Dr. Ved Vrat Verma

Associate Professor & Coordinator, Department of Biotechnology

School of Engineering and Technology, Noida International University

Qualification: Ph. D. (Biophysics), M. Tech (Bioinformatics), B. Tech (Biotechnology)

Area of Specialization: Computational Biology specialized in Structural Bioinformatics and Drug Designing

Experience (Research Experience):

Post-Ph. D experience: 5 Years

Pre-Ph. D. research experience: 6 Years

RESEARCH INTEREST

  • Breast Cancer
  • Identifying the deleterious effect of missense SNPs using various tools and algorithms.
  • Anti-microbial drug-resistant
  • Species-specific and Computer-aided drug designing (CADD).
  • Next Generation Sequencing
  • Calculations of thermodynamic parameters and protein folding analysis by using MD simulations.
  • Three-dimensional structure prediction of protein and biological macromolecules.
  • Annotation of structural and functional features in biological macromolecules.
  • Functional divergence & Amino Acid Network (AAN) analysis of proteins.
  • Structural and functional annotations of proteomics and genomics data using bioinformatics tools.
  • Understanding the biological macromolecular interactions (Protein-Protein/Protein-Drug/Protein-DNA/DNA-DNA) using atomistic simulations.

PUBLICATIONS

Total Publications: 12, h-index: 8, i-10-index: 6, Cumulative impact Factor: 47.469, Total Citation: 182

GoogleScholar: https://scholar.google.com/citations?user=V71EaAEAAAAJ&hl=en&oi=ao

List of publications in peered reviewed journals

  1. Verma VV , Bhargava L, Sajid M, Kumar A, Singh H, Bharadwaj M. Structure-based study to identify alkaloids as promising cytochrome P450 (CYP1A1) inhibitors: An in-silico approach using virtual screening, molecular dynamic simulations, and binding free energy calculation. J Cell Biochem. Jun 28, 2022;1-18. doi: 10.1002/jcb.30302. ( IF: 4.48 )
  2. Gautam H # , Verma VV # , Husain SA and Bharadwaj M. Forecasting most deleterious nsSNPs in human TLR9 gene and their cumulative impact on structural and functional features of respective protein: An analytical study using in-silico approaches. Systems biology in reproductive medicine. https://doi.org/10.1080/19396368.2022.2148837. ( IF: 3.06 ). #: Authors contributed equally.
  3. Sahu RK, Verma VV , Kumar A, Tandon S, Das BC, Hedau ST. In-silico prediction and interaction of resveratrol on methyl-CpG binding proteins by molecular docking and MD simulations study. RSC Adv. 2022 Apr 13;12(18):11493-11504. (IF: 4.036)
  4. Kaushik V, Verma VV , Goel M. Functional Divergence and comparative in-silico study of Cas4 proteins of DUF83 class. Journal of Molecular Recognition 2017 . DOI: 10.1002/jmr.2694. (IF: 2.89)
  5. Kashyap A, Rani Gupta1, Sharma R, Verma VV , Gupta S and Pradeep Goyal. New Delhi Metallo Beta-Lactamase: Menace and its Challenges. J Mol Genet Med 2017, 11:4. (Impact Score: 1.96)
  6. Syal P, Verma VV , Gupta R. Targeted mutations and MD simulations of a methanol-stable lipaseYLIP9 from Yarrowia lipolytica MSR80 to develop a biodiesel enzyme. International Journal of Biological Macromolecules 2017 , 104: 78–88. (IF: 8.025)
  7. Singh AK, Chauhan SS, Singh SK, Verma VV , Singh A, Arya RK, Maheshwari S, Akhtar MS, Sarkar J, Rangnekar VM, Chauhan PM, Datta D. Dual targeting of MDM2 with a novel small-molecule inhibitor overcomes TRAIL resistance in cancer. Carcinogenesis 2016 , 1-14. doi:10.1093/carcin/bgw088. (IF: 4.741)
  8. Singh Y, Gupta N, Verma VV , Goel M, Gupta R. Selective disruption of disulphide bonds lowered activation energy and improved catalytic efficiency in TALipB from Trichosporon asahii MSR54: MD simulations revealed flexible lid and extended substrate binding area in the mutant. Biochem Biophys Res Commun 2016 , 25; 472(1):223-30. (IF: 3.32) .
  9. Verma VV , Gupta R, Goel M. Phylogenetic and evolutionary analysis of functional divergence among Gamma glutamyl transpeptidase (GGT) subfamilies. Biology Direct . 2015 , 10:49. doi: 10.1186/s13062-015-0080-7. (IF: 7.173) .
  10. Sharma R, Verma VV , Gupta R. Functional characterization of an extracellular keratinolytic protease, Ker AP from Pseudomonas aeruginosa KS-1: A putative aminopeptidase with PA domain. J Mol Catal B Enzym 2013 , 91: 8-16. (IF: 2.269) .
  11. Rajput R, Verma VV , Chaudhary V, Gupta R. A hydrolytic c-glutamyl transpeptidase from thermo-acidophilic archaeon Picrophilus torridus : binding pocket mutagenesis and transpeptidation. Extremophiles 2013 , 17:29-41. (IF: 2.395) .
  12. Kumari A, Verma VV , Gupta R. Comparative biochemical characterization and in silico analysis of novel lipases Lip11 and Lip12 with Lip2 from Yarrowia lipolytica . World J Microbiol Biotechnol 2012 , 28:3103-3111. (IF: 3.12)

