Works in Journal of Biomolecular Structure & Dynamics, 2023, Vol 41, Issue 13

Results: 39

An exploration on the topologies of SARS-CoV-2/human protein-protein interaction network.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 6313, doi. 10.1080/07391102.2022.2108496

By:

Navish, A. A.;
Uthayakumar, R.

Publication type:

Article

Flap sub-domain dynamics of serine-threonine phosphatase (Stp1) of Staphylococcus aureus: an accelerated molecular dynamics simulation study.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 6413, doi. 10.1080/07391102.2022.2107575

By:

Mandal, Pranabesh;
Rani, Priyanka;
Chandra, Girish;
Singh, Durg Vijay

Publication type:

Article

Probing interactions of aminoacyl-adenylate with Mycobacterium tuberculosis methionyl-tRNA synthetase through in silico site-directed mutagenesis and free energy calculation.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 6450, doi. 10.1080/07391102.2022.2107574

By:

Volynets, Galyna P.;
Gudzera, Olga I.;
Usenko, Mariia O.;
Gorbatiuk, Oksana B.;
Yarmoluk, Sergiy M.;
Tukalo, Michael A.

Publication type:

Article

Binding energy analysis and molecular dynamic simulation studies of the designed orally active, non-toxic GABARAP modulators.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 6394, doi. 10.1080/07391102.2022.2107571

By:

Nambiar, Megha P.;
Ashwanikumar, N.;
Anoop, Anakuthil;
Biju, A. R.

Publication type:

Article

A multi-spectroscopic and computational simulations study to delineate the interaction between antimalarial drug hydroxychloroquine and human serum albumin.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 6377, doi. 10.1080/07391102.2022.2107077

By:

Azeem, Kashish;
Ahmed, Mofieed;
Mohammad, Taj;
Uddin, Amad;
Shamsi, Anas;
Hassan, Md. Imtaiyaz;
Singh, Shailja;
Patel, Rajan;
Abid, Mohammad

Publication type:

Article

To probe the activation mechanism of the Delta opioid receptor by an agonist ADL5859 started from inactive conformation using molecular dynamic simulations.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 6359, doi. 10.1080/07391102.2022.2107074

By:

Dean, Emily;
Kumar, Vikash;
McConnell, Ashleigh;
Pagnoncelli, Iohana B.;
Wu, Chun

Publication type:

Article

Seasonal variation of the composition of essential oils from Piper cernuum Vell and Piper rivinoides Kunth, ADMET study, DFT calculations, molecular docking and dynamics studies of major components as potent inhibitors of the heterodimer methyltransferase complex NSP16-NSP10 SARS COV-2 protein

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 6326, doi. 10.1080/07391102.2022.2107072

By:

Alves Borges Leal, Antonio Linkoln;
Fonseca Bezerra, Camila;
Ferreira e Silva, Andressa Kelly;
Everson da Silva, Luiz;
Bezerra, Lucas Lima;
Almeida-Neto, Francisco Wagner;
Marinho, Emanuelle Machado;
Celedonio Fernandes, Carla Freire;
Nunes da Rocha, Matheus;
Marinho, Marcia Machado;
Coutinho, Henrique D. M.;
Barreto, Humberto Medeiros;
Rafaela Freitas Dotto, Ana;
Amaral, Wanderlei do;
Santos, Hélcio Silva dos;
Lima-Neto, Pedro de;
Marinho, Emmanuel Silva

Publication type:

Article

Design, dynamic docking, synthesis, and in vitro validation of a novel DNA gyrase B inhibitor.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 6345, doi. 10.1080/07391102.2022.2107073

By:

Pudipeddi, Akhila;
Vasudevan, Sahana;
Shanmugam, Karthi;
Mohan S, Suma;
Vairaprakash, Pothiappan;
Neelakantan, Prasanna;
Balraj, Alex Stanley;
Solomon, Adline Princy

Publication type:

