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Hire Dr. Dr. Ankur C.

India

USD 10 /hr

Protein Design & Bioinformatics Expert | Molecular Docking, Structural Biology, Therapeutic Peptides | Consultant

Profile Summary

I am a computational biologist and bioinformatics consultant with expertise in protein design, molecular modeling, and structural bioinformatics. I help academic researchers, biotech startups, and pharmaceutical teams solve complex biological problems using advanced computational approaches. My work focuses on protein–protein interaction analysis, peptide and protein binder design, molecular docking, structural modeling, simulation and bioinformatics data analysis. I have hands-on experience with widely used tools such as AlphaFold, Protenix, RFdiffusion, ProteinMPNN, Rosetta, GROMACS, AutoDock, HDOCK, BindCraft and various Python-based bioinformatics pipelines. I have conducted research on designing de novo peptide and protein binders against viral proteins, including dengue virus targets, and analyzing mutation hotspots and evolutionary patterns from large genomic datasets. I also develop automated workflows for structural analysis, interface characterization, and machine-learning-ready dataset generation. With a strong background in microbiology, biochemistry, and computational biology, I combine biological insight with computational methods to support drug discovery, protein engineering, and therapeutic peptide development. I can assist clients with protein structure prediction, docking studies, peptide/protein design, bioinformatics data analysis, and preparation of publication-quality results and reports. 1. Protein Structure Prediction & Modeling A. AlphaFold structure prediction B. Homology modeling C. Structure refinement (Rosetta / MD) D. Model validation (Ramachandran, MolProbity) 2. Protein–Protein / Protein–Peptide Docking A. Docking using HDOCK, HADDOCK, AutoDock, ClusPro B. Binding interface analysis C. Binding affinity prediction (PRODIGY, PISA) D. Visualization and report 3. Peptide / Protein Binder Design A. De novo binder design B. RFdiffusion / ProteinMPNN pipelines C. BindCraft D. Protenix E. Binder screening and ranking F. Interface optimization 4. Bioinformatics Data Analysis A. Sequence analysis (BLAST, MSA, phylogeny) B. Mutation analysis C. Comparative genomics D. Viral genome analysis 5. Viral Mutation & Evolution Analysis A. Mutation hotspot analysis B. Variant comparison C. Evolution analysis 6. Molecular Dynamics Simulation A. GROMACS simulations B. Protein stability analysis C. Binding stability analysis 7. Research Paper writing Data Analysis A. docking analysis B. MD plots C. structural visualization 8. Research project writing for funding I was awarded two projects from Govt. of India A. Indian Council of Medical Research (ICMR) awarded project related with VoCs of SARS-CoV-2 B. DBT awarded project related with Dengue virus

Subject Matter Expertise

• ☆ Molecular Modeling
• ☆ Molecular Docking
• ☆ Chemoinformatics
• ☆ Computational Biology
• ☆ Biochemistry
• ☆ Structural Biology
• ☆ Biotechnology & Bioengineering
• ☆ Bioinformatics
• ☆ Chemical Biology
• ☆ Drug Discovery
• ☆ High Throughput Screening (HTS)
• ☆ Drug Target Identification
• ☆ Hit-to-Lead & Lead Optimization
• ☆ Medicinal Chemistry
• ☆ Drug Design
• ☆ Structure-Activity Relationship (SAR) Studies
• ☆ Vaccine Development
• ☆ Precision Medicine

Services

• Writing
• Research
• Consulting
• Data & AI

Writing Clinical Trial Documentation, Medical Writing, Non-Medical Regulatory Writing, Technical Writing

Research Market Research, User Research, Meta-Research, Feasibility Study, Gap Analysis, Gray Literature Search, Scientific and Technical Research, Systematic Literature Review

Consulting Scientific and Technical Consulting

Data & AI Predictive Modeling

Work Experience

DBT-RA

Indian Institute of Chemical Biology

April 2025 - Present

ICMR-RA

CSIR - Indian Institute of Chemical Biology

July 2022 - July 2024

Associate professor

Techno India University

March 2022 - June 2022

Guest Faculty

West Bengal State University

July 2018 - February 2022

Research Associate

West Bengal State University

April 2018 - January 2022

Education

Post-doctoral Fellow

CSIR-Indian Institute of Chemical Biology

April 2022 - Present

Certifications

• Certification details not provided.

