Designing of a multi-epitopes based vaccine against rubella virus using bioinformatics and immunoinformatics approach

Authors: Bushra Bibi, Arshad Iqbal, Muhammad Rahiyab, Syed Shujait Ali, Ishaq Khan, Shahid Ali, Zahid Hussain, Abbas Khan

Source: The Microbe, Vol 7, Iss , Pp 100323- (2025)

Subject Terms: Congenital Rubella syndrome, Structural polyprotein, Molecular docking, MD simulation, Immune simulation, In silico cloning, Microbiology, QR1-502

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Relation: http://www.sciencedirect.com/science/article/pii/S2950194625000913; https://doaj.org/toc/2950-1946

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Correction: Suleman et al. Immunoinformatics and Immunogenetics-Based Design of Immunogenic Peptides Vaccine against the Emerging Tick-Borne Encephalitis Virus (TBEV) and Its Validation through In Silico Cloning and Immune Simulation. Vaccines 2021, 9, 1210

Authors: Muhammad Suleman, Muhammad Tahir ul Qamar, Kiran, Samreen Rasool, Aneela Rasool, Aqel Albutti, Noorah Alsowayeh, Ameen S. S. Alwashmi, Mohammad Abdullah Aljasir, Sajjad Ahmad, Zahid Hussain, Muhammad Rizwan, Syed Shujait Ali, Abbas Khan, Dong-Qing Wei

Source: Vaccines, Vol 12, Iss 8, p 920 (2024)

Subject Terms: n/a, Medicine

File Description: electronic resource

Relation: https://www.mdpi.com/2076-393X/12/8/920; https://doaj.org/toc/2076-393X

Access URL: https://doaj.org/article/fb07759bf59c444198b97816e916987e

Exploring the medicinal potential of Dark Chemical Matters (DCM) to design promising inhibitors for PLpro of SARS-CoV-2 using molecular screening and simulation approaches

Authors: Abbas Khan, Ayesha Liaqat, Adan Masood, Syed Shujait Ali, Liaqat Ali, Abdulrahman Alshammari, Abdullah F. Alasmari, Anwar Mohammad, Yasir Waheed, Dong-Qing Wei

Source: Saudi Pharmaceutical Journal, Vol 31, Iss 10, Pp 101775- (2023)

Subject Terms: SARS-CoV-2 variants, PLpro, Drugs, Free energy, Conformational dynamics, Therapeutics. Pharmacology, RM1-950

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Relation: http://www.sciencedirect.com/science/article/pii/S1319016423002700; https://doaj.org/toc/1319-0164

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Structural vaccinology-based design of multi-epitopes vaccine against Streptococcus gordonii and validation using molecular modeling and immune simulation approaches

Authors: Syed Nouman Nasir, Ayesha Iftikhar, Farukh Zubair, Abdulrahman Alshammari, Metab Alharbi, Abdullah F. Alasmari, Abbas Khan, Muhammad Waseem, Syed Shujait Ali, Liaqat Ali, Yasir Waheed, Dong-Qing Wei

Source: Heliyon, Vol 9, Iss 5, Pp e16148- (2023)

Subject Terms: Streptococcus gordonii, Immunoinformatics, Multi-epitopes vaccine, Molecular docking, Immune simulation, Science (General), Q1-390, Social sciences (General), H1-99

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Relation: http://www.sciencedirect.com/science/article/pii/S2405844023033558; https://doaj.org/toc/2405-8440

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Structural insights into the effect of mutations in the spike protein of SARS-CoV-2 on the binding with human furin protein

Authors: Muhammad Suleman, Muhammad Luqman, Dong-Qing Wei, Shahid Ali, Syed Shujait Ali, Abbas Khan, Haji Khan, Zafar Ali, Wajid Khan, Muhammad Rizwan, Naeem Ullah

Source: Heliyon, Vol 9, Iss 4, Pp e15083- (2023)

Subject Terms: SARS COV-2, Furin, Molecular docking, Molecular simulation, S-Protein, Mutation, Science (General), Q1-390, Social sciences (General), H1-99

