Journal of Biomolecular Structure and Dynamics, Volume 39, Issue 2 (2021)

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Journal of Biomolecular Structure and Dynamics, Volume 39, Issue 2 (2021)

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Research Articles

Article
Elucidation the binding mechanism of Nelumbo nucifera-derived isoquinoline alkaloids as Rho-kinase 1 inhibitors by molecular docking and dynamic simulation
Jian Liu, Yang Lu, Guancong Li, Min Xiao, Guangming Yang & Yang Pan
Pages: 379-394
Published online: 25 Jan 2020
AbstractforElucidation the binding mechanism of Nelumbo nucifera-derived isoquinoline alkaloids as Rho-kinase 1 inhibitors by molecular docking and dynamic simulation | Full Text | References | PDF (4.2 MB) | EPUB
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Article
Screening of inhibitors as potential remedial against Ebolavirus infection: pharmacophore-based approach
Muthumanickam Sankar, Langeswaran K, Sangavi Jeyachandran & Boomi Pandi
Pages: 395-408
Published online: 30 Jan 2020
AbstractforScreening of inhibitors as potential remedial against Ebolavirus infection: pharmacophore-based approach | Full Text | References | PDF (3.5 MB) | EPUB | Supplemental
  • 267 Views
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Article
Delineating the folding perturbations and molecular mechanisms of Thr-Ala 642 mutation in Rab-GTPase activating protein Akt substrate of 160kDa and its impact on the aetiology of diabetes
Utkarsh Nagpal, D. Kamalesh, P. Raghuraman, Sriroopreddy Ramireddy & C. Sudandiradoss
Pages: 409-420
Published online: 18 Feb 2020
AbstractforDelineating the folding perturbations and molecular mechanisms of Thr-Ala 642 mutation in Rab-GTPase activating protein Akt substrate of 160kDa and its impact on the aetiology of diabetes | Full Text | References | PDF (2.9 MB) | EPUB
  • 158 Views
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Article
Targeting metacaspase-3 from Plasmodium falciparum towards antimalarial therapy: A combined approach of in-silico and in-vitro investigation
Bhumika Kumar, Taj Mohammad, Amaduddin, Afzal Hussain, Asimul Islam, Faizan Ahmad, Mohamed F. Alajmi, Shailja Singh, Kailash C. Pandey, Md. Imtaiyaz Hassan & Mohammad Abid
Pages: 421-430
Published online: 13 Jan 2020
AbstractforTargeting metacaspase-3 from Plasmodium falciparum towards antimalarial therapy: A combined approach of in-silico and in-vitro investigation | Full Text | References | PDF (2.9 MB) | EPUB | Supplemental
  • 274 Views
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Article
Identifying the key residues instrumental in imparting stability to amyloid beta protofibrils – a comparative study using MD simulations of 17–42 residues
Madhu Sudan Dutta & Soumalee Basu
Pages: 431-456
Published online: 13 Jan 2020
AbstractforIdentifying the key residues instrumental in imparting stability to amyloid beta protofibrils – a comparative study using MD simulations of 17–42 residues | Full Text | References | PDF (11.4 MB) | EPUB | Supplemental
  • 328 Views
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Article
Synthesis, characterization and anti-inflammatory activity evaluation of 1,2,4-triazole and its derivatives as a potential scaffold for the synthesis of drugs against prostaglandin-endoperoxide synthase
Bushra Khan, Abdullah Naiyer, Fareeda Athar, Shakir Ali & Sonu Chand Thakur
Pages: 457-475
Published online: 10 Jan 2020
AbstractforSynthesis, characterization and anti-inflammatory activity evaluation of 1,2,4-triazole and its derivatives as a potential scaffold for the synthesis of drugs against prostaglandin-endoperoxide synthase | Full Text | References | PDF (5.3 MB) | EPUB | Supplemental
  • 401 Views
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Article
Non-enzymatic glycation of human serum albumin modulates its binding efficacy towards bioactive flavonoid chrysin: A detailed study using multi-spectroscopic and computational methods
Sharat Sarmah, Somdev Pahari, Sourav Das, Vinay Kumar Belwal, Madhurima Jana & Atanu Singha Roy
Pages: 476-492