Publications

PREPRINT

Supriya Nath, Karan Chhetri, Aabid Hussain, Ankur Chaudhuri, Joydip Ghosh, Sondipon Chakraborty, Debarati Mukherjee, Mintu Karan, Bikramjit Raychaudhury, Krishnendu Acharya, et al. (2025). Lead optimization against drug-resistant Leishmania donovani infection: Semi-synthetic derivatives of ethyl linoleate isolated from Indian edible mushroom Meripilus giganteus .

Prateeka Borar, Tapan Biswas, Ankur Chaudhuri, Pallavi Rao T, Swasti Raychaudhuri, Tom Huxford, Saikat Chakrabarti, Gourisankar Ghosh, Smarajit Polley (2025). Dual-specific autophosphorylation of kinase IKK2 enables phosphorylation of substrate IκBα through a phosphoenzyme intermediate .

Prateeka Borar, Tapan Biswas, Ankur Chaudhuri, Pallavi T Rao, Swasti Raychaudhuri, Tom Huxford, Saikat Chakrabarti, Gourisankar Ghosh, Smarajit Polley (2025). Dual-specific autophosphorylation of kinase IKK2 enables phosphorylation of substrate IκBα through a phosphoenzyme intermediate .

Prateeka Borar, Tapan Biswas, Ankur Chaudhuri, Tom Huxford, Saikat Chakrabarti, Gourisankar Ghosh, Smarajit Polley (2024). Dual-specific autophosphorylation of kinase IKK2 enables phosphorylation of substrate IκBα through a phosphoenzyme intermediate .

Ankur Chaudhuri (2020). Comparative analysis of non structural protein 1 of SARS-CoV2 with SARS-CoV1 and MERS-CoV: An in silicostudy .

JOURNAL ARTICLE

Prateeka Borar, Tapan Biswas, Ankur Chaudhuri, Pallavi T Rao, Swasti Raychaudhuri, Tom Huxford, Saikat Chakrabarti, Gourisankar Ghosh, Smarajit Polley (2025). Dual-specific autophosphorylation of kinase IKK2 enables phosphorylation of substrate IκBα through a phosphoenzyme intermediate . eLife.

Prateeka Borar, Tapan Biswas, Ankur Chaudhuri, Pallavi T Rao, Swasti Raychaudhuri, Tom Huxford, Saikat Chakrabarti, Gourisankar Ghosh, Smarajit Polley (2025). Dual-specific autophosphorylation of kinase IKK2 enables phosphorylation of substrate IκBα through a phosphoenzyme intermediate . eLife.

Ankur Chaudhuri, Subhrangshu Das, Saikat Chakrabarti (2024). Mutational and evolutionary dynamics of non-structural and spike proteins from variants of concern (VOC) of SARS-CoV-2 in India . International Journal of Biological Macromolecules.

Ashikur Rahaman, Ankur Chaudhuri, Arnab Sarkar, Sibani Chakraborty, Shamee Bhattacharjee, Deba Prasad Mandal(2022). Eucalyptol targets PI3K/Akt/mTOR pathway to inhibit skin cancer metastasis . Carcinogenesis. 43. (6). p. 571--583. Oxford University Press ({OUP})

Ankur Chaudhuri(2021). Comparative analysis of non structural protein 1 of SARS-CoV2 with SARS-CoV1 and MERS-CoV: An in silico study . Journal of Molecular Structure. 1243. p. 130854. Elsevier {BV}

