शोधकौशलम्
डॉक्टरल् शोधात् जैवसूचनाशास्त्रीयशुष्कप्रयोगशालाकौशल्यम्
Research Focus
Bridging computational and experimental cancer research — from AI-driven drug discovery pipelines (SieveAI) and molecular dynamics simulations (coarse-grain MARTINI for membranes, atomistic CHARMM36 for proteins) to cell-based validation assays. Specializing in protein-ligand docking, protein-protein interactions, structure prediction (AlphaFold2, SwissModel, I-TASSER, Rosetta), MMPBSA binding free energy, and exosomal miRNA analysis. Automated workflows from PDB preparation through docking, MD, and result extraction — reducing months of manual work to hours.
जैवसूचनाशास्त्रम् सङ्गणकीयजीवविज्ञानम् च
सङ्गणकीयऔषधआвиष्कारे, आण्विकगतिकज्ञाने, अनुवंशिकीयदत्तांशविश्लेषणे, पाइपलाइनविकासे च विस्तृतानुभवः। बहुओपन्सोर्सोपकरणानि निर्मितानि प्रकशितानि च।
Protein-Ligand Docking
औषध-लक्ष्य-बन्धनस्य पूर्वानुमानाय आण्विक-बन्धनम् (Molecular docking) — AutoDock Vina, SwissDock, तथा PATCHDOCK इत्येतषां उपयोगं कृत्वा सहस्राणि यौगिकानि परीक्षितवान् तथा च कर्क-लक्ष्याणाम् (यथा CXCL9/10 तथा SKP2) कृते सम्भाव्य-चिकित्सा-प्रत्याशिनः चिह्नितवान्।
- AutoDock Vina — batch protein-ligand docking (1,950+ complexes)
- Protein-protein docking — HADDOCK, pyDockWeb, PatchDock, ClusPro
- Protein-protein interaction — CD151 cholesterol binding, TWIST1-OGT/OGase, survivin-caspase complexes
- Protein-complex docking — ternary systems (survivin + OBPHA + caspase-3/7/9)
- Peptide-peptide docking — TWIST1-OGT/OGase interactions
- Ligand preparation — AutoDockTools, OpenBabel, PubChemPy 3D SDF, SwissParam topology
- Post-docking analysis — ChimeraX H-bond/contact automation, PLIP, PRODIGY
- Cancer targets — CXCL9/10, SKP2, PPARγ, BRCA1, GRK2, CD63-VEGF, p53, Bcl-2, PDGFR
- DrugBank & FDA drug screening — 8K+ conformers, immune checkpoints (CD28, TIGIT, PD-1)
Molecular Dynamics Simulation
प्रोटिन-स्थायित्वस्य, लिगण्ड-बन्धन-गत्याः, तथा नैनोसेकण्ड-समयमानयोः संरचनात्मक-परिवर्तनानां अध्ययनाय GROMACS तथा WebGro इत्येताभ्यां सह आण्विक-गतिकी-सिमुलेशनम् — बन्धन-भविष्यवाणीनां प्रमाणीकरणाय अतिमहत्त्वपूर्णम्।
- GROMACS — full MD pipeline (pdb2gmx, editconf, solvate, genion, grompp, mdrun) up to 300ns
- Coarse-grain MD — MARTINI force field for lipid–ligand membrane systems (Lapatinib/DMPC/cholesterol)
- Atomistic MD — CHARMM36 force field for protein–ligand complexes; AMBER/CHARMM36 for membranes
- CHARMM-GUI membrane builder — DMPC, DOPC, DOPS, cholesterol bilayer preparation & embedding
- Desmond MD — local installation & WebGro cloud submission, trajectory analysis
- MMPBSA — gmx_MMPBSA binding free energy calculations (300ns trajectories)
- RMSD / RMSF / Rg / SASA / DSSP — protein stability, secondary structure, solvent analysis
- SwissParam & PRODRG — ligand topology/ITP generation for GROMACS CHARMM force field
- GMXvg — published GROMACS visualization & plotting tool
Protein Structure Prediction
AlphaFold2, SwissModel, I-TASSER, Rosetta च — प्रोटीन-संरचनापूर्वानुमानम्, म्यूटेंट-मॉडलिंग, ट्रांसमेम्ब्रेन-पूर्वानुमानम्, प्रोटीन-तुलना (RMSD) च।
- AlphaFold2 — protein structure prediction via Google Colab (IL27 complex, CD151, CD63)
- SwissModel — homology modeling + QA (quality assessment) for mutant proteins (3EQH-ALA76GLY)
