% SilicoScientia publication list: 32 peer reviewed papers. Titles, authors, journals and pages from Crossref; open access status from OpenAlex, checked 12 October 2026.

@article{Mangal2026NDM1,
  author = {Mangal, Parth and Shinde, Omkar and Chikhale, Sonali and Bhowmick, Shovonlal and Islam, Md Ataul},
  title = {{SilicoXplore: An integrated cloud platform coupling machine learning with physics-based modelling for end-to-end drug discovery, applied to the computational prioritisation of putative New Delhi metallo-{$\beta$}-lactamase-1 binders}},
  journal = {Journal of Molecular Graphics and Modelling},
  year = {2026},
  volume = {149},
  pages = {109566},
  doi = {10.1016/j.jmgm.2026.109566},
  url = {https://doi.org/10.1016/j.jmgm.2026.109566},
  keywords = {Antimicrobial resistance; SilicoXplore}
}

@article{Islam2026EGFR,
  author = {Islam, Md Ataul and Bhowmick, Shovonlal and Chikhale, Sonali},
  title = {{SilicoSAR: an integrated machine-learning QSAR module within the SilicoXplore platform for QSAR-based virtual screening, demonstrated by the discovery of natural-product EGFR inhibitors}},
  journal = {Computational Biology and Chemistry},
  year = {2026},
  volume = {126},
  pages = {109467},
  doi = {10.1016/j.compbiolchem.2026.109467},
  url = {https://doi.org/10.1016/j.compbiolchem.2026.109467},
  keywords = {Oncology; SilicoXplore}
}

@article{Alsarra2026GPIanchoredwalltr,
  author = {Alsarra, Ibrahim A. and Chikhale, Rupesh and Al-Mohizea, Abdullah M. and Islam, Md Ataul},
  title = {{Identification of GPI-Anchored Wall Transfer Protein 1 Modulators for Fungal Infections Through Generative AI and Physics-Based Approaches}},
  journal = {International Journal of Molecular Sciences},
  year = {2026},
  volume = {27},
  number = {11},
  pages = {4767},
  doi = {10.3390/ijms27114767},
  url = {https://doi.org/10.3390/ijms27114767},
  keywords = {Antifungal; SilicoXplore}
}

@article{Islam2026CYP51B,
  author = {Islam, Md Ataul and Ali, Mohammad Ajmal and Chikhale, Rupesh and Islam, Md Lutful and Wabaidur, Saikh Mohammad},
  title = {{Artificial Intelligence-Guided Design and Computational Evaluation of Candidate CYP51B Inhibitors as Potential Antifungal Agents}},
  journal = {ChemistrySelect},
  year = {2026},
  volume = {11},
  number = {34},
  pages = {e74407},
  doi = {10.1002/slct.74407},
  url = {https://doi.org/10.1002/slct.74407},
  keywords = {Antifungal; SilicoXplore}
}

@article{Shinde2026HCVIRES,
  author = {Shinde, Omkar and Patil, Pritee Chunarkar and Eldesoky, Gaber E. and Chikhale, Rupesh V.},
  title = {{Integrated machine-learning methods for identification of Hepatitis C viral IRES sub-domain-IIa inhibitors}},
  journal = {Canadian Journal of Chemistry},
  year = {2026},
  volume = {104},
  number = {3},
  pages = {289--302},
  doi = {10.1139/cjc-2025-0046},
  url = {https://doi.org/10.1139/cjc-2025-0046},
  keywords = {Antiviral}
}

@article{Parekh2026PDE10A,
  author = {Parekh, Vipra Ajay and Amina, Musarat and Islam, Md Lutful and Patil, Pritee Chunarkar and Ali, Mohammad Ajmal and Wabaidur, Saikh Mohammad and Islam, Md Ataul},
  title = {{Identification of phosphodiesterase 10 A modulators for neurodegenerative and psychiatric disorders: Combination of physics-based virtual screening and machine learning approaches}},
  journal = {Computational Biology and Chemistry},
  year = {2026},
  volume = {121},
  pages = {108875},
  doi = {10.1016/j.compbiolchem.2025.108875},
  url = {https://doi.org/10.1016/j.compbiolchem.2025.108875},
  keywords = {Neurological}
}

