All Stories

  1. QuPepFold: A python package for hybrid quantum-classical protein folding simulations with CVaR-optimized VQE

    Article • PLOS One, February 2026, PLOS

    Akshay Uttarkar

  2. Computational modeling and optimization of scFv-based receptors to support CAR-T design targeting CD19 for enhanced binding robustness and reduced off-target propensity

    Article • Biochemical and Biophysical Research Communications, February 2026, Elsevier

    Akshay Uttarkar

  3. In Silico Discovery of Tanshinone I, a Diterpenoid from Salvia miltiorrhiza (Danshen), as a Dual Antiviral Natural Inhibitor Targeting Conserved Allosteric Sites of HMPV and HRSV RNA-Dependent RNA Polymerases

    Article • Journal of Pharmaceutical Innovation, November 2025, Springer Science + Business Media

    Akshay Uttarkar

  4. Discovery of natural compounds as novel FMS-like tyrosine kinase-3 (FLT3) therapeutic inhibitors for the treatment of acute myeloid leukemia: An in-silico approach

    Article • Aspects of Molecular Medicine, June 2025, Elsevier

    Akshay Uttarkar

  5. Molecular dynamics simulation and docking studies reveals inhibition of NF-kB signaling as a promising therapeutic drug target for reduction in cytokines storms

    Article • Scientific Reports, April 2025, Springer Science + Business Media

    Dr Shaban Ahmad, Akshay Uttarkar

  6. Computational modeling and optimization of peptide-based CAR-T cell receptors targeting CD19 for enhanced efficacy and minimized toxicity

    Article • March 2025, Springer Science + Business Media

    Akshay Uttarkar

  7. Computational modeling and optimization of peptide-based CAR-T cell receptors targeting CD19 for enhanced efficacy and minimized toxicity

    Article • February 2025, Springer Science + Business Media

    Akshay Uttarkar

  8. In silico exploration natural compounds for the discovery of novel DNMT3A inhibitors as potential therapeutic agents for acute myeloid leukemia

    Article • In Silico Research in Biomedicine, January 2025, Elsevier

    Akshay Uttarkar

  9. Quantum Enabled Protein Folding of Disordered Regions in Ubiquitin C Via Error Mitigated VQE Benchamrked on Tensor Network Simulator and Aria 1

    Article • IEEE Transactions on Molecular Biological and Multi-Scale Communications, January 2025, Institute of Electrical & Electronics Engineers (IEEE)

    Akshay Uttarkar

  10. Targeting the G-quadruplex structure in the hTERT promoter for telomerase activity: in silico screening of phyto-compounds and long timescale replica exchange molecular dynamic simulations

    Article • Molecular Simulation, October 2024, Taylor & Francis

    Akshay Uttarkar

  11. Advanced Strategies in Quantitative Structure Activity Relationship (QSAR) Modeling

    Article • October 2024, IGI Global

    Akshay Uttarkar

  12. Computational Theories Shaping the Future of Drug Discovery

    Article • October 2024, IGI Global

    Akshay Uttarkar

  13. Molecular Dynamics Simulation and Docking Studies Reveals Inhibition of NF-kB signaling as a Promising Therapeutic Drug Target for reduction in Cytokines Storms

    Article • October 2024, Springer Science + Business Media

    Akshay Uttarkar

  14. Exploring VQE for Ground State Energy Calculations of Small Molecules With Higher Bond Orders

    Article • September 2024, Institute of Electrical & Electronics Engineers (IEEE)

    Akshay Uttarkar

  15. T-Gate Enabled Fault-Tolerant Ansatz Circuit Design for Variational Quantum Algorithms in Peptide Folding on Aria-1

    Article • September 2024, Institute of Electrical & Electronics Engineers (IEEE)

    Akshay Uttarkar

  16. In silicoExploration Natural Compounds for the Discovery of Novel DNMT3A Inhibitors as Potential Therapeutic Agents for Acute Myeloid Leukemia