- I-TASSER — 3D structure prediction for membrane & transmembrane proteins
- Rosetta — protein structure prediction and design
- Avogadro — energy minimization of small molecules & ligand 3D optimization
- Protein structure comparison — ChimeraX Matchmaker (RMSD, primary/secondary/tertiary structure)
- PDB processing — UniProt mapping, PDBTM for transmembrane, chain cleanup, HETATM separation
- O-GlcNAcylation site prediction — YinOYang, dbPTM, PhosphoSitePlus for GRK2 sites (S20, S121, S370)
- Membrane protein resources — PDBTM, TMDock, MemProtMD, PerMemDB, MBPpred, ProteinTools
अनुवंशिकीयट्रान्सक्रिप्टोमिक्स् च
GEOParse इत्यनेन सह GEO-दत्तांशसमूहानां विश्लेषणं, RNA-Seq तथा ncRNA-अभिव्यक्ति-रूपाणां अध्ययनं, कर्करोगे विसंगत-जीन्-नियामक-जालस्य च परिज्ञानाय मार्ग-संवर्धनं GO-टीकाकरणं च।
- GEO dataset mining — GEOParse querying, GDS database search, sample/platform/series filtering (GSE15852, GSE73002, GSE77348)
- Differential gene expression — PyDGE framework, MCF7 vs MCF10A, normal vs tumor expression analysis
- TCGA cancer genomics — GDC portal data download (gdc-client), TCGA-BRCA miRNA-seq, TNBC cohort filtering, sample type codes
- miRNA database consolidation — miRBase (2,693 mature), ExoCarta, EVmiRNA, miRCancer cross-referencing & Venn analysis
- miRNA target prediction — TargetScan, miRDB, DIANA, miRWalk, miRTarBase validated targets
- Exosomal miRNA analysis — miR-34a, miR-10b, miR-21, miR-9; ExoLoger prediction database
- ncRNA analysis — lncRNA, circRNA, siRNA, piRNA; RNAComposer, UNAFold, MXfold2 for 3D structure
- Pathway & network analysis — KEGG (KEGGScape), WikiPathways, Biocarta, STRING interaction networks, FunRich enrichment
- NCBI/Entrez queries — PubMed search, GDS metadata extraction, Gene database cross-referencing
- Cancer gene resources — IntOGen (BRCA driver genes), cBioPortal, OncoKB, COSMIC, CancerES (IIITD)
- PTM databases — dbPTM, PhosphoSitePlus, O-GlcNAc (oglcnac.mcw.edu), VerSeDa
Drug Discovery Pipeline
SieveAI इति स्वचालित-औषध-अन्वेषण-पाइपलाइनं निर्मितवान् यत् समूहेषु परीक्षणं, बन्धनं, मूल्याङ्कनं च सञ्चालयति — yeन मासानां हस्तश्रमः होरासु परिवर्तितः। Zenodo DOI इत्यनेन सह प्रकाशितं तथा च मुक्तस्रोतरूपेण प्रदत्तम्।
- SieveAI — end-to-end automated drug discovery pipeline: PDB prep → ligand prep → docking → result extraction → filtering
- Bulk docking automation — 576 cancer genes × 5 ligands = 1,950+ complexes; 9,127 Vina results parsed & filtered
- DrugBank high-throughput screening — GRK2 (3,894 complexes ~60h compute), immune checkpoints (8K+ conformers)
- Automated PDB processing — Python scripts for ATOM/HETATM separation, chain cleanup, grid box calculation, PDBQT conversion
- Bulk ligand preparation — AutoDockTools prepare_ligand4.py, OpenBabel batch PDB→SDF→SMILES, PubChemPy 3D SDF download
- Automated result extraction — Vina score parsing, ChimeraX H-bond/contact command generation, best-pose selection by residue interaction
- SwissADME bulk — automated SMILES submission, ADME radar scraping, property aggregation across 88+ compounds
- MDDAA-Mate — docking analysis assistant for validation & cross-checking against published results
