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PhD Scholar · Bioinformatician · Gold Medalist

Muhammad Nouman Majeed

I work on in silico vaccine design, molecular dynamics simulations and computational drug discovery, with a focus on protein–ligand interactions and multi-epitope vaccines.

  • Founder and Chief Executive Officer, BioInfoX (SMC-Private) Limited
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Muhammad Nouman Majeed
36Peer-reviewed articles
200Citations
10h-index
7i10-index

Citation metrics from Google Scholar.

About

PhD scholar and bioinformatician working from epitope to trajectory: designing vaccine and drug candidates in silico and testing them with molecular dynamics.

I specialise in in silico vaccine design, molecular dynamics simulations and computational drug discovery. My research focuses on protein–ligand interactions, molecular modelling and multi-epitope vaccine development, and I have contributed to research projects and publications in molecular dynamics, immunoinformatics and AI-assisted drug discovery.

I founded and lead BioInfoX (SMC-Private) Limited, which provides molecular docking, molecular dynamics, DFT and bioinformatics services to researchers worldwide and trains students across Pakistan.

In silico vaccine design

Epitope prediction and multi-epitope vaccine constructs against viral, bacterial and fungal pathogens.

Molecular dynamics

Protein–ligand and protein–membrane simulations with GROMACS, OpenMM and ACEMD3, and binding free energies.

Computational drug discovery

Docking, virtual screening, QSAR and AI-driven screening and optimisation of ligands.

Nanoinformatics and DFT

DFT, neural networks and simulation to study nanoparticles for therapy and environmental use.

Genomics

Whole-genome sequencing, assembly and NCBI submission of bacterial isolates.

AI in bioinformatics

Artificial neural networks for protein structure, genomics and biomarker discovery.

Honours

Awards and recognition

  • 28 Jan 2025

    Best Research Student Award 2024, University of Okara

    Presented by Vice Chancellor Dr. Sajjad Mubin for research in bioinformatics, molecular dynamics, and in silico drug and vaccine design.

  • 2 Nov 2024

    Best Research Poster Award, C-BICS 2024

    12th International Conference on Biological and Computational Sciences, Capital University of Science and Technology, Islamabad.

  • 9 Jul 2024

    1st Position, 9th Molecular Models and Bioinformatics Posters Competition

    University of Central Punjab, for the poster “In Silico Design of a Universal Multi-Epitope Vaccine for 14 Cancer Types”.

  • 8 Aug 2023

    Selected in the PMYP Laptop Scheme

    Prime Minister's Youth Programme.

  • 2 Aug 2023

    Best Project, Department of Biotechnology

    University of Okara.

Publications

Selected peer-reviewed publications

32 of 36 peer-reviewed articles, newest first; the complete list is on Google Scholar. My name is underlined where it appears in the author list.

