Journal of Biomolecular Structure and Dynamics, Volume 38, Issue 15 (2020)

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Journal of Biomolecular Structure and Dynamics, Volume 38, Issue 15 (2020)

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Research Articles

Article
Small-angle X-ray scattering based structure, modeling and molecular dynamics analyses of a family 5 glycoside hydrolase first endo-mannanase named as RfGH5_7 from Ruminococcus flavefaciens
Dishant Goyal, Krishan Kumar, Kedar Sharma & Arun Goyal
Pages: 4371-4384
Published online: 23 Oct 2019
AbstractforSmall-angle X-ray scattering based structure, modeling and molecular dynamics analyses of a family 5 glycoside hydrolase first endo-mannanase named as RfGH5_7 from Ruminococcus flavefaciens | Full Text | References | PDF (4.2 MB) | EPUB
  • 301 Views
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Article
Discovery of potent apoptosis signal-regulating kinase 1 inhibitors via integrated computational strategy and biological evaluation
Yuchen Wang, Shaohua Hou, Yu Tong, Hongmei Li, Yi Hua, Yuanrong Fan, Xingye Chen, Yan Yang, Haichun Liu, Tao Lu, Yadong Chen & Yanmin Zhang
Pages: 4385-4396
Published online: 23 Oct 2019
AbstractforDiscovery of potent apoptosis signal-regulating kinase 1 inhibitors via integrated computational strategy and biological evaluation | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 178 Views
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Article
Crystallographic structure versus homology model: a case study of molecular dynamics simulation of human and zebrafish histone deacetylase 10
Abdullahi Ibrahim Uba & Kemal Yelekçi
Pages: 4397-4406
Published online: 15 Nov 2019
AbstractforCrystallographic structure versus homology model: a case study of molecular dynamics simulation of human and zebrafish histone deacetylase 10 | Full Text | References | PDF (2.9 MB) | EPUB
  • 302 Views
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Article
Identification of therapeutic peptide scaffold from tritrpticin family for urinary tract infections using in silico techniques
S. R. Shruti & R. Rajasekaran
Pages: 4407-4417
Published online: 23 Oct 2019
AbstractforIdentification of therapeutic peptide scaffold from tritrpticin family for urinary tract infections using in silico techniques | Full Text | References | PDF (1.3 MB) | EPUB | Supplemental
  • 116 Views
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Article
Evolutionary significance and functional characterization of streptomycin adenylyltransferase from Serratia marcescens
Dhamodharan Prabhu, Sundaraj Rajamanikandan, Poopandi Saritha & Jeyaraman Jeyakanthan
Pages: 4418-4431
Published online: 29 Oct 2019
AbstractforEvolutionary significance and functional characterization of streptomycin adenylyltransferase from Serratia marcescens | Full Text | References | PDF (3.4 MB) | EPUB
  • 192 Views
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Article
Identification of novel inhibitor of protein tyrosine phosphatases delta: structure-based pharmacophore modeling, virtual screening, flexible docking, molecular dynamics simulation, and post-molecular dynamics analysis
Yang-Chun Ma, Bing Yang, Xin Wang, Liang Zhou, Wei-Ya Li, Wen-Shan Liu, Xin-Hua Lu, Zhi-Hui Zheng, Ying Ma & Run-Ling Wang
Pages: 4432-4448
Published online: 31 Oct 2019
AbstractforIdentification of novel inhibitor of protein tyrosine phosphatases delta: structure-based pharmacophore modeling, virtual screening, flexible docking, molecular dynamics simulation, and post-molecular dynamics analysis | Full Text | References | PDF (5 MB) | EPUB | Supplemental
  • 237 Views
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Article
Elucidation of role of an acetyltransferase like protein in paromomycin resistance in Leishmania donovani using in silico and in vitro approaches
Aditya Verma, Arnab Nayek, Amit Kumar, Ruchi Singh & Poonam Salotra
Pages: 4449-4460
Published online: 26 Oct 2019
AbstractforElucidation of role of an acetyltransferase like protein in paromomycin resistance in Leishmania donovani using in silico and in vitro approaches | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 156 Views
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Article
Discovery of selective farnesoid X receptor agonists for the treatment of hyperlipidemia from traditional Chinese medicine based on virtual screening and in vitro validation
