Journal of Biomolecular Structure and Dynamics, Volume 39, Issue 1 (2021)

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Journal of Biomolecular Structure and Dynamics, Volume 39, Issue 1 (2021)

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Vol 42, 2024 Vol 41, 2023 Vol 40, 2022 Volume 39, 2021 Vol 38, 2020 Vol 37, 2019 Vol 36, 2018 Vol 35, 2017 Vol 34, 2016 Vol 33, 2015 Vol 32, 2014 Vol 31, 2013 Vol 30, 2012 Vol 29, 2011-2012 Vol 28, 2010-2011 Vol 27, 2009-2010 Vol 26, 2008-2009 Vol 25, 2007-2008 Vol 24, 2006-2007 Vol 23, 2005-2006 Vol 22, 2004-2005 Vol 21, 2003-2004 Vol 20, 2002-2003 Vol 19, 2001-2002 Vol 18, 2000-2001 Vol 17, 1999-2000 Vol 16, 1998-1999 Vol 15, 1997-1998 Vol 14, 1996-1997 Vol 13, 1995-1996 Vol 12, 1994-1995 Vol 11, 1993-1994 Vol 10, 1992-1993 Vol 9, 1991-1992 Vol 8, 1990-1991 Vol 7, 1989-1990 Vol 6, 1988-1989 Vol 5, 1987-1988 Vol 4, 1986-1987 Vol 3, 1985-1986 Vol 2, 1984-1985 Vol 1, 1983-1984
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Research Articles

Article
Development of decision trees to discriminate HDAC8 inhibitors and non-inhibitors using recursive partitioning
Sk. Abdul Amin, Nilanjan Adhikari & Tarun Jha
Pages: 1-8
Published online: 18 Sep 2019
AbstractforDevelopment of decision trees to discriminate HDAC8 inhibitors and non-inhibitors using recursive partitioning | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 229 Views
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Article
Two-dimensional infrared spectral explorations into bilayer and monolayer self-assemblies of amphiphilic polypeptides
Jun Zhang
Pages: 9-19
Published online: 21 Jan 2020
AbstractforTwo-dimensional infrared spectral explorations into bilayer and monolayer self-assemblies of amphiphilic polypeptides | Full Text | References | PDF (2.6 MB) | EPUB
  • 222 Views
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Article
Predicting interfacial hot-spot residues that stabilize protein-protein interfaces in oligomeric membrane-toxin pores through hydrogen bonds and salt bridges
Rajat Desikan, Prabal K. Maiti & K. Ganapathy Ayappa
Pages: 20-34
Published online: 29 Jan 2020
AbstractforPredicting interfacial hot-spot residues that stabilize protein-protein interfaces in oligomeric membrane-toxin pores through hydrogen bonds and salt bridges | Full Text | References | PDF (3.8 MB) | EPUB
  • 278 Views
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Article
Investigation of conformational dynamics of Tyr89Cys mutation in protection of telomeres 1 gene associated with familial melanoma
Mohd. Amir, Shahzaib Ahamad, Taj Mohammad, Deeba Shamim Jairajpuri, Gulam Mustafa Hasan, Ravins Dohare, Asimul Islam, Faizan Ahmad & Md. Imtaiyaz Hassan
Pages: 35-44
Published online: 27 Dec 2019
AbstractforInvestigation of conformational dynamics of Tyr89Cys mutation in protection of telomeres 1 gene associated with familial melanoma | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 277 Views
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Research Article

Article
Identification of the potential dual inhibitor of protein tyrosine phosphatase sigma and leukocyte common antigen-related phosphatase by virtual screen, molecular dynamic simulations and post-analysis
Liang Zhou, Yang-Chun Ma, Xue Tang, Wei-Ya Li, Ying Ma & Run-Ling Wang
Pages: 45-62
Published online: 27 Dec 2019
AbstractforIdentification of the potential dual inhibitor of protein tyrosine phosphatase sigma and leukocyte common antigen-related phosphatase by virtual screen, molecular dynamic simulations and post-analysis | Full Text | References | PDF (3.8 MB) | EPUB | Supplemental
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Research Articles

Article
Computational investigation of imidazopyridine analogs as protein kinase B (Akt1) allosteric inhibitors by using 3D-QSAR, molecular docking and molecular dynamics simulations
Xi Gu, Ying Wang, Mingxing Wang, Jian Wang & Ning Li
Pages: 63-78
Published online: 26 Dec 2019
AbstractforComputational investigation of imidazopyridine analogs as protein kinase B (Akt1) allosteric inhibitors by using 3D-QSAR, molecular docking and molecular dynamics simulations | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 434 Views
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Article
Biomolecular study and conjugation of two para-aminobenzoic acid derivatives with serum proteins: drug binding efficacy and protein structural analysis
P. Chanphai, F. Cloutier, Y. Oufqir, M.-F. Leclerc, A.M. Eiján, C. Reyes-Moreno, G. Bérubé & H.A. Tajmir-Riahi
Pages: 79-90
Published online: 03 Feb 2020
AbstractforBiomolecular study and conjugation of two para-aminobenzoic acid derivatives with serum proteins: drug binding efficacy and protein structural analysis | Full Text | References | PDF (2.7 MB) | EPUB