Showing all 32

2026

  1. 1.Designing IL-24-P18 fusion protein through computational engineering for targeted breast cancer therapy. Naveed M, Asim M, Aziz T, Ibrahim S, Aqeel ZB, Majeed MN, Hussain N, et al. Journal of Computational Biophysics and Chemistry. 2026;25(1):109–23. Google Scholar
  2. 2.Immunoinformatics-based design and evaluation of a multi-epitope vaccine against Vibrio fluvialis. Naveed M, Husnain M, Aziz T, Qadir P, Asim M, Majeed MN, Aloufi AS, et al. Scientific Reports. 2026. Google Scholar
  3. 3.Nanoinformatics-guided inhibition of blaOXA in Staphylococcus nepalensis using cysteine-conjugated silver nanoparticles. Naveed M, Asim M, Aziz T, Majeed MN, Husnain M, Khan AA, Alshehri F, et al. ChemistrySelect. 2026;11(1):e04545. Google Scholar
  4. 4.Molecular identification of the blaOXA gene in Bacillus cereus and AI-driven optimization of natural phytochemicals for foodborne illness treatment. Naveed M, Asim M, Aziz T, Salah Ud Din M, Majeed MN, Binsaleh AY, et al. Antonie van Leeuwenhoek. 2026;119(2):29. Google Scholar
  5. 5.In silico design and immunoinformatics assessment of a multiepitope vaccine targeting borealpox virus. Naveed M, Asim M, Aziz T, Athar A, Majeed MN, Tombozara N, et al. Scientific Reports. 2026. Google Scholar
  6. 6.Identification of phytochemical inhibitors targeting the hylEfm gene in multidrug-resistant Enterococcus faecium using different approaches. Naveed M, Asim M, Aziz T, Ibrahim S, Ali A, Majeed MN, Binsaleh AY, et al. ChemistrySelect. 2026;11(1):e04341. Google Scholar
  7. 7.Multi-epitope vaccine against nucleoprotein and envelopment polyprotein of Batai orthobunyavirus using molecular docking and molecular dynamics studies. Naveed M, Asim M, Ali A, Amjad S, Majeed MN, Yolande Sandrine MN, et al. Scientific Reports. 2026;16(1):8973. Google Scholar
  8. 8.Immunoinformatics-guided design of a multi-epitope vaccine targeting the envelopment polyprotein of Oropouche virus. Naveed M, Athar A, Tariq A, Asim M, Majeed MN, El Hadi Mohamed RA, et al. Molecular Genetics and Genomics. 2026;301(1):43. Google Scholar
  9. 9.Computational design of a multiepitope vaccine targeting VP1 and VP2 capsid proteins of simian virus 40 (SV40) for enhanced immune activation. Naveed M, Asim M, Aziz T, Amjad S, Majeed MN, Jamal SB, et al. Open Medicine. 2026;21(1):20251284. Google Scholar
  10. 10.AI-driven optimization of cetirizine-derived ligands targeting histamine H1 and H2 receptors: a computational drug design study. Naveed M, Ali N, Nabi G, Aqeel ZB, Ali A, Naeem M, Majeed MN, et al. ChemistrySelect. 2026;11(6):e02976. Google Scholar
  11. 11.Identification of natural FGFR3 inhibitor for glioma using integrated computational and microRNA regulatory analysis. Javaid S, Ali N, Shahid S, Majeed MN. Scientific Reports. 2026. Google Scholar
  12. 12.Structure-based drug designing and pharmacological profiling of Withanolide A as potential EGFR inhibitors for glioblastoma treatment. Naveed M, Zafar A, Fatima M, Majeed MN, Khan AA, Binsaleh AY, et al. Letters in Drug Design & Discovery. 2026:100379. Google Scholar
  13. 13.In silico discovery and interaction analysis of a Datura stramonium defensin-like peptide targeting cancer-related receptors. Javaid S, Mushtaq Z, Jamil A, Shahid S, Ali N, Majeed MN. Scientific Reports. 2026. Google Scholar
  14. 14.Optimization of bioinformatics-designed thiazolide derivatives as SARS-CoV-2 nucleocapsid protein inhibitors. Naveed M, Arshad A, Aziz T, Asim M, Hanif N, Majeed MN, et al. Current Molecular Pharmacology. 2026. Google Scholar
  15. 15.Immunopharmacological and structural design of a polyprotein-based multi-epitope vaccine against Powassan virus. Kalsoom A, Abidi SH, Marwat SA, Shabbir G, Naveed M, Mughal AMA, et al. Naunyn-Schmiedeberg's Archives of Pharmacology. 2026:1–27. Google Scholar
  16. 16.Harnessing chromium-resistant bacteria from tannery wastewater: innovative in vitro and in silico strategies for bioremediation. Ashfaq H, Amin A, Cheema MT, Majeed MN. Water, Air, & Soil Pollution. 2026;237(11):674. Google Scholar
  17. 17.Elucidating the biodegradation potential of Nudix hydrolase from Bacillus paranthracis via different approaches. Naveed M, Hanif N, Zahid M, Haseeb MA, Salah Ud Din M, Majeed MN, et al. Zeitschrift für Naturforschung C. 2026. Google Scholar
  18. 18.Mitigating chronic granulomatous disease (CGD) through mutational analysis and de novo drug design targeting the CYBA gene through different approaches. Naveed M, Ibrahim S, Aziz T, Khatoon K, Asad M, Majeed MN, et al. Letters in Drug Design & Discovery. 2026:100325. Google Scholar
  19. 19.Structure-based drug discovery targeting fmhA in Staphylococcus warneri using extracts of Calliandra harrisii: an integrated ethnobotanical and in silico approach. Ali N, Naveed M, Waseem M, Majeed MN, Yolande Sandrine MN, et al. Zeitschrift für Naturforschung C. 2026. Google Scholar
  20. 20.Designing a multi-epitope vaccine against yellow fever virus using immunoinformatics approaches. Naveed M, Asim M, Aziz T, Toheed M, Athar A, Majeed MN, Khan AA, et al. Open Medicine. 2026;21(1):20261453. Google Scholar