Debarati Mukherjee and Md Yousuf and Somaditya Dey and Sondipon Chakraborty and Ankur Chaudhuri and Vinay Kumar and Biswajyoti Sarkar and Supriya Nath and Aabid Hussain and Aritri Dutta and Tanushree Mishra and Biswajit Gopal Roy and Sushma Singh and Sibani Chakraborty and Susanta Adhikari and Chiranjib Pal(2020). Targeting the Trypanothione Reductase of Tissue-Residing Leishmania in Hosts’ Reticuloendothelial System: A Flexible Water-Soluble Ferrocenylquinoline-Based Preclinical Drug Candidate . Journal of Medicinal Chemistry. 63. (24). p. 15621--15638. American Chemical Society ({ACS})

Ankur Chaudhuri, Roishinique Johnson, Kuntol Rakshit, Andrea Bednářová, Kimberly Lackey, Sibani Sen Chakraborty, Natraj Krishnan, Anathbandhu Chaudhuri(2020). Exposure to Spectracide® causes behavioral deficits in Drosophila melanogaster: Insights from locomotor analysis and molecular modeling . Chemosphere. 248. p. 126037. Elsevier {BV}

Chaudhuri, A., Johnson, R., Rakshit, K., Bednářová, A., Lackey, K., Chakraborty, S.S., Krishnan, N., Chaudhuri, A.(2020). Exposure to Spectracide® causes behavioral deficits in Drosophila melanogaster: Insights from locomotor analysis and molecular modeling . Chemosphere. 248.

Yuthika Dholey, Ankur Chaudhuri, Sibani Sen Chakraborty(2019). An integrated in silico approach to understand protein–protein interactions: human meprin-β with fetuin-A . Journal of Biomolecular Structure and Dynamics. p. 1--13. Informa {UK} Limited

Ankur Chaudhuri, Nandagopal Hudait, Sibani Sen Chakraborty(2019). Pharmacophore modeling coupled with molecular dynamic simulation approach to identify new leads for meprin-β metalloprotease . Computational Biology and Chemistry. 80. p. 292--306. Elsevier {BV}

Niladri Biswas, Ankur Chaudhuri, Sibani Chakraborty, Chirantan Roy Choudhury(2019). Example of square planar copper(II) biuret complex: crystal structure, DNA and protein binding activity and molecular docking study . Inorganic and Nano-Metal Chemistry. 48. (10). p. 495--507. Informa {UK} Limited

Niladri Biswas, Sumit Khanra, Arnab Sarkar, Shamee Bhattacharjee, Deba Prasad Mandal, Ankur Chaudhuri, Sibani Chakraborty, Chirantan Roy Choudhury(2019). Cytotoxicity activity, in silico molecular docking, protein- and DNA-binding study of a new Ni(II) Schiff base complex . Journal of Coordination Chemistry. 71. (16-18). p. 2740--2766. Informa {UK} Limited

Chaudhuri, A., Biswas, S., Chakraborty, S.(2019). Exploring protein–protein intermolecular recognition between meprin-α and endogenous protease regulator cystatinC coupled with pharmacophore elucidation . Journal of Biomolecular Structure and Dynamics. 37. (2). p. 440-453.

Biswas, N., Saha, S., Khanra, S., Sarkar, A., Prasad Mandal, D., Bhattacharjee, S., Chaudhuri, A., Chakraborty, S., Roy Choudhury, C.(2019). Example of two novel thiocyanato bridged copper (II) complexes derived from substituted thiosemicarbazone ligand: structural elucidation, DNA/albumin binding, biological profile analysis, and molecular docking study . Journal of Biomolecular Structure and Dynamics. 37. (11). p. 2801-2822.

Chaudhuri, A., Hudait, N., Chakraborty, S.S.(2019). Pharmacophore modeling coupled with molecular dynamic simulation approach to identify new leads for meprin-β metalloprotease . Computational Biology and Chemistry. 80. p. 292-306.

