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Hire Dr. Dakshinamurthy S.

United Arab Emirates

USD 75 /hr

Computational chemist with strong experience (Industry/Academia) in drug design, serving 17+years in Bioinformatics

Profile Summary

- Practicing structural bioinformatics for more than 17 years with 7+ years post Ph.D. exp. - Worked on identifying the crucial determinants of drug binding selectivity for highly similar proteins with profound experience in Molecular dynamics, QSAR, and Pharmacophore. - Hands-on working experience in different AI/ML methods (like RL(reinforcement learning), generative models, RNN-LSTM) in drug design and cheminformatics projects. - Excellent communication and networking skills, leadership, scientific writing and teamwork skills proved in multifaceted projects and various computational chemistry publications. - Reach me for 1 to 1 consultation and professional training on the broad areas of structural bioinformatics.

Subject Matter Expertise

• ☆ Catalysis
• ☆ Chemoinformatics
• ☆ Computational Chemistry
• ☆ Molecular Biology
• ☆ Next Generation Sequencing (NGS)
• ☆ Data Analysis
• ☆ Machine Learning
• ☆ Bioinformatics
• ☆ Structural Bioinformatics
• ☆ Personal Training
• ☆ Drug Discovery
• ☆ High Throughput Screening (HTS)
• ☆ Drug Target Identification
• ☆ Hit-to-Lead & Lead Optimization
• ☆ Drug Design
• ☆ Combinatorial Chemistry
• ☆ Structure-Activity Relationship (SAR) Studies
• ☆ Drug Development
• ☆ Small Molecule Drug Development
• ☆ Preclinical ADME/PK/PD

Services

• Writing
• Research
• Consulting
• Data & AI
• Product Development

Writing Medical Writing, Technical Writing, Copywriting, General Proofreading & Editing

Research User Research, Scientific and Technical Research, Systematic Literature Review, Secondary Data Collection

Consulting Scientific and Technical Consulting

Data & AI Data Visualization, Text Mining & Analytics, Data Mining, Data Cleaning, Data Processing, Data Insights

Product Development Concept Development

Work Experience

Discovery Scientist

Cresset Discovery, UK

March 2023 - October 2023

Senior Principal Scientist

PharmCADD

July 2020 - February 2023

Education

PhD

SASTRA Deemed University - India

April 2010 - March 2016

M.Tech Bioinformatics

SASTRA Deemed University - India

April 2004 - May 2006

Certifications

• Career Essentials in Generative AI by Microsoft and LinkedIn

  Microsoft

  https://www.linkedin.com/learning/certificates/3f3a2f60eab352d70226fed1faad120186aaedc6f30b030b4a6e2f46e53646a8?accountId=54550724&u=54550724&success=true&authUUID=wFzHDSzxT0+g/O4eyo5ISA==

  August 2023 - Present

• Complete Python Developer in 2023: Zero to Mastery

  udemy

  https://www.udemy.com/certificate/UC-0b9b7a03-7442-4b81-94db-ba4465970c0f/

  September 2022 - Present

Publications

JOURNAL ARTICLE

Dakshinamurthy Sivakumar, Seong Hun Jang, Sathish Kumar Mudedla, Jaehan Choi, Sungmin Lee, Minjun Jeon, Suneel Kumar Bvs, Jinha Hwang, Minsung Kang, Eun Gyeong Shin, et al.(2022). PCW-A1001, AI-assisted de novo design approach to design a selective inhibitor for FLT-3(D835Y) in acute myeloid leukemia . Frontiers in Molecular Biosciences. 9. Frontiers Media {SA}

Dakshinamurthy Sivakumar, Sangwook Wu (2022). Classical and Machine Learning Methods for Protein - Ligand Binding Free Energy Estimation . Current Drug Metabolism.

Dakshinamurthy Sivakumar, Sathishkumar Mudedla, Seonghun Jang, Hyunjun Kim, Hyunjin Park, Yonwon Choi, Joongyo Oh, Sangwook Wu(2021). Computational Study on Selective PDE9 Inhibitors on PDE9-Mg/Mg, PDE9-Zn/Mg, and PDE9-Zn/Zn Systems . Biomolecules. 11. (5). p. 709. {MDPI} {AG}

Dakshinamurthy Sivakumar, Sathishkumar Mudedla, Seonghun Jang, Hyunjun Kim, Hyunjin Park, Yonwon Choi, Joongyo Oh, Sangwook Wu (2021). Computational Study on Selective PDE9 Inhibitors on PDE9-Mg/Mg, PDE9-Zn/Mg, and PDE9-Zn/Zn Systems . Biomolecules.

Dakshinamurthy Sivakumar, Matthias Stein (2021). Binding of SARS-CoV Covalent Non-Covalent Inhibitors to the SARS-CoV-2 Papain-Like Protease and Ovarian Tumor Domain Deubiquitinases . Biomolecules.

Dakshinamurthy Sivakumar, Vikash Kumar, Michael Naumann, Matthias Stein(2020). Activation and selectivity of OTUB-1 and OTUB-2 deubiquitinylases . Journal of Biological Chemistry. 295. (20). p. 6972--6982. Elsevier {BV}

(2020). Activation and selectivity of OTUB-1 and OTUB-2 deubiquitinylases . Journal of Biological Chemistry.