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Relation: http://www.sciencedirect.com/science/article/pii/S2405844023022909; https://doaj.org/toc/2405-8440

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Mutational analysis of the spike protein of SARS-COV-2 isolates revealed atomistic features responsible for higher binding and infectivity

Authors: Muhammad Hanifa, Muhammad Salman, Muqaddas Fatima, Naila Mukhtar, Fahad N. Almajhdi, Nasib Zaman, Muhammad Suleman, Syed Shujait Ali, Yasir Waheed, Abbas Khan

Source: Frontiers in Cell and Developmental Biology, Vol 10 (2023)

Subject Terms: SARS-CoV-2, variants, genomes, spike protein, docking, simulation, Biology (General), QH301-705.5

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Relation: https://www.frontiersin.org/articles/10.3389/fcell.2022.940863/full; https://doaj.org/toc/2296-634X

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Sequence-structure functional implications and molecular simulation of high deleterious nonsynonymous substitutions in IDH1 revealed the mechanism of drug resistance in glioma

Authors: Muhammad Suleman, Syeda Umme-I-Hani, Muhammad Salman, Mohammed Aljuaid, Abbas Khan, Arshad Iqbal, Zahid Hussain, Syed Shujait Ali, Liaqat Ali, Hassan Sher, Yasir Waheed, Dong-Qing Wei

Source: Frontiers in Pharmacology, Vol 13 (2022)

Subject Terms: nsSNPs, IDH1, molecular docking, simulation, binding free energy, introduction, Therapeutics. Pharmacology, RM1-950

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Relation: https://www.frontiersin.org/articles/10.3389/fphar.2022.927570/full; https://doaj.org/toc/1663-9812

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Structural insights into the mechanism of RNA recognition by the N-terminal RNA-binding domain of the SARS-CoV-2 nucleocapsid phosphoprotein

Authors: Abbas Khan, Muhammad Tahir Khan, Shoaib Saleem, Muhammad Junaid, Arif Ali, Syed Shujait Ali, Mazhar Khan, Dong-Qing Wei

Source: Computational and Structural Biotechnology Journal, Vol 18, Iss , Pp 2174-2184 (2020)

Subject Terms: Nucleocapsid Phosphoprotein, RNA binding, Alanine scanning, PCA, DCCM, Free energy calculations, Biotechnology, TP248.13-248.65

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Relation: http://www.sciencedirect.com/science/article/pii/S2001037020303597; https://doaj.org/toc/2001-0370

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Sustainable production of biomass and industrially important secondary metabolites in cell cultures of selfheal (Prunella vulgaris L.) elicited by silver and gold nanoparticles

Authors: Hina Fazal, Bilal Haider Abbasi, Nisar Ahmad, Mohammad Ali, Syed Shujait Ali, Abbas Khan, Dong-Qing Wei

Source: Artificial Cells, Nanomedicine, and Biotechnology, Vol 47, Iss 1, Pp 2553-2561 (2019)

Subject Terms: Prunella vulgaris, cell culture, secondary metabolites, stress enzymes, nanoparticles, Biotechnology, TP248.13-248.65, Medical technology, R855-855.5

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Relation: https://doaj.org/toc/2169-1401; https://doaj.org/toc/2169-141X

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Structural and Biophysical Investigation of the Key Hotspots on the Surface of Epstein–Barr Nuclear Antigen 1 Essential for DNA Recognition and Pathogenesis

Authors: Huma Farooque Hashmi, Muhammad Waseem, Syed Shujait Ali, Zahid Hussain, Kaoshan Chen

Source: Frontiers in Molecular Biosciences, Vol 8 (2021)

Subject Terms: EBNA1, DNA recognition, MD simulation, in silico mutagenesis, free energy calculations, Biology (General), QH301-705.5

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Relation: https://www.frontiersin.org/articles/10.3389/fmolb.2021.664436/full; https://doaj.org/toc/2296-889X