Dholey, Y., Chaudhuri, A., Chakraborty, S.S.(2019). An integrated in silico approach to understand protein–protein interactions: human meprin-β with fetuin-A . Journal of Biomolecular Structure and Dynamics.

Sriparna Mukherjee, Nabonita Sengupta, Ankur Chaudhuri, Irshad Akbar, Noopur Singh, Sibani Chakraborty, Amol Ratnakar Suryawanshi, Arindam Bhattacharyya, Anirban Basu(2018). PLVAP and GKN3 Are Two Critical Host Cell Receptors Which Facilitate Japanese Encephalitis Virus Entry Into Neurons . Scientific Reports. 8. (1). Springer Science and Business Media {LLC}

Ankur Chaudhuri, Sibani Chakraborty(2018). Structure-activity Relationship of Astacin Metalloproteases: A Comparative Study Using EDTA . Current Enzyme Inhibition. 14. (2). p. 131--140. Bentham Science Publishers Ltd.

Ankur Chaudhuri, Sampa Biswas, Sibani Chakraborty(2018). Exploring protein–protein intermolecular recognition between meprin-α and endogenous protease regulator cystatinC coupled with pharmacophore elucidation . Journal of Biomolecular Structure and Dynamics. 37. (2). p. 440--453. Informa {UK} Limited

Chaudhuri, A., Chakraborty, S.(2018). Structure-activity relationship of astacin metalloproteases: A comparative study using EDTA . Current Enzyme Inhibition. 14. (2). p. 131-140.

Niladri Biswas, Sandeepta Saha, Sumit Khanra, Arnab Sarkar, Deba Prasad Mandal, Shamee Bhattacharjee, Ankur Chaudhuri, Sibani Chakraborty, Chirantan Roy Choudhury(2018). Example of two novel thiocyanato bridged copper (II) complexes derived from substituted thiosemicarbazone ligand: structural elucidation, DNA/albumin binding, biological profile analysis, and molecular docking study . Journal of Biomolecular Structure and Dynamics. 37. (11). p. 2801--2822. Informa {UK} Limited

Mukherjee, S., Sengupta, N., Chaudhuri, A., Akbar, I., Singh, N., Chakraborty, S., Suryawanshi, A.R., Bhattacharyya, A., Basu, A.(2018). PLVAP and GKN3 Are Two Critical Host Cell Receptors Which Facilitate Japanese Encephalitis Virus Entry Into Neurons . Scientific Reports. 8. (1).

Biswas, N., Khanra, S., Sarkar, A., Bhattacharjee, S., Prasad Mandal, D., Chaudhuri, A., Chakraborty, S., Roy Choudhury, C.(2018). Cytotoxicity activity, in silico molecular docking, protein- and DNA-binding study of a new Ni(II) Schiff base complex . Journal of Coordination Chemistry. 71. (16-18). p. 2740-2766.

Biswas, N., Chaudhuri, A., Chakraborty, S., Choudhury, C.R.(2018). Example of square planar copper(II) biuret complex: crystal structure, DNA and protein binding activity and molecular docking study . Inorganic and Nano-Metal Chemistry. 48. (10). p. 495-507.

Jyotirmay Maiti, Suman Biswas, Ankur Chaudhuri, Sandipan Chakraborty, Sibani Chakraborty, Ranjan Das(2017). Environment sensitive fluorescent analogue of biologically active oxazoles differentially recognizes human serum albumin and bovine serum albumin: Photophysical and molecular modeling studies . Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy. 175. p. 191--199. Elsevier {BV}

Maiti, J., Biswas, S., Chaudhuri, A., Chakraborty, S., Chakraborty, S., Das, R.(2017). Environment sensitive fluorescent analogue of biologically active oxazoles differentially recognizes human serum albumin and bovine serum albumin: Photophysical and molecular modeling studies . Spectrochimica Acta - Part A: Molecular and Biomolecular Spectroscopy. 175. p. 191-199.