AWARDS and HONORS

  • ICMR-Research Associate, BMI/II(27)/2020, 14 Jan 2021 to 17/08/2023

Indian Council of Medical Research-Research Associate (ICMR-RA)

Title of project: Identification of molecular landscape in Familial/Sporadic breast cancer

  • ICMR-PDF, 3/1/3/PDF (17)/2017-HRD, 27 March 2018

o Indian Council of Medical Research-Post Doctoral Fellowship (ICMR-PDF), 2018-2020, Monthly emolument Rs. 65000.00 + Rs. 300000.00 yearly as contingent grant (Total Grant for two years: Rs. 21,60000.00) . It was awarded through peered review of the project proposal followed by a personal discussion with the scientific committee of ICMR.

o Topic: “Alkaloids as augmented clinical inhibitors against human threat NDM-1: a fight against fate of multi drug resistant”.

  • ICMR-SRF, ISRM/11(09)/2017, 27 March 2018

o Indian Council of Medical Research-Senior Research Fellowship (ICMR-SRF) 2018-2020

o Topic: “A novel in-silico approach for drug design against pathogenic gamma glutamyltranspeptidase(GGT) proteins: employing functional divergence sites for generating species-specific inhibitors”

  • Abstract accepted for ICBCBBE-2017

o ICBCBBE-2017: 19th International Conference on Bioinformatics, Computational Biology and Biomedical Engineering, held at Paris, France, during February, 23-24, 2017.

o Topic: “Role of Functional Divergence in Specific Inhibitor Design: Using γ- Glutamyltranspeptidase (GGT) as a Model Protein”

  • ICMR-SRF, BIC/11(11)/2013, 01 Feb 2014-31 Jan 2018

o Indian Council of Medical Research-Senior Research Fellowship (ICMR-SRF), 2014-2017.

  • Topic: “Designing novel inhibitors against microbial gamma glutamyltranspeptidase using in-silico approaches”
  • First prize, Biophysical Chemistry (M. Tech), 2009

o SASTRA University, Thanjavur, Tamilnadu for the year 2008-2009.

LECTURES DELIVERED

  1. Deliver a lecture on the topic “Basics of Bioinformatics” in the “ 4 th DHR-ICMR-NICPR Workshop on Basic Molecular Biology Techniques Relevant to Cancer Research” at ICMR-National Institute of Cancer Prevention and Research (NICPR), Noida. From 28/02/2023 to 03/03/2023.
  2. Deliver a lecture on the topic “Basics of Bioinformatics” in the “ 3 rd DHR-ICMR-NICPR Workshop on Basic Molecular Biology Techniques Relevant to Cancer Research” at ICMR-National Institute of Cancer Prevention and Research (NICPR), Noida. From 31/01/2023 to 03/02/2023 .
  3. Deliver a lecture on the topic “Basics of Bioinformatics” in the “ 2 nd DHR-NICPR Workshop on Basic Molecular Biology Techniques Relevant to Cancer Research” at ICMR-National Institute of Cancer Prevention and Research (NICPR), Noida. From 30/11/2021 to 03/12/2021.