  • 261 Views
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Article
Synthesis, molecular docking and QSAR study of thiazole clubbed pyrazole hybrid as α-amylase inhibitor
Meenakshi Duhan, Rahul Singh, Meena Devi, Jayant Sindhu, Rimpy Bhatia, Ashwani Kumar & Parvin Kumar
Pages: 91-107
Published online: 27 Dec 2019
AbstractforSynthesis, molecular docking and QSAR study of thiazole clubbed pyrazole hybrid as α-amylase inhibitor | Full Text | References | PDF (2.4 MB) | EPUB | Supplemental
  • 536 Views
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Article
Light-induced effects in glycine aqueous solution studied by Fourier transform infrared-emission spectroscopy and ultraviolet-visible spectroscopy
Evgeni L. Terpugov, Maxim S. Kondratyev & Olga V. Degtyareva
Pages: 108-117
Published online: 25 Jan 2020
AbstractforLight-induced effects in glycine aqueous solution studied by Fourier transform infrared-emission spectroscopy and ultraviolet-visible spectroscopy | Full Text | References | PDF (1.7 MB) | EPUB | Supplemental
  • 345 Views
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Article
Observation of quantum signature in rivastigmine chemical bond break-up and quantum energetics, spectral studies of anti-Alzheimer inhibitors
M Rejwan Ali & Mihaly Mezei
Pages: 118-128
Published online: 10 Jan 2020
AbstractforObservation of quantum signature in rivastigmine chemical bond break-up and quantum energetics, spectral studies of anti-Alzheimer inhibitors | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 257 Views
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Article
Cellular prion protein gene polymorphisms linked to differential scrapie susceptibility correlate with distinct residue connectivity between secondary structure elements
Patricia Soto, India A. Claflin, Alyssa L. Bursott, Aimee D. Schwab-McCoy & Jason C. Bartz
Pages: 129-139
Published online: 08 Jan 2020
AbstractforCellular prion protein gene polymorphisms linked to differential scrapie susceptibility correlate with distinct residue connectivity between secondary structure elements | Full Text | References | PDF (2.2 MB) | EPUB | Supplemental
  • 220 Views
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Article
Deciphering molecular mechanism behind conformational change of the São Paolo metallo-β-lactamase 1 by using enhanced sampling
Jianzhong Chen, Jinan Wang, Laixue Pang, Wei Wang, Juan Zhao & Weiliang Zhu
Pages: 140-151
Published online: 28 Dec 2019
AbstractforDeciphering molecular mechanism behind conformational change of the São Paolo metallo-β-lactamase 1 by using enhanced sampling | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 217 Views
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Article
Quantitative structure–activity relationships analysis, homology modeling, docking and molecular dynamics studies of triterpenoid saponins as Kirsten rat sarcoma inhibitors
Mourad Stitou, Hamid Toufik, Mohammed Bouachrine & Fatima Lamchouri
Pages: 152-170
Published online: 06 Jan 2020
AbstractforQuantitative structure–activity relationships analysis, homology modeling, docking and molecular dynamics studies of triterpenoid saponins as Kirsten rat sarcoma inhibitors | Full Text | References | PDF (4 MB) | EPUB
  • 462 Views
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Article
Identification of potential inhibitors against pathogenic missense mutations of PMM2 using a structure-based virtual screening approach
D. Thirumal Kumar, Nikita Jain, S. Udhaya Kumar, C. George Priya Doss & Hatem Zayed
Pages: 171-187
Published online: 06 Jan 2020
AbstractforIdentification of potential inhibitors against pathogenic missense mutations of PMM2 using a structure-based virtual screening approach | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 465 Views
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Article
Exploring the different states of wild-type T-cell receptor and mutant conformational changes towards understanding the antigen recognition
Sunil Kumar Tripathi & Dinakar M. Salunke
Pages: 188-201
Published online: 08 Jan 2020
AbstractforExploring the different states of wild-type T-cell receptor and mutant conformational changes towards understanding the antigen recognition | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 258 Views
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Article
Molecular dynamics simulation and free energy calculation studies of the binding mechanism of allosteric inhibitors with TrkA kinase
Xiaoyun Wu, Qinlan Li, Shanhe Wan & Jiajie Zhang
Pages: 202-208
Published online: 30 Dec 2019
AbstractforMolecular dynamics simulation and free energy calculation studies of the binding mechanism of allosteric inhibitors with TrkA kinase | Full Text | References | PDF (1.4 MB) | EPUB