(2019). NADH oxidase from Lactobacillus reuteri: A versatile enzyme for oxidized cofactor regeneration . International Journal of Biological Macromolecules.

(2018). Insights into Cell-Free Conversion of CO2 to Chemicals by a Multienzyme Cascade Reaction . ACS Catalysis.

Dakshinamurthy Sivakumar, Vinoth Prasanna Gunasekaran, Kumari Nishi, Thirunavukkarasu Sivaraman, Ganeshan Mathan(2018). Identification of 2,4-dihydroxy-5-pyrimidinyl imidothiocarbomate as a novel inhibitor to Y box binding protein-1 (YB-1) and its therapeutic actions against breast cancer . European Journal of Pharmaceutical Sciences. 116. p. 2--14. Elsevier {BV}

Zhang, L., Singh, R., Sivakumar, D., Guo, Z., Li, J., Chen, F., He, Y., Guan, X., Kang, Y.C., Lee, J.-K.(2018). An artificial synthetic pathway for acetoin, 2,3-butanediol, and 2-butanol production from ethanol using cell free multi-enzyme catalysis . Green Chemistry. 20. (1). p. 230-242.

Dakshinamurthy Sivakumar, Thirunavukkarasu Sivaraman(2016). A Review on Structures and Functions of Bcl-2 Family Proteins from Homo sapiens . Protein & Peptide Letters. 23. (10). p. 932--941. Bentham Science Publishers Ltd.

Dakshinamurthy Sivakumar, SASTRA University, India, Thirunavukkarasu Sivaraman(2016). Crucial Residues Modulating Interface of hBcl-B - hBaxBH3 Heterodimer as Probed by Computational Methods . Brazilian Archives of Biology and Technology. 59. (0). {FapUNIFESP} ({SciELO})

Sivakumar, D., Surapaneni, K.M., Prabu, P.C., Hari, N., Thiruvasagam, P., Rajasekaran, M., Sivaraman, T.(2016). Evaluation of the anticancer properties of the predicted hBaxBH3-mimetic compound 2-hydroxy-3,5-dinitrobenzamide in a mammary carcinogenesis-induced rat model . RSC Advances. 6. (4). p. 2854-2869.

Sivakumar, D., Hari, N., Sivaraman, T.(2014). Computational analyses on delineating specificity of 2-hydroxy-3,5-dinitrobenzamide, a BH3-mimetic, towards anti-apoptotic proteins . Bangladesh Journal of Pharmacology. 9. (3). p. 307-311.

Anthony, J., Rangamaran, V.R., Gopal, D., Shivasankarasubbiah, K.T., Thilagam, M.L.J., Peter Dhassiah, M., Padinjattayil, D.S.M., Valsalan, V.K.N., Manambrakat, V., Dakshinamurthy, S., et al.(2014). Ultraviolet and 5′Fluorodeoxyuridine Induced Random Mutagenesis in Chlorella vulgaris and Its Impact on Fatty Acid Profile: A New Insight on Lipid-Metabolizing Genes and Structural Characterization of Related Proteins . Marine Biotechnology. 17. (1). p. 66-80.

Sivakumar, D., Lahiri, C., Chakravortty, D.(2013). Computational studies on histidine kinase protein BaeS to target multidrug-resistant Salmonella . Medicinal Chemistry Research. 22. (4). p. 1804-1811.

Sivakumar, D., Gorai, B., Sivaraman, T.(2013). Screening efficient BH3-mimetics to hBcl-B by means of peptidodynmimetic method . Molecular BioSystems. 9. (4). p. 700-712.

Sivakumar, D., Richa, T., Rajesh, S.S., Gorai, B., Sivaraman, T.(2012). In silico methods for designing antagonists to anti-apoptotic members of Bcl-2 family proteins . Mini-Reviews in Medicinal Chemistry. 12. (11). p. 1144-1153.

Dakshinamurthy Sivakumar, Thirunavukkarasu Sivaraman(2011). In silico Designing and Screening of Lead Compounds to NS5-Methyltransferase of Dengue Viruses . Medicinal Chemistry. 7. (6). p. 655--662. Bentham Science Publishers Ltd.

Dakshinamurthy Sivakumar, Abhishek A. Singh, Pallavi Somvanshi(2011). Cataloguing functionally relevant polymorphisms in gene DNA ligase I: a computational approach . 3 Biotech. 1. (1). p. 47--56. Springer Nature

Sivakumar, D., Sivaraman, T.(2011). In silico designing and screening of lead compounds to NS5- methyltransferase of dengue viruses . Medicinal Chemistry. 7. (6). p. 655-662.

Sivakumar, D., Aashis, R., Sivaraman, T.(2011). In silico rationalization for the differential bioavailability of ABT-737 and ABT-263 that antagonise the anti-apoptotic proteins . Journal of Pharmaceutical Sciences and Research. 3. (4). p. 1141-1145.

CONFERENCE PAPER

Sivakumar, D., Sivaraman, T.(2012). Designing of de novo dual inhibitors for Bcl-XL and Mcl-1 of Bcl2-family proteins by computational methods . IEEE-International Conference on Advances in Engineering, Science and Management, ICAESM-2012. p. 174-178.