Published online: 20 Jan 2020
AbstractforNon-enzymatic glycation of human serum albumin modulates its binding efficacy towards bioactive flavonoid chrysin: A detailed study using multi-spectroscopic and computational methods | Full Text | References | PDF (4.3 MB) | EPUB | Supplemental
  • 283 Views
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Article
Molecular dynamics simulations of cognate and non-cognate AspRS-tRNAAsp complexes
C. Ramakrishnan, R. Nagarajan, M. Sekijima & M. Michael Gromiha
Pages: 493-501
Published online: 20 Jan 2020
AbstractforMolecular dynamics simulations of cognate and non-cognate AspRS-tRNAAsp complexes | Full Text | References | PDF (2.3 MB) | EPUB
  • 276 Views
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Article
Exploring structural requirements of isoform selective histone deacetylase inhibitors: a comparative in silico study
Kriti Kashyap & Rita Kakkar
Pages: 502-517
Published online: 10 Jan 2020
AbstractforExploring structural requirements of isoform selective histone deacetylase inhibitors: a comparative in silico study | Full Text | References | PDF (3.2 MB) | EPUB | Supplemental
  • 288 Views
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Article
Effect of periphery cationic substituents of porphyrin on the B-Z transition of poly[d(A-T)2], poly[d(G-C)2] and their binding modes
Nayoung Kwon, Ji Hoon Han, Seog K. Kim & Yoon Jung Jang
Pages: 518-525
Published online: 24 Feb 2020
AbstractforEffect of periphery cationic substituents of porphyrin on the B-Z transition of poly[d(A-T)2], poly[d(G-C)2] and their binding modes | Full Text | References | PDF (1.7 MB) | EPUB | Supplemental
  • 136 Views
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Article
Computer-aided screening for suppressor of variegation 4-20 homolog 1 inhibitors and their preliminary activity validation in human osteosarcoma
Ruxiao Zheng, Danfeng Liang, Na Jiang, Jing Zhou, Xin Long, Xin Wang, Miaomiao Wu, Chuangfang Wu & Jinku Bao
Pages: 526-537
Published online: 31 Jan 2020
AbstractforComputer-aided screening for suppressor of variegation 4-20 homolog 1 inhibitors and their preliminary activity validation in human osteosarcoma | Full Text | References | PDF (3.1 MB) | EPUB | Supplemental
  • 182 Views
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Article
From normal to competo-allosteric regulation: insights into the binding pattern dynamics of DSPI protein of Pseudomonas aeruginosa
Naila Zaman & Syed Sikander Azam
Pages: 538-557
Published online: 21 Jan 2020
AbstractforFrom normal to competo-allosteric regulation: insights into the binding pattern dynamics of DSPI protein of Pseudomonas aeruginosa | Full Text | References | PDF (6.5 MB) | EPUB | Supplemental
  • 298 Views
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Article
In-silico profiling and structural insights into the impact of nSNPs in the P. falciparum acetyl-CoA transporter gene to understand the mechanism of drug resistance in malaria
Rahila Sardar, Nidhi Katyal, Shahzaib Ahamad, Dhananjay D. Jade, Shakir Ali & Dinesh Gupta
Pages: 558-569
Published online: 21 Jan 2020
AbstractforIn-silico profiling and structural insights into the impact of nSNPs in the P. falciparum acetyl-CoA transporter gene to understand the mechanism of drug resistance in malaria | Full Text | References | PDF (2.6 MB) | EPUB | Supplemental
  • 361 Views
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Article
Investigating the mechanism of binding of nalidixic acid with deoxyribonucleic acid and serum albumin: a biophysical and molecular docking approaches
Sharmin Siddiqui, Anam Mujeeb, Faisal Ameen, Hassan Mubarak Ishqi, Sayeed Ur Rehman & Mohammad Tabish
Pages: 570-585
Published online: 20 Jan 2020
AbstractforInvestigating the mechanism of binding of nalidixic acid with deoxyribonucleic acid and serum albumin: a biophysical and molecular docking approaches | Full Text | References | PDF (4 MB) | EPUB
  • 352 Views
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Article