    Article • August 2024, Cold Spring Harbor Laboratory Press

    Akshay Uttarkar

  17. Discovery of natural compounds as novel FMS-like tyrosine kinase-3 (FLT3) therapeutic inhibitors for the treatment of acute myeloid leukemia: anin silicoapproach

    Article • August 2024, Cold Spring Harbor Laboratory Press

    Akshay Uttarkar

  18. Computational Insights into Papaveroline as an In Silico Drug Candidate for Alzheimer’s Disease via Fyn Tyrosine Kinase Inhibition

    Article • Molecular Biotechnology, July 2024, Springer Science + Business Media

    Akshay Uttarkar

  19. Quantum synergy in peptide folding: A comparative study of CVaR-variational quantum eigensolver and molecular dynamics simulation

    Article • International Journal of Biological Macromolecules, July 2024, Elsevier

    Akshay Uttarkar

  20. Disaggregation of amyloid-beta fibrils via natural metabolites using long timescale replica exchange molecular dynamics simulation studies

    Article • Journal of Molecular Modeling, February 2024, Springer Science + Business Media

    Akshay Uttarkar

  21. A comparative insight into peptide folding with quantum CVaR-VQE algorithm, MD simulations and structural alphabet analysis

    Article • Quantum Information Processing, February 2024, Springer Science + Business Media

    Akshay Uttarkar

  22. Exploring the Role of Non-synonymous and Deleterious Variants Identified in Colorectal Cancer: A Multi-dimensional Computational Scrutiny of Exomes

    Article • Current Genomics, February 2024, Bentham Science Publishers

    Akshay Uttarkar

  23. Targeting the G-quadruplex structure in the hTERT promoter: In silico screening of phytocompounds and replica exchange molecular dynamics simulations

    Article • January 2024, Cold Spring Harbor Laboratory Press

    Akshay Uttarkar

  24. Deciphering the scope of in silico screening of novel natural lead molecules against putative molecular targets of multidrug-resistant bacterial pathogens

    Article • January 2024, Elsevier

    Akshay Uttarkar

  25. Protocol for the development of coarse-grained structures for macromolecular simulation using GROMACS v2

    Article • December 2023, Springer Science + Business Media

    Akshay Uttarkar

  26. BRCA1/TP53 tumor proteins inhibited by novel analogues of curcumin — Insight from computational modelling, dynamic simulation and experimental validation

    Article • International Journal of Biological Macromolecules, December 2023, Elsevier

    Akshay Uttarkar

  27. Investigating the Molecular Interactions of Quinoline Derivatives for Antibacterial Activity Against Bacillus subtilis: Computational Biology and In Vitro Study Interpretations

    Article • Molecular Biotechnology, November 2023, Springer Science + Business Media

    Akshay Uttarkar

  28. A Comparative Analysis of Quantum Computing Variational Quantum Eigensolver Algorithm and Molecular Dynamics Simulations for Peptide Folding

    Article • October 2023, Research Square

    Akshay Uttarkar

  29. Design of Novel Imidazopyrazine Derivative against Breast Cancer via Targeted NPY1R Antagonist

    Article • Anti-Cancer Agents in Medicinal Chemistry, September 2023, Bentham Science Publishers

    Akshay Uttarkar, Raviraj Kusanur

  30. Protocol for the development of coarse-grained structures for macromolecular simulation using GROMACS

    Article • PLOS One, August 2023, PLOS

    Akshay Uttarkar

  31. De Novo Design of Anti-COVID Drugs Using Machine Learning-Based Equivariant Diffusion Model Targeting the Spike Protein

    Article • Current Issues in Molecular Biology, May 2023, MDPI AG

    Akshay Uttarkar

  32. Carboxymuconolactone decarboxylase is a prospective molecular target for multi-drug resistant Acinetobacter baumannii-computational modeling, molecular docking and dynamic simulation studies

    Article • Computers in Biology and Medicine, May 2023, Elsevier

    Akshay Uttarkar

  33. Insights on Novel Effectors and Characterization of Metacaspase (RS107_6) as a Potential Cell Death-Inducing Protein in Rhizoctonia solani

