Journal of Biomolecular Structure and Dynamics, Volume 35, Issue 3 (2017)

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Journal of Biomolecular Structure and Dynamics, Volume 35, Issue 3 (2017)

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Research Articles

Article
Urea-induced denaturation of human calcium/calmodulin-dependent protein kinase IV: a combined spectroscopic and MD simulation studies
Huma Naz, Mohd. Shahbaaz, Md. Anzarul Haque, Krishna Bisetty, Asimul Islam, Faizan Ahmad & Md. Imtaiyaz Hassan
Pages: 463-475
Published online: 08 Mar 2016
AbstractforUrea-induced denaturation of human calcium/calmodulin-dependent protein kinase IV: a combined spectroscopic and MD simulation studies | Full Text | References | PDF (872.2 KB) | Supplemental
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Article
PPARγ non-covalent antagonists exhibit mutable binding modes with a similar free energy of binding: a case study
Filip Fratev
Pages: 476-485
Published online: 02 Aug 2016
AbstractforPPARγ non-covalent antagonists exhibit mutable binding modes with a similar free energy of binding: a case study | Full Text | References | PDF (431.3 KB) | Supplemental
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Article
Heterodimerization of the Entamoeba histolytica EhCPADH virulence complex through molecular dynamics and protein–protein docking
Sarita Montaño, Esther Orozco, José Correa-Basurto, Martiniano Bello, Bibiana Chávez-Munguía & Abigail Betanzos
Pages: 486-503
Published online: 18 Apr 2016
AbstractforHeterodimerization of the Entamoeba histolytica EhCPADH virulence complex through molecular dynamics and protein–protein docking | Full Text | References | PDF (1.5 MB) | Supplemental
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Article
Effects of the enlargement of polyglutamine segments on the structure and folding of ataxin-2 and ataxin-3 proteins
Jingran Wen, Daniel R. Scoles & Julio C. Facelli
Pages: 504-519
Published online: 20 May 2016
AbstractforEffects of the enlargement of polyglutamine segments on the structure and folding of ataxin-2 and ataxin-3 proteins | Full Text | References | PDF (1.7 MB)
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Article
The influence of nicotine on pioglitazone encapsulation into carbon nanotube: the investigation of molecular dynamic and density functional theory
Maryam Zaboli & Heidar Raissi
Pages: 520-534
Published online: 07 Apr 2016
AbstractforThe influence of nicotine on pioglitazone encapsulation into carbon nanotube: the investigation of molecular dynamic and density functional theory | Full Text | References | PDF (1.7 MB)
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Article
Steered molecular dynamics study reveals insights into the function of the repetitive B region of collagen- and fibrinogen-binding MSCRAMMs
D.S. Jemima Beulin & Karthe Ponnuraj
Pages: 535-550
Published online: 12 Apr 2016
AbstractforSteered molecular dynamics study reveals insights into the function of the repetitive B region of collagen- and fibrinogen-binding MSCRAMMs | Full Text | References | PDF (942.1 KB)
  • 547 Views
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Article
New insight into the shortening of the collagen fibril D-period in human cornea
Maria Jastrzebska, Dorota Tarnawska, Roman Wrzalik, Artur Chrobak, Michal Grelowski, Edward Wylegala, Dorota Zygadlo & Alicja Ratuszna
Pages: 551-563
Published online: 08 Mar 2016
AbstractforNew insight into the shortening of the collagen fibril D-period in human cornea | Full Text | References | PDF (1,014.9 KB)
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Article
Mapping intermolecular interactions and active site conformations: from human MMP-1 crystal structure to molecular dynamics free energy calculations
Anthony Nash, Helen L. Birch & Nora H. de Leeuw
Pages: 564-573
Published online: 25 Apr 2016
AbstractforMapping intermolecular interactions and active site conformations: from human MMP-1 crystal structure to molecular dynamics free energy calculations | Full Text | References | PDF (898.7 KB) | Supplemental
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Open Access
Article
Homology modeling and molecular dynamics study on Schwanniomyces occidentalis alpha-amylase
Yahya Sefidbakht, Omid Ranaei Siadat & Fatemeh Taheri
Pages: 574-584
Published online: 07 Apr 2016