Xi Chen, Fang Lu, Ganggang Luo, Yue Ren, Jing Ma & Yanling Zhang
Pages: 4461-4470
Published online: 16 Dec 2019
AbstractforDiscovery of selective farnesoid X receptor agonists for the treatment of hyperlipidemia from traditional Chinese medicine based on virtual screening and in vitro validation | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 211 Views
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Article
The pathogenicity, structural and functional exploration of human HMGB1 single nucleotide polymorphisms using in silico study
P. Santhiya, A. Christian Bharathi & B. Syed Ibrahim
Pages: 4471-4482
Published online: 29 Oct 2019
AbstractforThe pathogenicity, structural and functional exploration of human HMGB1 single nucleotide polymorphisms using in silico study | Full Text | References | PDF (2.8 MB) | EPUB | Supplemental
  • 156 Views
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Article
The structural basis of acid resistance in Mycobacterium tuberculosis: insights from multiple pH regime molecular dynamics simulations
Mohd Shahbaaz, Vladimir Potemkin, Maria Grishina, Krishna Bisetty & Imtaiyaz Hassan
Pages: 4483-4492
Published online: 08 Nov 2019
AbstractforThe structural basis of acid resistance in Mycobacterium tuberculosis: insights from multiple pH regime molecular dynamics simulations | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 229 Views
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Article
In silico mutation on a mutant lipase from Acinetobacter haemolyticus towards enhancing alkaline stability
Nurul Fatin Syamimi Khairul Anuar, Roswanira Abdul Wahab, Fahrul Huyop, Khairul Bariyyah Abd Halim & Azzmer Azzar Abdul Hamid
Pages: 4493-4507
Published online: 26 Oct 2019
AbstractforIn silico mutation on a mutant lipase from Acinetobacter haemolyticus towards enhancing alkaline stability | Full Text | References | PDF (3.4 MB) | EPUB
  • 225 Views
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Article
Uncovering the structure and function of Pseudomonas aeruginosa periplasmic proteins by an in silico approach
Silvia Caprari, Valentina Brandi, Andrea Pasquadibisceglie & Fabio Polticelli
Pages: 4508-4520
Published online: 30 Oct 2019
AbstractforUncovering the structure and function of Pseudomonas aeruginosa periplasmic proteins by an in silico approach | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 319 Views
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Article
Identification of potential inhibitors for HCV NS5b of genotype 4a by combining dynamic simulation, protein–ligand interaction fingerprint, 3D pharmacophore, docking and 3D QSAR
Mahmoud Abd El-Monem El-Hassab, Eman Esmat El-Bastawissy & Tarek Fathy El-Moselhy
Pages: 4521-4535
Published online: 07 Nov 2019
AbstractforIdentification of potential inhibitors for HCV NS5b of genotype 4a by combining dynamic simulation, protein–ligand interaction fingerprint, 3D pharmacophore, docking and 3D QSAR | Full Text | References | PDF (3.7 MB) | EPUB | Supplemental
  • 379 Views
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Article
Comprehensive analysis of the molecular docking of small molecule inhibitors to the Aβ1–40 peptide and its Osaka-mutant: insights into the molecular mechanisms of Aβ-peptide inhibition
Parveen Salahuddin, Rizwan Hasan Khan & Vladimir N. Uversky
Pages: 4536-4566
Published online: 09 Dec 2019
AbstractforComprehensive analysis of the molecular docking of small molecule inhibitors to the Aβ1–40 peptide and its Osaka-mutant: insights into the molecular mechanisms of Aβ-peptide inhibition | Full Text | References | PDF (3.6 MB) | EPUB
  • 261 Views
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Article
3D-QSAR, molecular docking, and molecular dynamics simulation of a novel thieno[3,4-d]pyrimidine inhibitor targeting human immunodeficiency virus type 1 reverse transcriptase
Han Chu, Qing-xiu He, Jun-wei Wang, Ya-ting Deng, Juan Wang, Yong Hu, Yuan-qiang Wang & Zhi-hua Lin
Pages: 4567-4578
Published online: 03 Dec 2019
Abstractfor3D-QSAR, molecular docking, and molecular dynamics simulation of a novel thieno[3,4-d]pyrimidine inhibitor targeting human immunodeficiency virus type 1 reverse transcriptase | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 194 Views
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Express Communication