@article{Wanode2026VEGFR2,
  author = {Wanode, Deepali M. and Islam, Md Ataul and Bhendarkar, Kumud P. and Ambatkar, Megha P. and Khedekar, Pramod B. and Chikhale, Rupesh},
  title = {{Applying artificial intelligence and machine learning framework for de novo design of pyrazole-based VEGFR-2 inhibitors}},
  journal = {Journal of Molecular Graphics and Modelling},
  year = {2026},
  volume = {146},
  pages = {109458},
  doi = {10.1016/j.jmgm.2026.109458},
  url = {https://doi.org/10.1016/j.jmgm.2026.109458},
  keywords = {Oncology; SilicoXplore}
}

@article{Islam2026Chk1,
  author = {Islam, Md Ataul and Ali, Mohammad Ajmal and Chikhale, Rupesh and Islam, Md Lutful and Wabaidur, Saikh Mohammad},
  title = {{Free energy perturbation-assisted identification of checkpoint kinase 1 targeted small-molecule inhibitors for cancer therapy using AI- and physics-driven molecular design}},
  journal = {Computational Biology and Chemistry},
  year = {2026},
  volume = {124},
  pages = {109203},
  doi = {10.1016/j.compbiolchem.2026.109203},
  url = {https://doi.org/10.1016/j.compbiolchem.2026.109203},
  keywords = {Oncology; SilicoXplore}
}

@article{Alsarra2026ERK2,
  author = {Alsarra, Ibrahim A. and Kolpe, Mahima Sudhir and Islam, Md Ataul},
  title = {{Identification of Novel Extracellular-Signal-Regulated Kinase 2 Inhibitors Through Machine Learning-Driven De Novo Design, Molecular Docking, and Free-Energy Perturbation}},
  journal = {Pharmaceuticals},
  year = {2026},
  volume = {19},
  number = {2},
  pages = {337},
  doi = {10.3390/ph19020337},
  url = {https://doi.org/10.3390/ph19020337},
  keywords = {Oncology}
}

@article{Deka2026CDC34UBC,
  author = {Deka, Hemchandra and Abdelghani, Heba Taha M. and Gangopadhyay, Aditi and Pawar, Atul Darasing and Patil, Pritee Chunarkar and Bhowmick, Shovonlal},
  title = {{Identification of potential allosteric inhibitors-modulators for the heterodimer CDC34-UBC protein-protein complex}},
  journal = {3 Biotech},
  year = {2026},
  volume = {16},
  number = {5},
  pages = {160},
  doi = {10.1007/s13205-026-04777-0},
  url = {https://doi.org/10.1007/s13205-026-04777-0},
  keywords = {Oncology}
}

@article{Islam2026MAP3K8,
  author = {Islam, Md Ataul and Iqbal, Aaherasha and Ali, Mohammad Ajmal and Chikhale, Rupesh and Islam, Md Lutful and Farah, Mohammad Abul},
  title = {{Free energy perturbation and machine learning-assisted identification of potential MAP3K8 hit molecules: a comprehensive structure- and ligand-based studies}},
  journal = {Molecular Diversity},
  year = {2026},
  doi = {10.1007/s11030-026-11696-y},
  url = {https://doi.org/10.1007/s11030-026-11696-y},
  keywords = {Oncology}
}

@article{Alsarra2026MenT3,
  author = {Alsarra, Ibrahim A. and Suryawanshi, Vikramsinh Sardarsinh and Al-Mohizea, Abdullah M. and Patil, Pritee Chunarkar and Chikhale, Rupesh and Islam, Md Ataul},
  title = {{Identification of potential MenT3 inhibitors for Mycobacterium tuberculosis using the generative artificial intelligence and SilicoXplore platform}},
  journal = {Scientific Reports},
  year = {2026},
  volume = {16},
  number = {1},
  pages = {18185},
  doi = {10.1038/s41598-026-49174-y},
  url = {https://doi.org/10.1038/s41598-026-49174-y},
  keywords = {Tuberculosis; SilicoXplore}
}

@article{Islam2026KasA,
  author = {Islam, Md Ataul and Ali, Mohammad Ajmal and Chikhale, Rupesh and Islam, Md Lutful and Farah, Mohammad Abul},
  title = {{Free energy perturbation and machine learning-assisted identification of novel molecules for the Mycobacterium tuberculosis KasA protein: a fragment-based drug design approach}},
  journal = {Molecular Diversity},
  year = {2026},
  doi = {10.1007/s11030-026-11726-9},
  url = {https://doi.org/10.1007/s11030-026-11726-9},
  keywords = {Tuberculosis; SilicoXplore}
}