Identification of high-affinity inhibitors of pyruvate dehydrogenase kinase-3: towards therapeutic management of cancer
Taj Mohammad, Kaynat Arif, Mohamed F. Alajmi, Afzal Hussain, Asimul Islam, Md. Tabish Rehman & Imtaiyaz Hassan
Pages: 586-594
Published online: 14 Jan 2020
AbstractforIdentification of high-affinity inhibitors of pyruvate dehydrogenase kinase-3: towards therapeutic management of cancer | Full Text | References | PDF (2.2 MB) | EPUB
  • 339 Views
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Article
Two novel bipyridine-based cobalt (II) complexes: synthesis, characterization, molecular docking, DNA-binding and biological evaluation
Tahere Kondori, Omolbanin Shahraki, Niloufar Akbarzadeh-T & Zahra Aramesh-Boroujeni
Pages: 595-609
Published online: 25 Jan 2020
AbstractforTwo novel bipyridine-based cobalt (II) complexes: synthesis, characterization, molecular docking, DNA-binding and biological evaluation | Full Text | References | PDF (2.4 MB) | EPUB
  • 409 Views
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Article
Pharmacophore model-based virtual screening, docking, biological evaluation and molecular dynamics simulations for inhibitors discovery against α-tryptophan synthase from Mycobacterium tuberculosis
Sadia Naz, Umar Farooq, Sara Khan, Rizwana Sarwar, Yahia Nasser Mabkhot, Maria Saeed, Abdulrahman Alsayari, Abdullatif Bin Muhsinah & Zaheer Ul-Haq
Pages: 610-620
Published online: 25 Jan 2020
AbstractforPharmacophore model-based virtual screening, docking, biological evaluation and molecular dynamics simulations for inhibitors discovery against α-tryptophan synthase from Mycobacterium tuberculosis | Full Text | References | PDF (2.6 MB) | EPUB
  • 677 Views
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Article
Syringaresinol as a novel androgen receptor antagonist against wild and mutant androgen receptors for the treatment of castration-resistant prostate cancer: molecular docking, in-vitro and molecular dynamics study
Divakar Selvaraj, Santhoshkumar Muthu, Satvik Kotha, Ramachandra Setty Siddamsetty, Sasikumar Andavar & Saravanan Jayaraman
Pages: 621-634
Published online: 25 Jan 2020
AbstractforSyringaresinol as a novel androgen receptor antagonist against wild and mutant androgen receptors for the treatment of castration-resistant prostate cancer: molecular docking, in-vitro and molecular dynamics study | Full Text | References | PDF (2.7 MB) | EPUB | Supplemental
  • 552 Views
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Article
Understanding structure-based dynamic interactions of antihypertensive peptides extracted from food sources
Gazal Kalyan, Vivek Junghare, Sourya Bhattacharya & Saugata Hazra
Pages: 635-649
Published online: 12 Feb 2020
AbstractforUnderstanding structure-based dynamic interactions of antihypertensive peptides extracted from food sources | Full Text | References | PDF (4.8 MB) | EPUB | Supplemental
  • 451 Views
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Article
pH-dependent complex formation of Zn-meso-tetra(4-N-hydroxyethylpyridyl) porphyrin with cancer DNA
Nelli H. Karapetyan, Gayane V. Ananyan & Yeva B. Dalyan
Pages: 650-655
Published online: 27 Jan 2020
AbstractforpH-dependent complex formation of Zn-meso-tetra(4-N-hydroxyethylpyridyl) porphyrin with cancer DNA | Full Text | References | PDF (943.3 KB) | EPUB
  • 118 Views
  • 2 CrossRef citations
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Article
Structure-based virtual screening, free energy of binding and molecular dynamics simulations to propose novel inhibitors of Mtb-MurB oxidoreductase enzyme
Sonam Nirwan, Varun Chahal & Rita Kakkar
Pages: 656-671
Published online: 25 Jan 2020
AbstractforStructure-based virtual screening, free energy of binding and molecular dynamics simulations to propose novel inhibitors of Mtb-MurB oxidoreductase enzyme | Full Text | References | PDF (4 MB) | EPUB | Supplemental
  • 257 Views
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Article
Prediction of the inhibitory concentrations of chloroquine derivatives using deep neural networks models
Zhe Du, Hong Yang, Wen-Juan Lv, Xiao-Yun Zhang & Hong-Lin Zhai