Article
What limits the primary sequence space of natural proteins?
Aditya Mittal, Anandkumar Madhavjibhai Changani & Sakshi Taparia
Pages: 4579-4583
Published online: 29 Oct 2019
AbstractforWhat limits the primary sequence space of natural proteins? | Full Text | References | PDF (683.2 KB) | EPUB
  • 693 Views
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Hypothesis Paper

Article
Mitogen activated protein kinase-1 and cell division control protein-42 are putative targets for the binding of novel natural lead molecules: a therapeutic intervention against Candida albicans
Dharshini Gopal, Aditi G Muddebihalkar, Sinosh Skariyachan, Akshay Uttarkar C, Prinith Kaveramma, Ulluvangada Praveen, Roshini Ravi Shankar, Tejaswini Venkatesan & Vidya Niranjan
Pages: 4584-4599
Published online: 29 Oct 2019
AbstractforMitogen activated protein kinase-1 and cell division control protein-42 are putative targets for the binding of novel natural lead molecules: a therapeutic intervention against Candida albicans | Full Text | References | PDF (5 MB) | EPUB | Supplemental
  • 283 Views
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Letters to the Editor

Letter
Identification of deleterious missense variants of human Piwi like RNA-mediated gene silencing 1 gene and their impact on PAZ domain structure, stability, flexibility and dimension: in silico analysis
Zouhair Elkarhat, Lamiaa Elkhattabi, Hicham Charoute, Imane Morjane, Abdellatif Errouagui, Francis Carey, Boubker Nasser, Abdelhamid Barakat & Hassan Rouba
Pages: 4600-4606
Published online: 17 Oct 2019
AbstractforIdentification of deleterious missense variants of human Piwi like RNA-mediated gene silencing 1 gene and their impact on PAZ domain structure, stability, flexibility and dimension: in silico analysis | Full Text | References | PDF (2 MB) | EPUB
  • 115 Views
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Letter
Design and activity detection of BH3-mimetic peptide based on Bcl-XL binding potency
Chenggong Fu, Longhe Zhao, Xiangmin Tan, Jiazhong Li & Xin Wang
Pages: 4607-4616
Published online: 01 Nov 2019
AbstractforDesign and activity detection of BH3-mimetic peptide based on Bcl-XL binding potency | Full Text | References | PDF (2.9 MB) | EPUB
  • 301 Views
  • 1 CrossRef citations
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Letter
Structure-based methoxyflavone derivatives with potent inhibitory activity against various influenza neuraminidases
Yongjian Zang, Dongxiao Hao, He Wang, Zhiwei Yang, Huadong Liu & Shengli Zhang
Pages: 4617-4624
Published online: 25 Oct 2019
AbstractforStructure-based methoxyflavone derivatives with potent inhibitory activity against various influenza neuraminidases | Full Text | References | PDF (2.5 MB) | EPUB | Supplemental
  • 174 Views
  • 4 CrossRef citations
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Letter
Virtual high-throughput screening of natural compounds in-search of potential inhibitors for protection of telomeres 1 (POT1)
Mohd Amir, Taj Mohammad, Kartikay Prasad, Gulam Mustafa Hasan, Vijay Kumar, Ravins Dohare, Asimul Islam, Faizan Ahmad & Md. Imtaiyaz Hassan
Pages: 4625-4634
Published online: 31 Oct 2019
AbstractforVirtual high-throughput screening of natural compounds in-search of potential inhibitors for protection of telomeres 1 (POT1) | Full Text | References | PDF (2.8 MB) | EPUB
  • 190 Views
  • 27 CrossRef citations
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Letter
Quantum chemical and well-tempered metadynamics study to design adenine analogs for orthogonal Preq1 riboswitch
Kalyanashis Jana, Padmaja D. Wakchaure, Shibaji Ghosh, Tusar Bandyopadhyay & Bishwajit Ganguly
Pages: 4635-4643
Published online: 30 Oct 2019
AbstractforQuantum chemical and well-tempered metadynamics study to design adenine analogs for orthogonal Preq1 riboswitch | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 204 Views
  • 0 CrossRef citations
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Letter
Bovine serum albumin/gold nanoparticles as a drug delivery system for Curcumin: experimental and computational studies
Bahareh Khodashenas, Mehdi Ardjmand, Mazyar Sharifzadeh Baei, Ali Shokuhi Rad & Azim Akbarzadeh Khiyavi
Pages: 4644-4654
Published online: 30 Oct 2019
AbstractforBovine serum albumin/gold nanoparticles as a drug delivery system for Curcumin: experimental and computational studies | Full Text | References | PDF (3.3 MB) | EPUB
  • 274 Views
  • 13 CrossRef citations
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Letter
In vitro and in silico studies of nitrobenzamide derivatives as potential anti-neuroinflammatory agents
Seda Savranoglu Kulabas, Ferah Comert Onder, Yakup Berkay Yılmaz, Adem Ozleyen, Serdar Durdagi, Kader Sahin, Mehmet Ay & Tugba Boyunegmez Tumer
Pages: 4655-4668
Published online: 05 Nov 2019
AbstractforIn vitro and in silico studies of nitrobenzamide derivatives as potential anti-neuroinflammatory agents | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 607 Views
  • 3 CrossRef citations
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