Computational chemist

Vaisali Balasubramaniam

LinkedIn +1-206-***-**** ***********@*****.*** Redmond, Washington, 98052 Skills

• Molecular Docking Molecular Dynamics Simulation Gene Expression Profiling Nucleotide Sequence Analysis Complex conformational analysis Structure-based target design and evaluation

• Target design Homology modeling Protein primary and secondary structure characterization Protein sequence similarity comparison Pharmacokinetics and pharmacodynamics ADMETox prediction MMGBSA/PBSA analysis

• Bio-molecular networking Protein-protein interaction (PPI) Protein Drug Interaction (PDI) Free energy analysis Evolutionary compound library preparation

• Structure activity relationship (SAR) studies Ligand-based pharmacophore modeling Computational virtual screening Gene enrichment analysis Binding site assessment

Software Experience

•

• Schrodinger AutoDock Biovia Discovery Studio Material Studio CytoScape DataWarrior MOE NAMD GROMACS CHARMM OpenBabel Latex

• Agile Scrum Basic AI & ML Documentation Cloud Technologies AWS Azure GCP SQL BioInformatics Tools

• SNP Nexus- SIFT PolyPhen MethPrimer ProtParamtool SOPMA Prosite COSMIC

• BaCelLo SwissModel SAVES ADMETLab BLAST: Basic Local Alignment Search Tool Computed Atlas of Surface Topography of proteins (CASTp)

• ClinVar BioGRID Ensembl Variant Effect Predictor (VEP) ToppGene Expert Protein Analysis System (ExPASy) Translate tool Protein Structure Analysis tool (ProSA) CABS-flex

Databases Used

• Protein databank (RCSBPDB) Uniprot Ensembl Clinicaltrials.gov Open target Genecards The Comparative Toxicogenomics Database (CTD) PubMed PubChem GWAS catalogue

• Drugbank ChEMBL National Institutes of Health (NIH) Dr. Duke's database STRING The Cancer Genome Atlas (TCGA) National Center for Biotechnology Information (NCBI)

• The Human Metabolome Database (HMDB) ICGC KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway database The Expression Atlas Journal Publications

• B. Vaisali, Parvathy C. R, Hima Vyshnavi A. M, P. K Krishnan Namboori “Tumor Hypoxia Diagnosis’ using Deep CNN Learning strategy a theranostic pharmacogenomic approach”, International Journal of Prognostics and Health Management, 10, 2019: 007.

• B. Vaisali, P. K Krishnan Namboori “Tumor hypoxia mutation detection using deeplearning-a deep drug designing strategy”, International journal of scientific & technology research, 8, 2019.

• B. Vaisali, P. K Krishnan Namboori “Design and development of pharmacogenomic target models to study individual variation in drug action and side effects associated with anti-tumour hypoxic molecules”, Journal of Pharmacy And Bioallied Sciences, 13.4, 2021: 387-393.

• Pooja S, Bhagyalakshmi Nair, Vaisali B, Prashanth S, P K. Krishnan Namboori and Lekshmi R Nath. “Evaluation of Kaempferol as AKT dependent mTOR regulator via targeting FKBP-12 in Hepatocellular carcinoma: an in silico approach”, Letters in Drug Design & Discovery, 17.11, 2020: 1401 – 1408. Conference Publications

• Pooja S Srinidhi. P V, Akshayaa. S, B. Vaisali and P.K Krishnan Namboori. “DNA repair mutation detection using Deep learning strategy- A pharmacogenomic perspective”, Innovations in Power and Advanced Computing Technologies (i-PACT 2019), 2019.

• Anju Elizabath babu, Dr. Athira K.V, Vaisali. B and Dr. P K Krishnan Namboori “Therapeutic implications of ‘passiflora edulis’ extract towards depression-cardiovascular disorder- a pharmacogenomic approach”, International Conference on Recent Trends in Science, Engineering and Mathematics

(ICRTSEM 2020), 2020.

• Vaisali B, P. K Krishnan Namboori “Control of tumor hypoxia using phytochemicals”, Amrita pharmaceutical conference (APC2019), 2019. Papers Communicated

• B.Vaisali, P. K Krishnan Namboori, “The role of HIF1A in Silent Hypoxia of COVID patients: A Molecular Networking Perspective”.

• B. Vaisali, P. K Krishnan Namboori, “Population wise customized drug design strategy for Tumor hypoxia: A computational approach”. Experience Teaching associate Amrita University

India 09/18 – 03/21

• Computer-aided drug discovery for M.Pharm, Amrita School of Pharmacy

• Bioinformatics for M.Tech, Bio-medical engineering, Amrita school of engineering

• Computer-aided drug design and Pharmacoinformatics for M.Sc, Amrita school of Biotechnology Python RdKit NumPy Pandas PyTorch MatPlotLib Basic R SAS Research assistant

Amrita Molecular Modelling

and Research Lab

India

08/18 – 05/22

• Analyzed the efficiency of Passiflora edulis extract in controlling cardiovascular dysfunction caused by major depression disorder (MDD).

• Evaluated phytoconstituent Kaempferol for its potential to interact more favorably with Rapamycin target for the inhibition of mTORC1 in Hepatocellular carcinoma

Intern

BioPharma Solutions

India

07/21 – 08/22

• Investigated the kinase mutations, IGF1R and EGFR, and their Pharmacogenomic contributions.

• Supervised research projects for master's students and produced products for journals and conferences

•. Conducted training sessions on Computational drug discovery and development for Industrial candidates and researchers from various Institutions like NIT, VIT, IIT etc.

Education PhD in Computational Engineering

and Networking

Amrita University 9.38 2018- 2022

• Thesis: Design and Identification of Bio-Reductive and Pharmacogenomic P4 Anti-cancer drugs to control tumor hypoxia Masters in technology in

Biomedical Engineering

Amrita University 7.45 2016- 2018

• Thesis: Anti-hypoxia potentiation for anticancer drugs – a pharmacogenomic approach 7.44 Bachelor of Engineering in

Biomedical Engineering

Dr. N.G.P Institute of Technology 2012- 2016

• Thesis: Stand Alone Oxygen Analyzer

Certifications

• Cambridge Business English Certificate (BEC), Vintage Level

• Summer Internship at Research Centre Imarat (RCI) lab, Defence Research and Development Organization - DRDO, Ministry of Defence, Government of India.

Awards

• Honoured as a Distinguished Alumni from the batch of 2012-16 at Dr.NGP Institute of Technology

• Member of the Department Advisory Board (DAB), Biomedical Engineering at Dr.NGP Institute of Technology

• In collaboration with the career development center, delivered lectures and webinars on drug discovery in various biomedical forums. Hobbies

• Fabric Painting, Hand crafts

• Cooking

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