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Mutational Landscape of Pirin and Elucidation of the Impact of Most Detrimental Missense Variants That Accelerate the Breast Cancer Pathways: A Computational Modelling Study

Authors: Muhammad Suleman, Muhammad Tahir ul Qamar, Shoaib Saleem, Sajjad Ahmad, Syed Shujait Ali, Haji Khan, Fazal Akbar, Wajid Khan, Adel Alblihy, Faris Alrumaihi, Muhammad Waseem, Khaled S. Allemailem

Source: Frontiers in Molecular Biosciences, Vol 8 (2021)

Subject Terms: nsSNPs, PIR protein, breast cancer, MD simulations, PIR, Biology (General), QH301-705.5

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Relation: https://www.frontiersin.org/articles/10.3389/fmolb.2021.692835/full; https://doaj.org/toc/2296-889X

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Insights Into Mutations Induced Conformational Changes and Rearrangement of Fe2+ Ion in pncA Gene of Mycobacterium tuberculosis to Decipher the Mechanism of Resistance to Pyrazinamide

Authors: Asma Sindhoo Nangraj, Abbas Khan, Shaheena Umbreen, Sana Sahar, Maryam Arshad, Saba Younas, Sajjad Ahmad, Shahid Ali, Syed Shujait Ali, Liaqat Ali, Dong-Qing Wei

Source: Frontiers in Molecular Biosciences, Vol 8 (2021)

Subject Terms: PZA, simulation, mutations, PCA, free energy, Biology (General), QH301-705.5

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Relation: https://www.frontiersin.org/articles/10.3389/fmolb.2021.633365/full; https://doaj.org/toc/2296-889X

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Ultra-Large-Scale Screening of Natural Compounds and Free Energy Calculations Revealed Potential Inhibitors for the Receptor-Binding Domain (RBD) of SARS-CoV-2

Authors: Lisha Guo, Faryar Zafar, Nawal Moeen, Fahad M. Alshabrmi, Junqi Lin, Syed Shujait Ali, Muhammad Munir, Abbas Khan, Dongqing Wei

Source: Molecules, Vol 27, Iss 21, p 7317 (2022)

Subject Terms: SARS-CoV-2, Deltacron, structure-based drugs, molecular simulations, free energy, Organic chemistry, QD241-441

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Relation: https://www.mdpi.com/1420-3049/27/21/7317; https://doaj.org/toc/1420-3049

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Cation/Proton Antiporter Genes in Tomato: Genomic Characterization, Expression Profiling, and Co-Localization with Salt Stress-Related QTLs

Authors: Zahid Hussain, Habiba Khan, Muhammad Imran, Muhmmad Kashif Naeem, Sabir Hussain Shah, Arshad Iqbal, Syed Shujait Ali, Muhammad Rizwan, Shahid Ali, Muhammad Atif Muneer, Emilie Widemann, Sarfraz Shafiq

Source: Agronomy, Vol 12, Iss 2, p 245 (2022)

Subject Terms: CPA, CHX, KEA, NHX, ion transporter, tomato, Agriculture

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Relation: https://www.mdpi.com/2073-4395/12/2/245; https://doaj.org/toc/2073-4395

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Structural-Dynamics and Binding Analysis of RBD from SARS-CoV-2 Variants of Concern (VOCs) and GRP78 Receptor Revealed Basis for Higher Infectivity

Authors: Abbas Khan, Anwar Mohammad, Inamul Haq, Mohammad Nasar, Waqar Ahmad, Qudsia Yousafi, Muhammad Suleman, Sajjad Ahmad, Aqel Albutti, Taimoor Khan, Sulaiman K. Marafie, Eman Alshawaf, Syed Shujait Ali, Jehad Abubaker, Dong-Qing Wei

Source: Microorganisms, Vol 9, Iss 11, p 2331 (2021)

Subject Terms: COVID-19, SARS-CoV-2, new variants, GRP78, infectivity, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.mdpi.com/2076-2607/9/11/2331; https://doaj.org/toc/2076-2607