Pages: 672-680
Published online: 25 Jan 2020
AbstractforPrediction of the inhibitory concentrations of chloroquine derivatives using deep neural networks models | Full Text | References | PDF (986.5 KB) | EPUB | Supplemental
  • 120 Views
  • 1 CrossRef citations
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Article
Identifying new piperazine-based PARP1 inhibitors using text mining and integrated molecular modeling approaches
Kader Sahin & Serdar Durdagi
Pages: 681-690
Published online: 12 Feb 2020
AbstractforIdentifying new piperazine-based PARP1 inhibitors using text mining and integrated molecular modeling approaches | Full Text | References | PDF (1.9 MB) | EPUB | Supplemental
  • 656 Views
  • 10 CrossRef citations
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Article
Exploring the combination characteristics of lumefantrine, an antimalarial drug and human serum albumin through spectroscopic and molecular docking studies
Kabiru Abubakar Musa, Nor Farrah Wahidah Ridzwan, Saharuddin B. Mohamad & Saad Tayyab
Pages: 691-702
Published online: 22 Jan 2020
AbstractforExploring the combination characteristics of lumefantrine, an antimalarial drug and human serum albumin through spectroscopic and molecular docking studies | Full Text | References | PDF (1.8 MB) | EPUB | Supplemental
  • 225 Views
  • 8 CrossRef citations
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Article
In silico identification of hydantoin derivatives: a novel natural prolyl hydroxylase inhibitor
Mahesh Kumar Teli, Surendra Kumar, Dharmendra Kumar Yadav & Mi-hyun Kim
Pages: 703-717
Published online: 25 Jan 2020
AbstractforIn silico identification of hydantoin derivatives: a novel natural prolyl hydroxylase inhibitor | Full Text | References | PDF (4.1 MB) | EPUB | Supplemental
  • 220 Views
  • 8 CrossRef citations
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Article
Pharmacophore model and atom-based 3D quantitative structure activity relationship (QSAR) of human immunodeficiency virus-1 (HIV-1) capsid assembly inhibitors
R. P. Bhole, C. G. Bonde, S. C. Bonde, R. V. Chikhale & R. D. Wavhale
Pages: 718-727
Published online: 25 Jan 2020
AbstractforPharmacophore model and atom-based 3D quantitative structure activity relationship (QSAR) of human immunodeficiency virus-1 (HIV-1) capsid assembly inhibitors | Full Text | References | PDF (2 MB) | EPUB | Supplemental
  • 232 Views
  • 13 CrossRef citations
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Article
Virtual screening, molecular dynamics, density functional theory and quantitative structure activity relationship studies to design peroxisome proliferator-activated receptor-γ agonists as anti-diabetic drugs
Sinthyia Ahmed, Nazrul Islam, Md Shahinozzaman, Sayo O. Fakayode, Nadia Afrin & Mohammad A. Halim
Pages: 728-742
Published online: 25 Jan 2020
AbstractforVirtual screening, molecular dynamics, density functional theory and quantitative structure activity relationship studies to design peroxisome proliferator-activated receptor-γ agonists as anti-diabetic drugs | Full Text | References | PDF (3 MB) | EPUB | Supplemental
  • 501 Views
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Article
Molecular basis of SMAC-XIAP binding and the effect of electrostatic polarization
Shuaizhen Tian, Changge Ji & John Z. H. Zhang
Pages: 743-752
Published online: 27 Jan 2020
AbstractforMolecular basis of SMAC-XIAP binding and the effect of electrostatic polarization | Full Text | References | PDF (1.8 MB) | EPUB
  • 372 Views
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Article
RETRACTED ARTICLE: Protein blueprint and their interactions while approachability struggle for amino acids
Aman Chandra Kaushik, Aamir Mehmood, Muhammad Tahir Khan, Ajay Kumar, Xiaofeng Dai & Dong-Qing Wei
Pages: i-ix
Published online: 30 Jan 2020
First Page PreviewforRETRACTED ARTICLE: Protein blueprint and their interactions while approachability struggle for amino acids | Full Text | PDF (2.4 MB) | EPUB
  • 211 Views
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