2025

  1. 21.Computational drug design for neurosyphilis disease by targeting phosphoglycerate kinase in Treponema pallidum with enhanced binding affinity and reduced toxicity. Naveed M, Ibrahim S, Aziz T, Asim M, Majeed MN, Khan AA, et al. Scientific Reports. 2025;15(1):10311. Google Scholar
  2. 22.In-silico and computational active site-driven design and characterization of beta-NGF-A fusion protein as a novel and targeted Alzheimer's disease therapy. Naveed M, Ibrahim S, Aziz T, Khatoon K, Asim M, Majeed MN, Hussain N, et al. Journal of Computational Biophysics and Chemistry. 2025;24(8):1023–38. Google Scholar
  3. 23.Combining network pharmacology and computational approaches for screening of Apiaceae-derived phytochemicals as inhibitors of DNA polymerase III in Streptococcus pyogenes. Naveed M, Asim M, Aziz T, Ayyaz M, Ibrahim S, Majeed MN, Khan AA, et al. Chinese Journal of Analytical Chemistry. 2025:100632. Google Scholar
  4. 24.Scrutinizing the evidence of anthracene toxicity on adrenergic receptor beta-2 and its bioremediation by fungal manganese peroxidase via in silico approaches. Naveed M, Khatoon K, Aziz T, Naveed R, Majeed MN, Salah Ud Din M, et al. Scientific Reports. 2025;15(1):3795. Google Scholar
  5. 25.Dual functional cobalt-doped CdFe2O4 nanoflakes for promising photocatalysts and supercapacitor electrodes. Siddique S, Hussain MF, Khan ZA, Majeed MN, Ullah S. Journal of Innovative Technology. 2025;7(1):9–20. Google Scholar
  6. 26.Computational design of a multi-epitope peptide vaccine against the opportunistic fungus Aspergillus fumigatus in lung cancer patients. Haider SA, Biniyam PD, Sarfraz I, Majeed MN, Ditta A, Fajar F, et al. 2025. Google Scholar
  7. 27.Computational identification and analysis of miRNAs targeting TP53 and tumor suppressor genes in squamous cell lung carcinoma. Haider SA, Shahid S, Sarfaraz I, Yousaf B, Azhar S, Majeed MN. 2025. Google Scholar

2024

  1. 28.Designing a multi-epitope vaccine candidate to MERS-CoV: an in silico approach. Majeed MN, Iqbal A, Murtaza N, Herrera-Zúñiga LD, Siddique S, Raza M, et al. Innovative Biosystems and Bioengineering. 2024;8(3):3–17. Google Scholar
  2. 29.Rational computational design and development of an immunogenic multiepitope vaccine incorporating transmembrane proteins of Staphylococcus lugdunensis. Naveed M, Fatima F, Aziz T, Iftikhar MA, Javed T, Majeed MN, et al. International Immunopharmacology. 2024;143:113345. Google Scholar
  3. 30.Exploring the complex relationship between insulin resistance, lipid metabolism, and cardiovascular risk. Majeed MN, Khan A, Amin H, Bhattarai B, et al. Journal of Population Therapeutics and Clinical Pharmacology. 2024;31(2):185–206. DOIGoogle Scholar
  4. 31.Natural substances in modern healthcare: an exploration of the role of natural substances, including phytotherapeutics and herbal products, in the context of modern healthcare. Bangash SA, Budhathoki H, Sohail S, Alshehri B, Khan UA, Majeed MN. Journal of Population Therapeutics and Clinical Pharmacology. 2024;31(2):2739–45. DOIGoogle Scholar