Bioinformatics Data Mining
PubMed-साहित्य-खननाय विशिष्ट-जाल-अपमार्जन-तन्त्राणि (scraping frameworks) विकसितानि, येन सहस्राणि संक्षेपेभ्यः वैज्ञानिक-जाल-स्रोतोभ्यः च व्यवस्थित-समीक्षाभ्यः संरचित-दत्तांशः निष्कासितः।
- PubMed querying & full-text mining — biopubmed CLI tool
- Scientific literature meta-analysis — systematic review automation
- Web scraping framework (Scrapper) — GEO, DrugBank, UniProt, ZINC, PubChem data extraction
- API integration — PubChemPy 3D SDF download, RCSB ligand fetch, KEGG KGML pathway
- miR literature curation — exosomal miR article classification & filtering
Biomedical Text Mining
अनुसन्धान-संक्षेपेभ्यः नामाङ्कित-सत्ता-प्रत्यभिज्ञानस्य (NER) कीवर्ड-सह-उत्पत्ति-विश्लेषणस्य च कृते जैववैद्यकीय-NLP — विशालग्रन्थेभ्यः स्वचालित-साहित्य-संश्लेषणं परिकल्पना-निर्माणं च सक्षमं करोति।
- Biomedical NLP — keyword co-occurrence, named entity recognition, spaCy POS/lemma extraction
- Text mining — structured extraction from thousands of PubMed results
- Exosomal miR prediction — NLP + clustering for unvalidated miR identification
- Regex-based data extraction — SMILES conversion, gene ID mapping, UniProt batch queries
Machine Learning for Bioinformatics
SMILES/SMARTS-अङ्गुलीमुद्रा-उपयोगेन मेटाबोलाइट-वर्गीकरणाय गम्भीर-नाडी-जालानि (DNN), यत् रैंडम फ़ॉरेस्ट, SVM, तथा XGBoost प्रतिरूपैः दृढ-मूल्याङ्कनेन (AUC, F1, MCC) सह पूरितम् अस्ति।
- DNN for metabolite classification — SMILES/SMARTS fingerprinting
- Random Forest / SVM / XGBoost — cancer gene expression classifiers
- Model evaluation — AUC, F1, MCC metrics
- PCA & one-hot encoding — miRNA sequence analysis & dimensionality reduction
Research Software & Tools
सङ्गणकीय-सॉफ्टवेयर्-उपकरणानि रचितवान् प्रकाशितवान् च — SieveAI (औषध-अन्वेषणम्), ExoLoger (एक्सोसोमल miRNA-पूर्वानुमानम्), GMXvg (GROMACS दृश्यावलोकनम्, Zenodo DOI), miRvim (3D miRNA-संरचना-दत्तांशकोशः), तथा UtilityLib (पायथन्-उपयोगिताः, Zenodo DOI)।
- SieveAI — automated drug discovery pipeline
- ExoLoger — exosomal miRNA prediction database
- GMXvg — GROMACS visualization & plotting
- miRVim — 3D miRNA structure database
- UtilityLib — Python utility library (PyPI v2.21.4)
- TheBiomics — Drupal education platform (17K+ users)
- biopubmed — PubMed scraping & processing CLI
- Scrapper — scientific web data extraction framework
- MDDAA-Mate — docking analysis assistant & validation tool
- PyDGE — differential gene expression analysis framework
शुष्कप्रयोगशाला प्रयोगात्मकजीवविज्ञानम् च
कर्चरजीवविज्ञाने औषधविज्ञाने च कोशिकासंवर्धने, आण्विकजीवविज्ञानपरीक्षासु, प्रोटीनकार्ये, काचान्तर्गतअध्ययनेषु च प्रायोगिकानुभवः।
कोशिकासंवर्धनम् अनुरक्षणम् च
कठोर-पूतिबाध-रहित (aseptic) तन्त्रेण स्तनधारि-कोशिका-रेखाणां (MG63, MCF7, MM231, LN229) परिरक्षणं कृतवान् — यस्मिन् शीत-परिरक्षणं, उप-संवर्धनम्, प्रेषणम्, ट्रान्सफेक्शन-अनुकूलनम्, माइकोप्लाज्मा-परीक्षणं च अन्तर्भवति।
- Mammalian cell culture — MG63, MCF7, MDA-MB-231, LN229, A549
- Animal cell culture — aseptic technique, laminar flow hood, CO₂ incubator operation
- Cell line maintenance — sub-culturing, passaging, cell counting (hemocytometer), viability assessment
- Cryopreservation — liquid nitrogen storage, freeze-thaw recovery, DMSO cryoprotectant protocols