  • 255 Views
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Article
Small angle X-ray scattering based structure, modeling and molecular dynamics analyses of family 43 glycoside hydrolase α-L-arabinofuranosidase from Clostridium thermocellum
Kedar Sharma, Carlos M. G. A. Fontes, Shabir Najmudin & Arun Goyal
Pages: 209-218
Published online: 30 Dec 2019
AbstractforSmall angle X-ray scattering based structure, modeling and molecular dynamics analyses of family 43 glycoside hydrolase α-L-arabinofuranosidase from Clostridium thermocellum | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 318 Views
  • 3 CrossRef citations
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Article
Multi-epitope based vaccine against yellow fever virus applying immunoinformatics approaches
Stephane Fraga de Oliveira Tosta, Mariana Santana Passos, Rodrigo Kato, Álvaro Salgado, Joilson Xavier, Arun Kumar Jaiswal, Siomar C. Soares, Vasco Azevedo, Marta Giovanetti, Sandeep Tiwari & Luiz Carlos Junior Alcantara
Pages: 219-235
Published online: 06 Jan 2020
AbstractforMulti-epitope based vaccine against yellow fever virus applying immunoinformatics approaches | Full Text | References | PDF (3.6 MB) | EPUB | Supplemental
  • 722 Views
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Article
Effect of tetracycline family of antibiotics on actin aggregation, resulting in the formation of Hirano bodies responsible for neuropathological disorders
Samridhi Pathak, Sarita Tripathi, Nayan Deori, Basir Ahmad, Hriday Verma, Rama Lokhande, Shirisha Nagotu & Avinash Kale
Pages: 236-253
Published online: 28 Jan 2020
AbstractforEffect of tetracycline family of antibiotics on actin aggregation, resulting in the formation of Hirano bodies responsible for neuropathological disorders | Full Text | References | PDF (3.3 MB) | EPUB | Supplemental
  • 370 Views
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Article
The effect of putrescine on stability and structural properties of bovine serum albumin
Elham Ziaee, Behzad Shareghi, Sadegh Farhadian, Lida Momeni & Fatemeh Heibati-Goojani
Pages: 254-262
Published online: 31 Mar 2020
AbstractforThe effect of putrescine on stability and structural properties of bovine serum albumin | Full Text | References | PDF (1.6 MB) | EPUB
  • 161 Views
  • 1 CrossRef citations
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Article
Design and synthesis of a sulphur containing Schiff base drug: DNA binding studies and theoretical calculations
Urmila Saha, Malay Dolai, Saugata Konar, Amit Das, Ray J. Butcher, Gopinatha Suresh Kumar & Subrata Mukhopadhyay
Pages: 263-271
Published online: 08 Jan 2020
AbstractforDesign and synthesis of a sulphur containing Schiff base drug: DNA binding studies and theoretical calculations | Full Text | References | PDF (1.9 MB) | EPUB | Supplemental
  • 166 Views
  • 3 CrossRef citations
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Article
Investigating into the molecular interactions of flavonoids targeting NS2B-NS3 protease from ZIKA virus through in-silico approaches
Rakhi Yadav, Chandrabose Selvaraj, Murali Aarthy, Prateek Kumar, Ankur Kumar, Sanjeev Kumar Singh & Rajanish Giri
Pages: 272-284
Published online: 10 Jan 2020
AbstractforInvestigating into the molecular interactions of flavonoids targeting NS2B-NS3 protease from ZIKA virus through in-silico approaches | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 645 Views
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Article
A-CaMP: a tool for anti-cancer and antimicrobial peptide generation
Aman Chandra Kaushik, Aamir Mehmood, Shaoliang Peng, Yu-Juan Zhang, Xiaofeng Dai & Dong-Qing Wei
Pages: 285-293
Published online: 06 Jan 2020
AbstractforA-CaMP: a tool for anti-cancer and antimicrobial peptide generation | Full Text | References | PDF (2.1 MB) | EPUB | Supplemental
  • 544 Views
  • 8 CrossRef citations
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Article
Structural and functional alterations of nitric oxide synthase 3 due to missense variants associate with high-altitude pulmonary edema through dynamic study
Hema Kanipakam, Kavita Sharma, Tashi Thinlas, Ghulam Mohammad & M. A. Qadar Pasha
Pages: 294-309
Published online: 17 Jan 2020
AbstractforStructural and functional alterations of nitric oxide synthase 3 due to missense variants associate with high-altitude pulmonary edema through dynamic study | Full Text | References | PDF (4.4 MB) | EPUB | Supplemental
  • 247 Views
  • 10 CrossRef citations
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Article
Why the first self-binding peptide of human c-Src kinase does not contain class II motif but can bind to its cognate Src homology 3 domain in class II mode?