@article{Chikhale2026TMK,
  author = {Chikhale, Rupesh V. and Islam, Md Ataul and Suryawanshi, Vikramsinh Sardarsinh and Alsarra, Ibrahim A.},
  title = {{Free energy perturbation-derived identification of natural compounds targeting Mycobacterium tuberculosis thymidylate kinase}},
  journal = {Scientific Reports},
  year = {2026},
  volume = {16},
  number = {1},
  pages = {16272},
  doi = {10.1038/s41598-026-46983-z},
  url = {https://doi.org/10.1038/s41598-026-46983-z},
  keywords = {Tuberculosis}
}

@article{Islam2026DNAgyraseB,
  author = {Islam, Md Ataul and Islam, Md Lutful and Iqbal, Aaherasha and Ali, Mohammad Ajmal and Chikhale, Rupesh and Farah, Mohammad Abul},
  title = {{Screening and optimization of potential molecules targeting DNA gyrase B in Mycobacterium tuberculosis: a generative artificial intelligence, free energy perturbation, and de novo design approach}},
  journal = {Chemical Papers},
  year = {2026},
  doi = {10.1007/s11696-026-05622-7},
  url = {https://doi.org/10.1007/s11696-026-05622-7},
  keywords = {Tuberculosis}
}

@article{Suryawanshi2025AChE,
  author = {Suryawanshi, Vikramsinh Sardarsinh and Islam, Md Lutful and Eldesoky, Gaber E. and Patil, Pritee Chunarkar and Bhowmick, Shovonlal and Islam, Md Ataul},
  title = {{Identification of Acetylcholinesterase Inhibitors Through a Pharmacophore-Guided Deep Learning Approach for Therapeutic Applications in Alzheimer's Disease}},
  journal = {ChemistrySelect},
  year = {2025},
  volume = {10},
  number = {25},
  pages = {e00492},
  doi = {10.1002/slct.202500492},
  url = {https://doi.org/10.1002/slct.202500492},
  keywords = {Neurological}
}

@article{Choudhary2025Pks13,
  author = {Choudhary, Rinku and Bhowmick, Shovonlal and Abdelghani, Heba Taha M. and Patil, Pritee Chunarkar and Chikhale, Rupesh V.},
  title = {{Pharmacophore guided deep learning approach to identify novel inhibitors targeting mycobacterial polyketide synthase Pks13-TE domain}},
  journal = {Journal of Molecular Structure},
  year = {2025},
  volume = {1319},
  pages = {139360},
  doi = {10.1016/j.molstruc.2024.139360},
  url = {https://doi.org/10.1016/j.molstruc.2024.139360},
  keywords = {Tuberculosis}
}

@article{Chikhale2025EthR,
  author = {Chikhale, Rupesh V. and Choudhary, Rinku and Eldesoky, Gaber E. and Kolpe, Mahima Sudhir and Shinde, Omkar and Hossain, Dilnawaz},
  title = {{Generative AI, molecular docking and molecular dynamics simulations assisted identification of novel transcriptional repressor EthR inhibitors to target Mycobacterium tuberculosis}},
  journal = {Heliyon},
  year = {2025},
  volume = {11},
  number = {4},
  pages = {e42593},
  doi = {10.1016/j.heliyon.2025.e42593},
  url = {https://doi.org/10.1016/j.heliyon.2025.e42593},
  keywords = {Tuberculosis}
}

@article{Battula2025DosR,
  author = {Battula, Monishka and Bhor, Samiksha and Bhowmick, Shovonlal and Eldesoky, Gaber E. and Chikhale, Rupesh V.},
  title = {{Targeting Mycobacterial Dormancy Survival Regulator (DosR) With Generative Artificial Intelligence and Omics Methods}},
  journal = {Chemistry \& Biodiversity},
  year = {2025},
  pages = {e02926},
  doi = {10.1002/cbdv.202402926},
  url = {https://doi.org/10.1002/cbdv.202402926},
  keywords = {Tuberculosis}
}

@article{Battula2024RibosomalRNA,
  author = {Battula, Monishka and Bhowmick, Shovonlal and Patil, Pritee Chunarkar and Eldesoky, Gaber E. and Chikhale, Rupesh V.},
  title = {{Investigating the Ribosomal-RNA: Protein Interactions and AI-Assisted Discovery of Novel Inhibitors}},
  journal = {ChemistrySelect},
  year = {2024},
  volume = {9},
  number = {43},
  pages = {e202403459},
  doi = {10.1002/slct.202403459},
  url = {https://doi.org/10.1002/slct.202403459},
  keywords = {Antimicrobial resistance}
}