- Transfection optimization — lipid-based and electroporation methods
- Mycoplasma testing & contamination control
- Cancer cell to adipocyte differentiation (PPARγ agonist studies)
प्रोटीनाकलनम् परीक्षाः च
प्रोटिन-मात्रा-निर्धारणं (Bradford, BCA), SDS-PAGE तथा वेस्टर्न ब्लॉटिंग् इत्येतेषां माध्यमेन पृथक्करणं प्रत्यभिज्ञानं च, तथा च ELISA तथा सह-प्रतिरक्षी-अवक्षेपणैः (co-immunoprecipitation) सह परस्परक्रिया-अध्ययनम्।
- Protein estimation — Bradford & BCA assay (standard curve preparation)
- SDS-PAGE & Western blotting — Vimentin, target protein detection
- Wet blot transfer — tank transfer system for protein membrane immobilization
- Dry blot transfer — semi-dry transfer for rapid protein detection
- Gel Doc imaging — documentation & analysis of electrophoresis gels and blots
- ELISA — quantitative protein interaction analysis
- Co-immunoprecipitation — protein-protein interaction validation
- A280 protein quantification
आण्विकजीवविज्ञानतन्त्राणि
मानक-आण्विक-जीवविज्ञान-कार्यप्रवाहः — TRIzol इत्यनेन सह RNA-निष्कर्षणम्, cDNA-संश्लेषणम्, जीन्-अभिव्यक्तये qPCR/RT-PCR, एगरोज़-जैल-वैद्युतकणसञ्चलनम्, तथा क्लोनिङ्ग्-प्राइमर-रूपरेखाभिः सह प्लास्मिड-पृथक्करणम्।
- RNA extraction — TRIzol method
- cDNA synthesis & gene expression analysis
- RT-PCR & qPCR — reverse transcription, quantitative expression profiling
- Agarose gel electrophoresis — nucleic acid separation & Gel Doc visualization
- Plasmid isolation, cloning & primer design
- Competent cell transformation
काचान्तर्गतअध्ययनानि
औषध-परीक्षणाय कोशिका-आधारित-परीक्षणाः — MTT/XTT व्यवहार्यता, वसा-निर्माणं, व्रण-निवारण-प्रवासनं, आक्रमण-परीक्षाः, एपोप्टोसिस-प्रत्यभिज्ञानं (Annexin V), तथा औषध-संयोजन-परस्परप्रवाहः (CI सूचकाङ्कः)।
- MTT & XTT viability assays — dose-response drug screening, IC₅₀ determination
- Colony formation assay — clonogenic survival quantification
- Wound healing migration assay — scratch assay for cell motility
- Invasion assays — transwell migration & Matrigel invasion
- Apoptosis detection — Annexin V / PI staining
- Drug combination synergy — Combination Index (CI) method
- Cancer cell vs normal cell comparative studies
Instruments & Equipment
कोशिका-संवर्धन-आणविकजीवविज्ञान-प्रोटीनविश्लेषण-वर्णलेखन-कार्यप्रवाहायाः प्रयोगशाला-उपकरणानि उपस्कराः च।
- Gel Doc system — gel documentation, blot imaging & densitometry analysis
- CO₂ incubator — mammalian cell culture environment control
- Laminar flow hood — aseptic technique & sterile workspace
- Microplate reader — absorbance/fluorescence for MTT, Bradford, BCA, ELISA
- Centrifuge — refrigerated & bench-top, cell pelleting, fractionation
- PCR thermal cycler — RT-PCR & qPCR amplification
- Electrophoresis apparatus — vertical SDS-PAGE & horizontal agarose gel
- Wet & dry blot transfer systems — tank & semi-dry protein transfer
- HPLC system — basic operation & familiarization with analytical chromatography devices
वर्णलेखनम् HPLC च
यौगिक-प्रत्यभिज्ञानाय शुद्धता-विश्लेषणाय च HPLC-सञ्चालनं पद्धति-विकासः च, सहैव स्तम्भ-तनुस्तर-वर्णलेखन-तन्त्राणि (column and thin-layer chromatography)।
- Chromatography basics — column, thin-layer & basic HPLC familiarization
- Column & thin-layer chromatography
- Standard curve & peak integration