Peng Zhou, Fugang Yan, Qingqing Miao, Zheng Chen & Heyi Wang
Pages: 310-318
Published online: 06 Jan 2020
AbstractforWhy the first self-binding peptide of human c-Src kinase does not contain class II motif but can bind to its cognate Src homology 3 domain in class II mode? | Full Text | References | PDF (1.7 MB) | EPUB
  • 161 Views
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Article
Non-symmetrical structural behavior of a symmetric protein: the case of homo-trimeric TRAF2 (tumor necrosis factor-receptor associated factor 2)
Velia Minicozzi, Almerinda Di Venere, Eleonora Nicolai, Alessandro Giuliani, Anna Maria Caccuri, Luisa Di Paola & Giampiero Mei
Pages: 319-329
Published online: 13 Feb 2020
AbstractforNon-symmetrical structural behavior of a symmetric protein: the case of homo-trimeric TRAF2 (tumor necrosis factor-receptor associated factor 2) | Full Text | References | PDF (2 MB) | EPUB
  • 91 Views
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Article
Are zinc oxide nanoparticles safe? A structural study on human serum albumin using in vitro and in silico methods
Marziyeh Hassanian, Hassan Aryapour, Alireza Goudarzi & Masoud Bezi Javan
Pages: 330-335
Published online: 29 Jan 2020
AbstractforAre zinc oxide nanoparticles safe? A structural study on human serum albumin using in vitro and in silico methods | Full Text | References | PDF (1 MB) | EPUB
  • 246 Views
  • 14 CrossRef citations
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Article
Unravelling the interaction of glipizide with human serum albumin using various spectroscopic techniques and molecular dynamics studies
Razique Anwer, Khalid I. AlQumaizi, Shafiul Haque, Pallavi Somvanshi, Nazia Ahmad, Saleh M. AlOsaimi & Tasneem Fatma
Pages: 336-347
Published online: 10 Jan 2020
AbstractforUnravelling the interaction of glipizide with human serum albumin using various spectroscopic techniques and molecular dynamics studies | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 272 Views
  • 8 CrossRef citations
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Article
Identification of a novel binding mechanism of Quinoline based molecules with lactate dehydrogenase of Plasmodium falciparum
Rahul Singh, Vijay Bhardwaj & Rituraj Purohit
Pages: 348-356
Published online: 20 Jan 2020
AbstractforIdentification of a novel binding mechanism of Quinoline based molecules with lactate dehydrogenase of Plasmodium falciparum | Full Text | References | PDF (1.9 MB) | EPUB | Supplemental
  • 641 Views
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Article
Structural heterogeneity in RNA recognition motif 2 (RRM2) of TAR DNA-binding protein 43 (TDP-43): clue to amyotrophic lateral sclerosis
Amresh Prakash, Vijay Kumar, Atanu Banerjee, Andrew M. Lynn & Rajendra Prasad
Pages: 357-367
Published online: 22 Jan 2020
AbstractforStructural heterogeneity in RNA recognition motif 2 (RRM2) of TAR DNA-binding protein 43 (TDP-43): clue to amyotrophic lateral sclerosis | Full Text | References | PDF (3.8 MB) | EPUB | Supplemental
  • 353 Views
  • 13 CrossRef citations
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Letter to the Editor

Letter
Discovery of new AKT1 inhibitors by combination of in silico structure based virtual screening approaches and biological evaluations
Filip Fratev, Denisse A. Gutierrez, Renato J. Aguilera, Ashish Tyagi, Chendil Damodaran & Suman Sirimulla
Pages: 368-377
Published online: 12 Feb 2020
AbstractforDiscovery of new AKT1 inhibitors by combination of in silico structure based virtual screening approaches and biological evaluations | Full Text | References | PDF (2.1 MB) | EPUB
  • 271 Views
  • 5 CrossRef citations
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