@article{Deka2024Peregrin,
  author = {Deka, Hemchandra and Pawar, Atul Darasing and Battula, Monishka Srinivas and Eldesoky, Gaber E. and Shinde, Omkar Dilip and Patil, Pritee Chunarkar and Mistri, Tapan Kumar and Shahare, Hitesh Vishwanath and Bhowmick, Shovonlal},
  title = {{Identification of Peregrin inhibitors-modulators by harnessing the computational prowess of molecular simulation and machine learning algorithms}},
  journal = {Journal of Molecular Liquids},
  year = {2024},
  volume = {411},
  pages = {125782},
  doi = {10.1016/j.molliq.2024.125782},
  url = {https://doi.org/10.1016/j.molliq.2024.125782},
  keywords = {Oncology}
}

@article{Bhowmick2024Hsp90,
  author = {Bhowmick, Shovonlal and Malhotra, Jagriti and Choudhary, Rinku and Shinde, Omkar Dilip and Metwally, Ahmed Sayed M. and Patil, Pritee Chunarkar},
  title = {{Machine Learning Aided De Novo Design Identifies Novel Benzimidazolone Based Inhibitor-Modulators for Heat Shock Protein 90 (HSP90)}},
  journal = {ChemistrySelect},
  year = {2024},
  volume = {9},
  number = {31},
  pages = {e202402147},
  doi = {10.1002/slct.202402147},
  url = {https://doi.org/10.1002/slct.202402147},
  keywords = {Oncology}
}

@article{Suryawanshi2024ERK2,
  author = {Suryawanshi, Vikramsinh Sardarsinh and Pawar, Surbhi Pravin and Kolpe, Mahima Sudhir and Abdelghani, Heba Taha M. and Chikhale, Sonali and Patil, Pritee Chunarkar and Bhowmick, Shovonlal},
  title = {{Machine learning-integrated and fingerprint-based similarity search against immuno oncology library for identification of novel ERK2 inhibitors}},
  journal = {Structural Chemistry},
  year = {2024},
  volume = {36},
  number = {2},
  pages = {681--700},
  doi = {10.1007/s11224-024-02397-z},
  url = {https://doi.org/10.1007/s11224-024-02397-z},
  keywords = {Oncology}
}

@article{Kolpe2024CHK2,
  author = {Kolpe, Mahima Sudhir and Suryawanshi, Vikramsinh Sardarsinh and Eldesoky, Gaber E. and Hossain, Dilnawaz and Patil, Pritee Chunarkar and Bhowmick, Shovonlal},
  title = {{Identification of Potent CHK2 Inhibitors-Modulators for Therapeutic Application in Cancer: A Machine Learning Integrated Fragment-Based Drug Design Approach}},
  journal = {ChemistrySelect},
  year = {2024},
  volume = {9},
  number = {39},
  pages = {e202403302},
  doi = {10.1002/slct.202403302},
  url = {https://doi.org/10.1002/slct.202403302},
  keywords = {Oncology}
}

@article{Kolpe2024AuroraAkinase,
  author = {Kolpe, Mahima Sudhir and Pawar, Surbhi Pravin and Suryawanshi, Vikramsinh Sardarsinh and Abdelghani, Heba Taha M. and Patil, Pritee Chunarkar and Bhowmick, Shovonlal},
  title = {{Identification of Aurora A kinase allosteric inhibitors: A comprehensive virtual screening through fingerprint-based similarity search, molecular docking, machine learning and molecular dynamics simulation}},
  journal = {Journal of Molecular Liquids},
  year = {2024},
  volume = {414},
  pages = {126115},
  doi = {10.1016/j.molliq.2024.126115},
  url = {https://doi.org/10.1016/j.molliq.2024.126115},
  keywords = {Oncology}
}

@article{Pawar2024AuroraAkinase,
  author = {Pawar, Surbhi Pravin and Kolpe, Mahima Sudhir and Suryawanshi, Vikramsinh Sardarsinh and Chikhale, Sonali and Tighezza, Ammar M. and Patil, Pritee Chunarkar and Bhowmick, Shovonlal},
  title = {{Molecular simulations and machine learning methods for the identification of novel aurora A kinase inhibitors}},
  journal = {Journal of Biomolecular Structure and Dynamics},
  year = {2024},
  volume = {43},
  number = {14},
  pages = {7797--7810},
  doi = {10.1080/07391102.2024.2435058},
  url = {https://doi.org/10.1080/07391102.2024.2435058},
  keywords = {Oncology}
}