In press

  1. 32.Genome sequence announcement of Bacillus paranthracis MBBL1 strain, isolated from petroleum-polluted soil in Lahore. Hanif N, Naveed M, Waseem M, Arshad A, Majeed MN, Sohail H, et al. In press. Google Scholar

NCBI submissions

Genomes and sequences deposited at NCBI

Whole-genome sequences of three Bacillus strains and 16S rRNA gene sequences of three isolates.

Whole-genome sequences

OrganismStrainAccessionBioProjectBioSampleAssemblySRA
Bacillus paranthracisMBBL1JBKOHK000000000PRJNA1205345SAMN46046895ASM4676398v1SRX27225424
Bacillus subtilisMBBL2JBKICF000000000PRJNA1205758SAMN46063101ASM4657322v1SRX27234169
Bacillus cereusMBBL3JBTHGN010000000PRJNA1393390SAMN54299749ASM5434347v1SRX31628070

16S rRNA gene sequences (partial)

OrganismStrainAccession
Ureibacillus chungkukjangiMBBL33PQ568249.1
Bacillus cereusMBBL36PQ732226.1
Bacillus cereusMBBL37PV014952.1

Activities

Talks, training and skills

Conference presentations

  • Rational In Silico Design and Molecular Dynamics Evaluation of a Multi-Epitope Vaccine Against Monkeypox Virus Targeting O2L, J1L, and B5R Proteins12th International Conference on Biological and Computational Sciences (C-BICS 2024), Capital University of Science and Technology, Islamabad · 2 Nov 2024
  • Integrating AI-Driven Protein Modeling, DFT, ANN and Molecular Dynamics to Evaluate Zinc Oxide Nanoparticles for Diabetes TherapyNational Conference on Recent Advances in Biological Sciences (RABS-2025)

Training and events

  • Trainer and organizer, 6th National Hands-on Training Workshop on Advanced Bioinformatics and Recombinant BiotechnologyUniversity of Central Punjab, Lahore · 22 Aug 2024 · Sessions on “Molecular Dynamics Simulation in Ubuntu” and “The Use of Biopython in Bioinformatics”, alongside Dr. Muhammad Naveed.
  • Organizer, 10th Final Year Project Exhibition, Open House Job Interviews and Bioinformatics Poster Competition “Innovating Tomorrow”University of Central Punjab, Lahore · 4 Feb 2025
  • Organizer, 2nd International Conference on Emerging Horizons in Science and TechnologyUniversity of Central Punjab · 21–22 Nov 2024
  • Organizer, one-day workshop on Biosafety and Biosecurity in the era of antimicrobial resistanceUniversity of Okara · Nov 2022
  • Participant, one-day awareness webinar on GMO Detection of RiceNational Institute for Biotechnology and Genetic Engineering

Skills

Molecular simulation
GROMACS, OpenMM, ACEMD3, AMBER and CHARMM force fields, MM-GBSA and MM-PBSA
Drug and vaccine design
Molecular docking, virtual screening, in silico vaccine design, immunoinformatics, pharmacokinetics (ADMET), QSAR
Computation and AI
DFT, artificial neural networks, AI-driven drug screening, Biopython, Ubuntu Linux, biostatistics
Laboratory
Microbiological techniques, nanoparticle synthesis, protein chemistry, biosafety and biosecurity
Languages
Urdu (native), English

Courses

  • SARS-CoV-2 Protein Modeling and Drug DockingInstructor: Bhagesh Hunakunti
  • AI For EveryoneDeepLearning.AI · Verify credential
  • HTML5: From Basics to Advanced LevelEdYoda Digital University · Jul 2025 · View certificate
  • Windows 10 System Administration & Basic Computer SkillsUdemy, instructor John Courteny · View certificate
  • The Fundamentals of Digital MarketingGoogle · Jun 2020

Contact

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