CONFERENCES and WORKSHOPS

  1. Organizing team member of “ 4 th DHR-ICMR-NICPR Workshop on Basic Molecular Biology Techniques Relevant to Cancer Research” at ICMR-National Institute of Cancer Prevention and Research (NICPR), Noida. From 28/02/2023 to 03/03/2023.
  2. Organizing team member of “ 3 rd DHR-ICMR-NICPR Workshop on Basic Molecular Biology Techniques Relevant to Cancer Research” at ICMR-National Institute of Cancer Prevention and Research (NICPR), Noida. From 31/01/2023 to 03/02/2023 .
  3. Organizing team member of “ 2 nd DHR-NICPR Workshop on Basic Molecular Biology Techniques Relevant to Cancer Research” at ICMR-National Institute of Cancer Prevention and Research (NICPR), Noida. From 30/11/2021 to 03/12/2021.
  4. Presented a poster ( Title: “Identifying the deleterious nsSNP in IL-6 gene and correlating their therapeutic aspects in breast cancer: an analytical study using in-silico algorithms and MD simulations ”) at the 11 th General Assembly of Asia Pacific Organization for Cancer Prevention (APOCP 11) Conference on Cancer Prevention (8-10 Dec 2022) at Kolkata. Organized by the CANCER FOUNDATION OF INDIA.
  5. Oral presentation (Title: Alkaloids as potential drug lead for fighting against multi drug resistant: a case study of NDM-1 from Klebsiella pneumonia as drug target ) in “ International Conference on “Recent Trends in Structural Bioinformatics and Computer Aided Drug Design (ICSBCADD'2019)”. Department of Bioinformatics, Alagappa University, Karaikudi-630003, Tamilnadu, India on 11 th to 13 h December 2019.
  6. Present a poster in International Conference on Innovative Research in Bioscience, Bioinformatics, Biomedical Engineering, Cancer Biology and Applied Biotechnology (BCA-2019) 15th June 2019 held at JNU, New Delhi . Title: “Alkaloids as lead hit against human threat ndm-1: a fight against fate of drug resistant”.
  7. Oral presentation (Title: In-silico prediction of high specificity inhibitors against HpGGT: Implications of divergent sites in drug design ) in “ International Conference on Advances in Biosciences and Biotechnology - ICABB-2018” (February 01-03, 2018). Organized by Department of Biotechnology, Jaypee Institute of Information Technology (JIIT), Noida (INDIA).
  8. Oral presentation (Title: Functional divergence analysis among Gamma glutamyl transpeptidase protein family ) in “NCDD 2018: National Conference on Diseases and Drugs: Emerging Trends and Challenges” (Jan 31-Feb 01, 2018). Organized by Department of Zoology, Zakir Husain Delhi College, Delhi University, New Delhi (India).
  9. Attend a workshop titled “Instructional workshop on computational methods in Drug Discovery” held at SCMM&SCIS, JNU , New Delhi from 9-11 Aug 2016.
  10. Attend a workshop titled “Computational Biotechnology at the Nanoscale: CCP4 Workshop (ICCP4-2016)” at “RCB” Faridabad (Haryana) from February 15-20, 2016.
  11. Present a poster in National Science Day at UDSC, New Delhi, 27-28 Feb 2015 .
  12. Attend an India International Science Festival (IISF)-2015 at IIT Delhi, 04-08 Dec 2015.
  13. Present a poster in INDO-US International Conference/Workshop on “Recent Advances in Structural Biology and Drug Discovery” RASBDD , October 9-11, 2014, Department of Biotechnology, Indian Institute of Technology Roorkee. Title: “γ-glutamyltranspeptidase (GGT): Acceptor site characterization by functional divergence and molecular dynamics simulations for drug design”.
  14. Science Conclave-2014 ” at IIIT Allahabad from 08 to 12 December 2014.
  15. Paper presentation on QSAR MODEL in National Bioinformatics Seminar, at Karunya University, Tamilnadu in August 2008.
  16. Attend a work shop on APPLICATION OF BIOINFORMATICS , Biotech Park Lucknow (UP) in June 2009.

SCIENTIFIC MEMBERSHIPS

  • Editorial Board member for “EC Proteomics and Bioinformatics”
  • Editorial Board Member for the “Austin Arthritis”
  • Associate Editor for “Sleep Medicine and Disorders: International Journal”
  • Editorial Board member for “Journal of Microbiology and Infection ” (https://www.reseaprojournals.com/jmi/index.php?page=editorial_board)
  • Reviewer “Frontier in Bioinformatics”
  • Reviewer “Frontiers in Immunology”
  • Reviewer “Frontiers in Molecular Biosciences

BIOINFORMATICS TECHNICAL SKILLS

Functional Divergence analysis: Diverge 3.0

Positive Selection analysis: Codmel program inbuilt with PALM package

Amino acid Network (ANN) analysis: RIN analyzer, RING server, Cytoscape, STRING database

Molecular Docking: Glide-Maestro, Autodock, Patchdock, ZDOCK

Drug-Designing tools: Schrodinger package, Discovery studio, Accelrys

Molecular Dynamic Simulations: GROMACS

Comparative SNPs analysis to identify their deleterious effect with respect to cancer and other diseases: Databases: NCBI, dbSNP, TCGA (GDC Portal), UniProt, Protein Data Bank and STRING. Deleterious SNPs identification tools: PROVEAN, Meta-SNP, PredictSNP, PhD-SNP, SIFT, PolyPhen-1, PolyPhen-2, SNAP, SNAP-2, PANTHER, MutPred, IMutant, ConSurf, MuPro.

Gene analysis tools: cBioPortal, GEPIA, Kaplan-Meier plotter, and CanSAR BLACK

Next Generation Sequencing tools: Fastqc, Trimomatic, Bowtie, Tophat, Cufflinks, Cuffmerge, cuffdiff, Trinity, Masurca, AsmQC, Augustus, Blast, GATK, Annovar

Molecular modeling: Modeller, Phyre 2.0, LOMETS, Swiss Model, I-Tasser, 3D-Star

Molecular visualization tools: Pymol, Deep viewer, VMD, Chimera, COOT

Other software: MEGA, Muscle, ClustalW, Espript, Phylip, BLAST, MATLAB, Chemdraw, Chemsketch,

Open Babel, DiNNA, VADAR, DALI server, PRODRG server, Protparam, Swissparam

Graphical Analysis: Sigma plot, XMGRACE

Operating system: Linux, Window

Programming languages: Linux scripting and PERL

Solving X-Ray diffraction data: CCP4, Phenix, COOT

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