    Article • Microorganisms, April 2023, MDPI AG

    Akshay Uttarkar

  34. Protocol for the development of coarse-grained structures for macromolecular simulation using GROMACS v1

    Article • February 2023, Springer Science + Business Media

    Akshay Uttarkar

  35. Transcription factors controlling the expression of oxidative stress associated genes in rice (Oryza sativa L.)

    Article • Plant Biotechnology Reports, February 2023, Springer Science + Business Media

    Akshay Uttarkar

  36. High Throughput Ligand Interaction Profiler v1

    Article • January 2023, Springer Science + Business Media

    Akshay Uttarkar

  37. Computational design of prospective molecular targets for Burkholderia cepacia complex by molecular docking and dynamic simulation studies

    Article • Proteins Structure Function and Bioinformatics, January 2023, Wiley

    Akshay Uttarkar

  38. Design of Novel Coumarin Derivatives as NUDT5 Antagonists That Act by Restricting ATP Synthesis in Breast Cancer Cells

    Article • Molecules, December 2022, MDPI AG

    Akshay Uttarkar

  39. Novel 1,2,5-Trisubstituted Benzimidazoles Potentiate Apoptosis by Mitochondrial Dysfunction in Panel of Cancer Cells

    Article • ACS Omega, December 2022, American Chemical Society (ACS)

    Akshay Uttarkar

  40. A Machine Learning-Based Approach Using Multi-omics Data to Predict Metabolic Pathways

    Article • October 2022, Springer Science + Business Media

    Akshay Uttarkar

  41. Mycobacterium Time-Series Genome Analysis Identifies AAC2′ as a Potential Drug Target with Naloxone Showing Potential Bait Drug Synergism

    Article • Molecules, September 2022, MDPI AG

    Akshay Uttarkar

  42. A Simple and Rapid Oxidative Stress Screening Method of Small Molecules for Functional Studies of Transcription Factor

    Article • Rice Science, September 2022, Elsevier

    Akshay Uttarkar

  43. Correction to: Scope of repurposed drugs against the potential targets of the latest variants of SARS-CoV-2

    Article • Structural Chemistry, August 2022, Springer Science + Business Media

    Akshay Uttarkar

  44. Brefeldin A variant via combinatorial screening acts as an effective antagonist inducing structural modification in EPAC2

    Article • Molecular Simulation, August 2022, Taylor & Francis

    Akshay Uttarkar

  45. Scope of repurposed drugs against the potential targets of the latest variants of SARS-CoV-2

    Article • Structural Chemistry, August 2022, Springer Science + Business Media

    Akshay Uttarkar

  46. Protocol for In-silico Design, Docking and Molecular Dynamic Simulation of Antisense Oligonucleotides v1

    Article • August 2022, ZappyLab, Inc.

    Akshay Uttarkar

  47. Novel small molecules targeting bZIP23 TF improve stomatal conductance and photosynthesis under mild drought stress by regulating ABA

    Article • European Journal of Biochemistry, May 2022, Wiley

    Akashata Dawane, Akshay Uttarkar

  48. Long Short Term Memory model for accurate predictions of Single Nucleotide Polymorphisms in Mycobacterium tuberculosis from timeseries genome analysis

    Article • April 2022, Research Square

    Akshay Uttarkar

  49. Molecular dynamics simulation and docking analysis of NF-κB protein binding with sulindac acid

    Article • Bioinformation, March 2022, Biomedical Informatics

    Dr Shaban Ahmad, Akshay Uttarkar

  50. Well-tempered Metadynamics protocol v2

    Article • February 2022, ZappyLab, Inc.