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Annotation of Potential Vaccine Targets and Design of a Multi-Epitope Subunit Vaccine against Yersinia pestis through Reverse Vaccinology and Validation through an Agent-Based Modeling Approach

Authors: Azaz Ul Haq, Abbas Khan, Jafar Khan, Shamaila Irum, Yasir Waheed, Sajjad Ahmad, N. Nizam-Uddin, Aqel Albutti, Nasib Zaman, Zahid Hussain, Syed Shujait Ali, Muhammad Waseem, Fariha Kanwal, Dong-Qing Wei, Qian Wang

Source: Vaccines, Vol 9, Iss 11, p 1327 (2021)

Subject Terms: Yersinia pestis, vaccine targets, epitope mining, in silico cloning, immune simulation, Medicine

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Relation: https://www.mdpi.com/2076-393X/9/11/1327; https://doaj.org/toc/2076-393X

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Dynamics Insights Into the Gain of Flexibility by Helix-12 in ESR1 as a Mechanism of Resistance to Drugs in Breast Cancer Cell Lines

Authors: Abbas Khan, Ashfaq-Ur-Rehman, Muhammad Junaid, Cheng-Dong Li, Shoaib Saleem, Fahad Humayun, Shazia Shamas, Syed Shujait Ali, Zainib Babar, Dong-Qing Wei

Source: Frontiers in Molecular Biosciences, Vol 6 (2020)

Subject Terms: ESR1 estrogen receptor, mutation, resistance, simulation, molecular docking, molecular dynamics (MD) simulation, Biology (General), QH301-705.5

File Description: electronic resource

Relation: https://www.frontiersin.org/article/10.3389/fmolb.2019.00159/full; https://doaj.org/toc/2296-889X

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Immunoinformatics and Immunogenetics-Based Design of Immunogenic Peptides Vaccine against the Emerging Tick-Borne Encephalitis Virus (TBEV) and Its Validation through In Silico Cloning and Immune Simulation

Authors: Muhammad Suleman, Muhammad Tahir ul Qamar, Kiran, Samreen Rasool, Aneela Rasool, Aqel Albutti, Noorah Alsowayeh, Ameen S. S. Alwashmi, Mohammad Abdullah Aljasir, Sajjad Ahmad, Zahid Hussain, Muhammad Rizwan, Syed Shujait Ali, Abbas Khan, Dong-Qing Wei

Source: Vaccines, Vol 9, Iss 11, p 1210 (2021)

Subject Terms: Tick-borne encephalitis (TBE), proteome mining, vaccine construct, in silico cloning, immune simulation, Medicine

File Description: electronic resource

Relation: https://www.mdpi.com/2076-393X/9/11/1210; https://doaj.org/toc/2076-393X

Access URL: https://doaj.org/article/d0c671d475e144ab999527a760bdbdef

Towards an Ensemble Vaccine against the Pegivirus Using Computational Modelling Approaches and Its Validation through In Silico Cloning and Immune Simulation

Authors: Bowen Zheng, Muhammad Suleman, Zonara Zafar, Syed Shujait Ali, Syed Nouman Nasir, Namra, Zahid Hussain, Muhammad Waseem, Abbas Khan, Fakhrul Hassan, Yanjing Wang, Dongqing Wei

Source: Vaccines, Vol 9, Iss 8, p 818 (2021)

Subject Terms: Pegivirus, epitopes, vaccine designing, in silico cloning, immune simulation, Medicine

File Description: electronic resource

Relation: https://www.mdpi.com/2076-393X/9/8/818; https://doaj.org/toc/2076-393X

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Pakistan as a major obstacle in global end to poliomyelitis program: background and 2016 update

Authors: Abdul Waheed Khan, Shahid Ali, Syed Shujait Ali

Source: Brazilian Journal of Infectious Diseases, Vol 20, Iss 5, Pp 518-520 (2016)

Subject Terms: Infectious and parasitic diseases, RC109-216, Microbiology, QR1-502

File Description: electronic resource

Relation: http://www.sciencedirect.com/science/article/pii/S1413867016301283; https://doaj.org/toc/1413-8670

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