Article

Insights into the microevolution of SARS-ACE2 interactions: in silico analysis of glycosylation and SNP pattern.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 6442, doi. 10.1080/07391102.2022.2106517

By:

Madasu, Pavan K;
Maity, Arpita;
Ghosh, Surya K.;
Chandran, Thyageshwar

Publication type:

Article

Design, synthesis, extra-precision docking, and molecular dynamics simulation studies of pyrrolidin-2-one derivatives as potential acetylcholinesterase inhibitors.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 6282, doi. 10.1080/07391102.2022.2106515

By:

Gupta, Mohan;
Kumar, Avinash;
Prasun, Chakrawarti;
Nair, Maya S.;
Kini, Suvarna G.;
Yadav, Divya;
Nain, Sumitra

Publication type:

Article

Structural modelling and in silico pharmacology of β-carboline alkaloids as potent 5-HT1A receptor antagonists and reuptake inhibitors.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 6219, doi. 10.1080/07391102.2022.2104376

By:

Ayipo, Yusuf Oloruntoyin;
Alananzeh, Waleed A.;
Ahmad, Iqrar;
Patel, Harun;
Mordi, Mohd Nizam

Publication type:

Article

Structural, vibrational spectroscopy, molecular docking, DFT studies and antibacterial activity of (E)-N1-(3-chlorobenzylidene)benzene-1,4-diamine.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 6295, doi. 10.1080/07391102.2022.2106516

By:

Hajam, Towseef Ahmad;
H., Saleem;
Mashood Ahamed, F. M.

Publication type:

Article

Insight on the interaction between the scorpion toxin blocker Discrepin on potassium voltage-gated channel Kv4.3 by molecular dynamics simulations.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 6272, doi. 10.1080/07391102.2022.2106514

By:

Montero-Domínguez, Pavel A.;
Mares-Sámano, Sergio;
Garduño-Juárez, Ramón

Publication type:

Article

Molecular dynamics simulations reveal the inhibitory mechanism of Withanolide A against α-glucosidase and α-amylase.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 6203, doi. 10.1080/07391102.2022.2104375

By:

Oyewusi, Habeebat Adekilekun;
Wu, Yuan-Seng;
Safi, Sher Zaman;
Wahab, Roswanira Abdul;
Hatta, Mohd Hayrie Mohd;
Batumalaie, Kalaivani

Publication type:

Article

In silico analysis of the C-terminal domain of big defensin from the Pacific oyster.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 6236, doi. 10.1080/07391102.2022.2105957

By:

Dhar, Dipanjana;
Dey, Debayan

Publication type:

Article

Efficient DNA-ligand interaction framework using fuzzy C-means clustering based glowworm swarm optimization (FCMGSO) method.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 6249, doi. 10.1080/07391102.2022.2105958

By:

Kiruba Nesamalar, E;
SatheeshKumar, J;
Amudha, T

Publication type:

Article

Human TMPRSS2 non-catalytic ectodomain and SARS-CoV-2 S2' subunit interaction mediated SARS-CoV-2 endocytosis: a model proposal with virtual screening for potential drug molecules to inhibit this interaction.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 6422, doi. 10.1080/07391102.2022.2105956

By:

Konduru, Guruprasad Varma;
Nagarajaram, Hampapathalu Adimurthy

Publication type:

Article

Evaluation of DNA damage induced by acesulfame potassium: spectroscopic, molecular modeling simulations and toxicity studies.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 6262, doi. 10.1080/07391102.2022.2105955

By:

Hadidi, Saba;
Varmira, Kambiz;
Soltani, Leila

Publication type:

Article

Evaluation of the dual effects of antiviral drugs on SARS-CoV-2 receptors and the ACE2 receptor using structure-based virtual screening and molecular dynamics simulation.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 6051, doi. 10.1080/07391102.2022.2103735

By:

Jahantigh, Hamid Reza;
Ahmadi, Nahid;
Shahbazi, Behzad;
Lovreglio, Piero;
Habibi, Mehri;
Stufano, Angela;
Gouklani, Hamed;
Ahmadi, Khadijeh