    Akshay Uttarkar

  51. Coumarin derivative as a potent drug candidate against triple negative breast cancer targeting the frizzled receptor of wingless-related integration site signaling pathway

    Article • Journal of Biomolecular Structure and Dynamics, January 2022, Taylor & Francis

    Akshay Uttarkar

  52. Carbon fullerene and nanotube are probable binders to multiple targets of SARS-CoV-2: Insights from computational modeling and molecular dynamic simulation studies

    Article • Infection Genetics and Evolution, December 2021, Elsevier

    DHARSHINI GOPAL, Akshay Uttarkar

  53. Molecular Docking and Interaction Studies of Identified Abscisic Acid Receptors in Oryza sativa: An In-Silico Perspective on Comprehending Stress Tolerance Mechanisms

    Article • Current Genomics, December 2021, Bentham Science Publishers

    Akshay Uttarkar

  54. Study of SARS-nCoV2 Indian Isolates Gaining Insights into Mutation Frequencies, Protein Stability and Prospective Effect on Pathogenicity

    Article • Coronaviruses, October 2021, Bentham Science Publishers

    Akshay Uttarkar

  55. Understanding the Xylooligosaccharides Utilization Mechanism of Lactobacillus brevis and Bifidobacterium adolescentis: Proteins Involved and Their Conformational Stabilities for Effectual Binding

    Article • Molecular Biotechnology, September 2021, Springer Science + Business Media

    Akshay Uttarkar

  56. Molecular dynamics simulation and docking studies reveal NF-κB as a promising therapeutic drug target for COVID-19

    Article • May 2021, Springer Science + Business Media

    Akshay Uttarkar

  57. Structural insights on the interaction potential of natural leads against major protein targets of SARS-CoV-2: Molecular modelling, docking and dynamic simulation studies

    Article • Computers in Biology and Medicine, May 2021, Elsevier

    Akshay Uttarkar, DHARSHINI GOPAL

  58. Re-profiling of natural inhibitor via combinatorial drug screening: Brefeldin A variant design as an effective antagonist leading to EPAC2 structure modification and antibody design for identification

    Article • April 2021, Cold Spring Harbor Laboratory Press

    Akshay Uttarkar

  59. Spiro Benzodiazepine Substituted Fluorocoumarins as Potent Anti-Anxiety Agents

    Article • Russian Journal of Bioorganic Chemistry, March 2021, Pleiades Publishing Ltd

    Akshay Uttarkar

  60. Stress-Induced Detoxification Enzymes in Rice Have Broad Substrate Affinity

    Article • ACS Omega, January 2021, American Chemical Society (ACS)

    Akshay Uttarkar

  61. Structural and molecular basis of the interaction mechanism of selected drugs towards multiple targets of SARS-CoV-2 by molecular docking and dynamic simulation studies- deciphering the scope of repurposed drugs

    Article • Computers in Biology and Medicine, November 2020, Elsevier

    Akshay Uttarkar, DHARSHINI GOPAL

  62. Response regulator GacA and transcriptional activator RhlR proteins involved in biofilm formation of Pseudomonas aeruginosa are prospective targets for natural lead molecules: Computational modelling, molecular docking and dynamic simulation studies

    Article • Infection Genetics and Evolution, November 2020, Elsevier

    Akshay Uttarkar, DHARSHINI GOPAL

  63. Natural epiestriol-16 act as potential lead molecule against prospective molecular targets of multidrug resistant Acinetobacter baumannii-Insight from in silico modelling and in vitro investigations

    Article • Infection Genetics and Evolution, August 2020, Elsevier

    Akshay Uttarkar

  64. Carbon fullerene acts as potential lead molecule against prospective molecular targets of biofilm-producing multidrug-resistant Acinetobacter baumanni and Pseudomonas aerugenosa: computational modeling and MD simulation studies

    Article • Journal of Biomolecular Structure and Dynamics, February 2020, Taylor & Francis

    Akshay Uttarkar

  65. Mitogen activated protein kinase-1 and cell division control protein-42 are putative targets for the binding of novel natural lead molecules: a therapeutic intervention against Candida albicans

    Article • Journal of Biomolecular Structure and Dynamics, October 2019, Taylor & Francis

    Professor SINOSH SKARIYACHAN, Prinith Kaveramma Uluvangada Praveen , DHARSHINI GOPAL, Akshay Uttarkar

  66. Genome Resequencing Reveals Single Nucleotide Polymorphism and Repeat Regions in Giardia lamblia Indian Isolate

    Article • Journal of Next Generation Sequencing & Applications, January 2017, OMICS Publishing Group

    Akshay Uttarkar