • 301 Views
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Article
Pharmacophore model prediction, 3D-QSAR and molecular docking studies on vinyl sulfones targeting Nrf2-mediated gene transcription intended for anti-Parkinson drug design
Mohd Athar, Mohsin Yousuf Lone, Vijay M. Khedkar & Prakash Chandra Jha
Pages: 1282-1297
Published online: 23 Nov 2015
AbstractforPharmacophore model prediction, 3D-QSAR and molecular docking studies on vinyl sulfones targeting Nrf2-mediated gene transcription intended for anti-Parkinson drug design | Full Text | References | PDF (660.7 KB)
  • 614 Views
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Article
Conformational variability of recombination R-triplex formed by the mammalian telomeric sequence
Anna K. Shchyolkina, Dmitry N. Kaluzhny, Olga F. Borisova, Donna J. Arndt-Jovin, Thomas M. Jovin & Victor B. Zhurkin
Pages: 1298-1306
Published online: 15 Oct 2015
AbstractforConformational variability of recombination R-triplex formed by the mammalian telomeric sequence | Full Text | References | PDF (401.2 KB)
  • 863 Views
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Open Access
Article
Computational studies of acetylcholinesterase complexed with fullerene derivatives: a new insight for Alzheimer disease treatment
Arlan da Silva Gonçalves, Tanos Celmar Costa França & Osmair Vital de Oliveira
Pages: 1307-1316
Published online: 15 Oct 2015
AbstractforComputational studies of acetylcholinesterase complexed with fullerene derivatives: a new insight for Alzheimer disease treatment | Full Text | References | PDF (830.9 KB)
  • 319 Views
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Article
Structure–function discrepancy in Clostridium botulinum C3 toxin for its rational prioritization as a subunit vaccine
R. Prathiviraj, A. Prisilla & P. Chellapandi
Pages: 1317-1329
Published online: 02 Sep 2015
AbstractforStructure–function discrepancy in Clostridium botulinum C3 toxin for its rational prioritization as a subunit vaccine | Full Text | References | PDF (960.2 KB) | Supplemental
  • 147 Views
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Article
Molecular modeling, in silico screening and molecular dynamics of PfPRL-PTP of P. falciparum for identification of potential anti-malarials
Sachin Patel, Deepti Joshi, Rani Soni, Drista Sharma & Tarun Kumar Bhatt
Pages: 1330-1344
Published online: 22 Sep 2015
AbstractforMolecular modeling, in silico screening and molecular dynamics of PfPRL-PTP of P. falciparum for identification of potential anti-malarials | Full Text | References | PDF (984.5 KB)
  • 235 Views
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Article
An in silico approach towards the identification of novel inhibitors of the TLR-4 signaling pathway
Jarjapu Mahita, K. Harini, Mallikarjuna Rao Pichika & Ramanathan Sowdhamini
Pages: 1345-1362
Published online: 02 Sep 2015
AbstractforAn in silico approach towards the identification of novel inhibitors of the TLR-4 signaling pathway | Full Text | References | PDF (910.1 KB) | Supplemental
  • 519 Views
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Article
Biased signaling: potential agonist and antagonist of PAR2
Kavita Kumari Kakarala & Kaiser Jamil
Pages: 1363-1376
Published online: 19 Oct 2015
AbstractforBiased signaling: potential agonist and antagonist of PAR2 | Full Text | References | PDF (1 MB) | Supplemental
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