@article{Chikhale2024TMK,
  author = {Chikhale, Rupesh V. and Pawar, Surbhi Pravin and Kolpe, Mahima Sudhir and Shinde, Omkar Dilip and Dahlous, Kholood A. and Mohammad, Saikh and Patil, Pritee Chunarkar and Bhowmick, Shovonlal},
  title = {{Identification of mycobacterial Thymidylate kinase inhibitors: a comprehensive pharmacophore, machine learning, molecular docking, and molecular dynamics simulation studies}},
  journal = {Molecular Diversity},
  year = {2024},
  volume = {28},
  number = {4},
  pages = {1947--1964},
  doi = {10.1007/s11030-024-10967-w},
  url = {https://doi.org/10.1007/s11030-024-10967-w},
  keywords = {Tuberculosis}
}

@article{Deka2024PknB,
  author = {Deka, Hemchandra and Pawar, Atul and Battula, Monishka and Ghfar, Ayman A. and Assal, Mohamed E. and Chikhale, Rupesh V.},
  title = {{Identification and Design of Novel Potential Antimicrobial Peptides Targeting Mycobacterial Protein Kinase PknB}},
  journal = {The Protein Journal},
  year = {2024},
  volume = {43},
  number = {4},
  pages = {858--868},
  doi = {10.1007/s10930-024-10218-9},
  url = {https://doi.org/10.1007/s10930-024-10218-9},
  keywords = {Tuberculosis}
}

@article{Chikhale2024Pks13,
  author = {Chikhale, Rupesh V. and Choudhary, Rinku and Malhotra, Jagriti and Eldesoky, Gaber E. and Mangal, Parth and Patil, Pritee Chunarkar},
  title = {{Identification of novel hit molecules targeting M. tuberculosis polyketide synthase 13 by combining generative AI and physics-based methods}},
  journal = {Computers in Biology and Medicine},
  year = {2024},
  volume = {176},
  pages = {108573},
  doi = {10.1016/j.compbiomed.2024.108573},
  url = {https://doi.org/10.1016/j.compbiomed.2024.108573},
  keywords = {Tuberculosis}
}

@article{Pawar2024MmpL3,
  author = {Pawar, Atul and Almutairi, Tahani Mazyad and Shinde, Omkar and Chikhale, Rupesh},
  title = {{Gen-AI Methods, Molecular Docking and Molecular Dynamics Simulations for Identification of Novel Inhibitors of MmPL3 Transporter of Mycobacterium tuberculosis}},
  journal = {Journal of Computational Biophysics and Chemistry},
  year = {2024},
  volume = {24},
  number = {04},
  pages = {471--489},
  doi = {10.1142/S2737416524500674},
  url = {https://doi.org/10.1142/S2737416524500674},
  keywords = {Tuberculosis}
}

@article{Chikhale2024InhA,
  author = {Chikhale, Rupesh V. and Abdelghani, Heba Taha M. and Deka, Hemchandra and Pawar, Atul Darasing and Patil, Pritee Chunarkar and Bhowmick, Shovonlal},
  title = {{Machine learning assisted methods for the identification of low toxicity inhibitors of Enoyl-Acyl Carrier Protein Reductase (InhA)}},
  journal = {Computational Biology and Chemistry},
  year = {2024},
  volume = {110},
  pages = {108034},
  doi = {10.1016/j.compbiolchem.2024.108034},
  url = {https://doi.org/10.1016/j.compbiolchem.2024.108034},
  keywords = {Tuberculosis}
}

@article{Chikhale2024EthR,
  author = {Chikhale, Rupesh V. and Eldesoky, Gaber E. and Kolpe, Mahima Sudhir and Suryawanshi, Vikramsinh Sardarsinh and Patil, Pritee Chunarkar and Bhowmick, Shovonlal},
  title = {{Identification of Mycobacterium tuberculosis transcriptional repressor EthR inhibitors: Shape-based search and machine learning studies}},
  journal = {Heliyon},
  year = {2024},
  volume = {10},
  number = {5},
  pages = {e26802},
  doi = {10.1016/j.heliyon.2024.e26802},
  url = {https://doi.org/10.1016/j.heliyon.2024.e26802},
  keywords = {Tuberculosis}
}