AbstractforHomology modeling and molecular dynamics study on Schwanniomyces occidentalis alpha-amylase | Full Text | References | PDF (4.3 MB) | Supplemental
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Article
The conformational and vibrational behavior of the inhibitory neuropeptide derived from beta-endorphin
Serda Kecel-Gunduz, Sefa Celik, Aysen E. Ozel & Sevim Akyuz
Pages: 585-602
Published online: 01 Jul 2016
AbstractforThe conformational and vibrational behavior of the inhibitory neuropeptide derived from beta-endorphin | Full Text | References | PDF (1.1 MB)
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Article
Studies on the interaction between nanodiamond and human hemoglobin by surface tension measurement and spectroscopy methods
Leila Pishkar, Saba Taheri, Somayeh Makarem, Hojjat Alizadeh Zeinabad, Arash Rahimi, Ali Akbar Saboury & Mojtaba Falahati
Pages: 603-615
Published online: 12 Jul 2016
AbstractforStudies on the interaction between nanodiamond and human hemoglobin by surface tension measurement and spectroscopy methods | Full Text | References | PDF (460.7 KB)
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Article
Genetics-directed drug discovery for combating Mycobacterium tuberculosis infection
Yuan Quan, Le Xiong, Jing Chen & Hong-Yu Zhang
Pages: 616-621
Published online: 27 Jun 2016
AbstractforGenetics-directed drug discovery for combating Mycobacterium tuberculosis infection | Full Text | References | PDF (182.7 KB) | Supplemental
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Article
An in silico approach to understand the structure–function properties of a serine protease (Bacifrinase) from Bacillus cereus and experimental evidence to support the interaction of Bacifrinase with fibrinogen and thrombin
Bandana Bora, Akash Deep Biswas, Arun Bahadur Gurung, Atanu Bhattacharjee, Venkata Satish Kumar Mattaparthi & Ashis K. Mukherjee
Pages: 622-644
Published online: 08 Jul 2016
AbstractforAn in silico approach to understand the structure–function properties of a serine protease (Bacifrinase) from Bacillus cereus and experimental evidence to support the interaction of Bacifrinase with fibrinogen and thrombin | Full Text | References | PDF (1.9 MB)
  • 438 Views
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Article
Dynamic properties of SOD1 mutants can predict survival time of patients carrying familial amyotrophic lateral sclerosis
Nikolay A. Alemasov, Nikita V. Ivanisenko, Sergey P. Medvedev, Suren M. Zakian, Nikolay A. Kolchanov & Vladimir A. Ivanisenko
Pages: 645-656
Published online: 17 Mar 2016
AbstractforDynamic properties of SOD1 mutants can predict survival time of patients carrying familial amyotrophic lateral sclerosis | Full Text | References | PDF (1.1 MB)
  • 437 Views
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Article
Lipoxygenase directed anti-inflammatory and anti-cancerous secondary metabolites: ADMET-based screening, molecular docking and dynamics simulation
Swati Singh, Manika Awasthi, Veda P. Pandey & Upendra N. Dwivedi
Pages: 657-668
Published online: 21 Mar 2016
AbstractforLipoxygenase directed anti-inflammatory and anti-cancerous secondary metabolites: ADMET-based screening, molecular docking and dynamics simulation | Full Text | References | PDF (546.4 KB) | Supplemental
  • 401 Views
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Article
A new mechanism of post-transfer editing by aminoacyl-tRNA synthetases: catalysis of hydrolytic reaction by bacterial-type prolyl-tRNA synthetase
Konstantin S. Boyarshin, Anastasia E. Priss, Alexsey V. Rayevskiy, Mykola M. Ilchenko, Igor Ya. Dubey, Ivan A. Kriklivyi, Anna D. Yaremchuk & Michael A. Tukalo
Pages: 669-682
Published online: 08 Mar 2016
AbstractforA new mechanism of post-transfer editing by aminoacyl-tRNA synthetases: catalysis of hydrolytic reaction by bacterial-type prolyl-tRNA synthetase | Full Text | References | PDF (626.1 KB) | Supplemental
  • 299 Views
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Letter to the Editor

Letter
MethyRNA: a web server for identification of N6-methyladenosine sites
Wei Chen, Hua Tang & Hao Lin
Pages: 683-687
Published online: 04 May 2016
First Page PreviewforMethyRNA: a web server for identification of N6-methyladenosine sites | Full Text | References | PDF (171.3 KB)
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