Niladri Biswas, Sumit Khanra, Arnab Sarkar, Shamee Bhattacharjee, Deba Prasad Mandal, Ankur Chaudhuri, Sibani Chakraborty, Chirantan Roy Choudhury(2017). One new azido bridged dinuclear copper(ii) thiosemicarbazide complex: synthesis, DNA/protein binding, molecular docking study and cytotoxicity activity . New J. Chem. 41. (21). p. 12996--13011. Royal Society of Chemistry ({RSC})

Biswas, N., Khanra, S., Sarkar, A., Bhattacharjee, S., Prasad Mandal, D., Chaudhuri, A., Chakraborty, S., Roy Choudhury, C.(2017). One new azido bridged dinuclear copper(II) thiosemicarbazide complex: Synthesis, DNA/protein binding, molecular docking study and cytotoxicity activity . New Journal of Chemistry. 41. (21). p. 12996-13011.

Ankur Chaudhuri, Asim K. Bera, Indrani Sarkar, Sibani Chakraborty(2016). Insights from Analysis of Binding Sites of Human Meprins: Screening of Inhibitors by Molecular Dynamics Simulation Study . Combinatorial Chemistry & High Throughput Screening. 19. (3). p. 246--258. Bentham Science Publishers Ltd.

Suvadip Mallick, Aritri Dutta, Ankur Chaudhuri, Debasri Mukherjee, Somaditya Dey, Subhadra Halder, Joydip Ghosh, Debarati Mukherjee, Sirin Salma Sultana, Gunjan Biswas, et al.(2016). Successful Therapy of Murine Visceral Leishmaniasis with Astrakurkurone, a Triterpene Isolated from the Mushroom Astraeus hygrometricus, Involves the Induction of Protective Cell-Mediated Immunity and TLR9 . Antimicrobial Agents and Chemotherapy. 60. (5). p. 2696--2708. American Society for Microbiology

Mallick, S., Dutta, A., Chaudhuri, A., Mukherjee, D., Dey, S., Halder, S., Ghosh, J., Mukherjee, D., Sultana, S.S., Biswas, G., et al.(2016). Successful therapy of murine visceral leishmaniasis with astrakurkurone, a triterpene isolated from the Mushroom Astraeus hygrometricus, involves the induction of protective cell-mediated immunity and TLR9 . Antimicrobial Agents and Chemotherapy. 60. (5). p. 2696-2708.

Chaudhuri, A., Bera, A.K., Sarkar, I., Chakraborty, S.(2016). Insights from analysis of binding sites of human meprins: Screening of inhibitors by molecular dynamics simulation study . Combinatorial Chemistry and High Throughput Screening. 19. (3). p. 246-258.

Chaudhuri, A., Sarkar, I., Chakraborty, S.(2014). Comparative analysis of binding sites of human meprins with hydroxamic acid derivative by molecular dynamics simulation study . Journal of Biomolecular Structure and Dynamics. 32. (12). p. 1969-1978.

Ankur Chaudhuri, Indrani Sarkar, Sibani Chakraborty(2013). Comparative analysis of binding sites of human meprins with hydroxamic acid derivative by molecular dynamics simulation study . Journal of Biomolecular Structure and Dynamics. 32. (12). p. 1969--1978. Informa {UK} Limited

Isolation of a major host plant- terpenoid and its probable impact on the degenerative growth of female Indian lac insect, Kerrialacca (Kerr.) Vol 4, No 4, 1351- 1358, 2016. Journal of Entomology and Zoology Studies.

BOOK CHAPTER

Chakraborty, S., Bera, A.K., Chaudhuri, A., Sen, S.(2017). Metalloproteases and human diseases: The astacin family . Proteases in Human Diseases. p. 227-245.

Chakraborty, S., Chaudhuri, A., Bera, A.K.(2017). Role of BMP1/tolloid like proteases in bone morphogenesis and tissue remodeling . Proteases in Physiology and Pathology. p. 77-88.