Publication type:

Article

A strategy to optimize the peptide-based inhibitors against different mutants of the spike protein of SARS-CoV-2.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 6191, doi. 10.1080/07391102.2022.2103587

By:

Priya, Prerna;
Basit, Abdul;
Bandyopadhyay, Pradipta

Publication type:

Article

Implementing accelerated dynamics to unravel the effects of high-fidelity Cas9 mutants on target DNA and guide RNA hybrid stability.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 6178, doi. 10.1080/07391102.2022.2103032

By:

Vora, Dhvani Sandip;
Jaiswal, Atul Kumar;
Sundar, Durai

Publication type:

Article

Identification of second generation benzylidene chromanone analogues as novel, potent DHODH inhibitors in acute myeloid leukemia cells.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 6168, doi. 10.1080/07391102.2022.2103031

By:

Abohassan, Mohammad;
Al Shahrani, Mesfer;
Rajagopalan, Prasanna

Publication type:

Article

Synthesis of aminochalcones and in silico evaluation of their antiparasitic potential against Leishmania.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 6434, doi. 10.1080/07391102.2022.2103030

By:

Bezerra, Lucas Lima;
Almeida-Neto, Francisco Wagner Queiroz;
Marinho, Márcia Machado;
Santos Oliveira, Larissa;
Teixeira, Alexandre Magno Rodrigues;
Bandeira, Paulo Nogueira;
dos Santos, Hélcio Silva;
Lima-Neto, Pedro de;
Marinho, Emmanuel Silva

Publication type:

Article

DPP-4 inhibition mediated antidiabetic potential of phytoconstituents of an aqueous fruit extract of Withania coagulans (Stocks) Dunal: in-silico, in-vitro and in-vivo assessments.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 6145, doi. 10.1080/07391102.2022.2103029

By:

Kumar, Pramod;
Ram, Heera;
Kala, Chandra;
Kashyap, Priya;
Singh, Garima;
Agnihotri, Charu;
Singh, Bhim Pratap;
Kumar, Ashok;
Panwar, Anil

Publication type:

Article

Structural basis for the selectivity of 3rd generation EGFR inhibitors: a molecular dynamics study.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 6134, doi. 10.1080/07391102.2022.2103028

By:

Gad, Mazen M.;
Abdelwaly, Ahmad;
Helal, Mohamed A.

Publication type:

Article

Designing ferritin nanocage based vaccine candidates for SARS-CoV-2 by in silico engineering of its HLA I and HLA II epitope peptides.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 6121, doi. 10.1080/07391102.2022.2103027

By:

Manickavasagam, Pratibha;
Abhishek, Suman;
Rajakumara, Eerappa

Publication type:

Article

Molecular docking and molecular dynamic simulations of apoptosis proteins with potential anticancer compounds present in Clinacanthus nutans extract using gas chromatography–mass spectrometry.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 6104, doi. 10.1080/07391102.2022.2101530

By:

Ismail, Noor Zafirah;
Mohamed, Wan Ahmad Syazani;
Ab. Rahim, Nurhidayah;
Hashim, Nor Munira;
Adebayo, Ismail Abiola;
Mohamad Zain, Nur Nadhirah;
Arsad, Hasni

Publication type:

Article

Pharmacophore-based virtual screening, molecular docking and molecular dynamics simulations study for the identification of LIM kinase-1 inhibitors.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 6089, doi. 10.1080/07391102.2022.2101529

By:

Singh, Ravi;
Pokle, Ankit Vyankatrao;
Ghosh, Powsali;
Ganeshpurkar, Ankit;
Swetha, Rayala;
Singh, Sushil Kumar;
Kumar, Ashok

Publication type:

Article

Anti-apoptotic Bcl-2 protein in apo and holo conformation anchored to the membrane: comparative molecular dynamics simulations.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 6074, doi. 10.1080/07391102.2022.2101145

By:

Caro-Gómez, Luis Alberto;
Rosas-Trigueros, Jorge L.;
Mixcoha, Edgar;
Zamorano-Carrillo, Absalom;
Martínez-Martínez, Jesús;
Benítez-Cardoza, Claudia Guadalupe

Publication type:

Article

Free energy simulations to study mutational effect of a conserved residue, Trp24, on stability of human serum retinol-binding protein.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 6040, doi. 10.1080/07391102.2022.2100829

By:

Lee, Kyung-Hoon;
Kuczera, Krzysztof

Publication type:

Article

Efficient proton shuttle makes SazCA an excellent CO<sub>2</sub> hydration enzyme.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 6001, doi. 10.1080/07391102.2022.2100828

By:

Kumar, Shashi;
Deshpande, Parag A.

Publication type:

Article

Modeling and computational characterization of a Xanthomonas sp. Hypothetical protein identifies a remote ortholog of Burkholderia lethal factor 1.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 6027, doi. 10.1080/07391102.2022.2100827

By:

Muhamad Ismail, Nur Afiqah Shalihin;
Yap, Su Hui;
Mohamad Yussoff, Mohamad Ariff;
Nor Muhammad, Nor Azlan;
Firdaus-Raih, Mohd;
Quay, Doris Huai Xia

Publication type:

Article

Structure based virtual screening and molecular dynamics of natural anti-biofilm compounds against SagS response regulator/sensor kinase in Pseudomonas aeruginosa.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 6011, doi. 10.1080/07391102.2022.2100482

By:

Behera, Santosh Kumar;
Panda, Amrita Kumari;
Mishra, Rojita;
Mahanty, Arabinda;
Bisht, Satpal Singh

Publication type:

Article

Chemically synthesised flavone and coumarin based isoxazole derivatives as broad spectrum inhibitors of serine β-lactamases and metallo-β-lactamases: a computational, biophysical and biochemical study.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 5990, doi. 10.1080/07391102.2022.2099977

By:

Farhat, Nabeela;
Ali, Abid;
Waheed, Mohd;
Gupta, Divya;
Khan, Asad U.

Publication type:

Article

DFT evaluation of structural, electronic and variation properties for complex carbohydrates with biological interest.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 5981, doi. 10.1080/07391102.2022.2099975

By:

Adjir, Khadidja;
Sekkal-Rahal, Majda;
Springborg, Michael

Publication type:

Article

Bis-1,2,4-triazol derivatives: Synthesis, characterization, DFT, antileishmanial activity and molecular docking study.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 5970, doi. 10.1080/07391102.2022.2098825

By:

Süleymanoğlu, Nevin;
Ustabaş, Reşat;
Güler, Halil İbrahim;
Direkel, Şahin;
Çelik, Fatih;
Ünver, Yasemin

Publication type:

Article

Evaluating the accuracy of the AMBER protein force fields in modeling dihydrofolate reductase structures: misbalance in the conformational arrangements of the flexible loop domains.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 5946, doi. 10.1080/07391102.2022.2098823

By:

Love, Olivia;
Pacheco Lima, Maria Carolina;
Clark, Casey;
Cornillie, Sean;
Roalstad, Shelly;
Cheatham III, Thomas E.

Publication type:

Article

Intercalation of diafenthiuron insecticide with calf thymus DNA: spectroscopic and molecular dynamics analysis.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 5961, doi. 10.1080/07391102.2022.2098824

By:

Ponkarpagam, S.;
Vennila, K. N.;
Elango, Kuppanagounder P.

Publication type:

Article

Evaluation of apigenin-based biflavonoid derivatives as potential therapeutic agents against viral protease (3CLpro) of SARS-CoV-2 via molecular docking, molecular dynamics and quantum mechanics studies.

Published in:

Journal of Biomolecular Structure & Dynamics, 2023, v. 41, n. 13, p. 5915, doi. 10.1080/07391102.2022.2098821

By:

Abdizadeh, Rahman;
Hadizadeh, Farzin;
Abdizadeh, Tooba

Publication type:

Article