Department of Bioinformatics

• • Lab facility

Extensive infrastructure facilities have been developed for rigorous training and to carry out research activities. The computer labs have are equipped with latest computers of high configuration having intel i7 multi-core processors. All computers are connected with high band-width internet connection powered by 1 GBPS National Knowledge Network (NKN) of Government of India. These labs have several HP, Dell, Fujitsu & Tyrone workstations and servers for high performance computing.

• • List of instruments& Softwares in the Lab
    • Multiple HP and Dell workstations and servers
    • 26-intel i7 desktop computers
    • Accelrys, Schrodinger, AMBER & various open source/commercial softwares
  • Lab staffs and their contact
    • Priyatam Manohar Mrinal – Laboratory Attendant
      Qualification: B.Sc.( Zoology)
      Email: priyatammrinal@cub.ac.in
      Contact: 0631-2229-
    • Atul Kumar Tripathi – Laboratory Attendant
      Qualification: M.Sc.
      Email: atulkumar@cub.ac.in
      Contact: 0631-2229-

• Project
  1. Dr. Durg Vijay Singh PI, UGC (2013-15; 6 lacs) project entitled Design and development of inhibitors against Nucleotide Binding Domain of P-gp for enhancing Bioavailability and reversal of multidrug resistance
  2. Dr. Durg Vijay Singh, PI, DST Kiran (2014-15; 3.26 lacs) project entitled Design and Development of herbicide against carboxyl-terminal (CT) domain of ACCase of P.minor to regain resistivity in resistance biotypes
  3. Dr. Vijay Kr. Singh PI, SERB (2016-20; 14 Lakh) project entitled Identification of molecular species that have potential to compete with insulin for receptor binding
  4. Dr. Durg Vijay Singh PI DST-SERB (2016-19; 31 lacs) project entitled Design and Development of Herbicide to Regain Sensitivity in Phalaris Minor Resistant Biotypes
  5. Dr. Ajay Kr. Singh, PI Dr. Anil Kumar (Co-PI) ICMR (2019-Ongoing; 35 lacs) project entitled In-Silico study on potent inhibitors against iron overload and cardiac arrhythmia in beta-thalassemia (RP-56).
  6. Dr. Durg Vijay Singh (PI) and Dr. Girish Chandra (Co-PI) ICMR (2020-ongoing; 31 lacs) project entitled Rational approach of antibiotic discovery and development against, a staphylococcus aureus serine-threonine phosphatases (Stp) protein (Project ID RP-60).
  7. Dr. Vijay Kr. Singh Dr. K.K. Ojha (Co-PI) ICMR (2020-Ongoing; 20 lacs) project entitled Gene interaction landscape inferred from expression data to search for diabetes effector molecules (Ref. 2020-3854)
  8. Dr. Durg Vijay Singh (PI), Prof. RS Rathore (Co-PI), Dr. Girish Chandra (Co-PI) (2021 Ongoing 50.37 Lakh) Development of herbicides against Acetyl CoA Carboxylase to address resistance and cross-resistance against Phalaris minor: A weed of wheat crop field.”

   

• Specific areas of research

  Disease Biology using modeling and omics approaches: The research in the Department of Bioinformatics, is primarily focused towards understanding the underlying process in disorders, with special emphasis on neurodegenerative, respiratory, monogenic & metabolic disorders, infectious disease & cancer.

  1. New algorithms and database have been developed to provide solution for drug and biologics design such as Databases of therapeutic targets and novel leads pertaining to natural products (MedPServer), de novo peptide design (Conflore), curcumin analogs and their molecular & disease targets (CRDB), a workflow for complete 3D-QSAR modeling, virtual screening & design (3D-QServer), simple sequence repeats database, and online server to detect simple sequence repeats with length variation etc.
  2. Analysis of muscle transcriptome to identify biologically relevant class of diabetic patient: We are analyzing large transcriptome datasets to identify subset of diabetic subjects having homogeneous expression of genes related to selected biological processes/pathways.
  3. Genome characterization of gall bladder cancer from Indo-Gangetic belt of India
  4. Evolutionary sequence analysis to detect drug resistance in pathogens
  5. Role of lnc RNA in oral and cervical cancer to understand the mechanism and its significance in oncogenesis.
  6. In silico study on potent inhibitors against iron overload and Cardiac arrhythmia in beta thalassemia
  7. Development (Design, Synthesis and Biological Evaluation) of novel Dual-binding Cation-π Inhibitors of AChE:
  8. Design of flavonoid based SARS-CoV-2 MPRO inhibitors
  9. Identification of Herb-based Lead Molecules, Optimization and Testing using case study of herbs available in Indian sub-continent for Asthma & Respiratory-tract Infection
  10. Other areas:
      Design and development of active molecule against herbicide resistance weeds & validation of leads through wet-lab and field assay as multiple and cross resistances in weeds is a major threat in grain production.
      o Comparative genomics of prokaryotes: To estimate the origin of replication site based on the nucleotide frequency of the prokaryotic genomes.
• Research Publications

  2022

  1. Haldar, A., Singh, A.K. The association of long non-coding RNA in the prognosis of oral squamous cell carcinoma. Genes Genom (2022). https://doi.org/10.1007/s13258-021-01194-w.

  2021

  1. PA Meetei, P. Nongdam, A Kiran Kumar, RS Rathore., (2021), Phenylbenzopyrone of flavonoids as a potential scaffold to prevent SARS-CoV-2 replication by inhibiting its M PRO main protease. Current Pharmaceutical Biotechnology. In press.
  2. Mahesha N, Yathirajan HS, Nagma Banu HA, Kalluraya B, Rathore RS and Glidewell CG. Formation of 1-(thia­zol-2-yl)-4,5-di­hydropyrazoles from simple precursors: synthesis, spectroscopic characterization and the structures of an inter­mediate and two products. Acta Crystallographica Section E: Crystallographic Communications (IUCr/Wiley). (2021). E77, 975-981
  3. Prasanna, P., Kumar, R., Singh, V. K., & Upadhyay, A. (2021). Cloning, purification, and homology modeling of Histone deacetylase in Leishmania donovani. Infection, Genetics and Evolution, 104738. (IF - 2.77)
  4. Priya P, Shanker A (2021) Coevolutionary forces shaping the fitness of SARS-CoV-2 spike glycoprotein against human receptor ACE2. Infection, Genetics and Evolution 87: 104646
  5. Nandan Kumar, Priyanka Rani, Shikha Agarwal Durg Vijay Singh "6-Ethoxy-4-N-(2-Morpholin-4-Ylethyl)-2-N-Propan-2- yl-1,3,5-Triazine-2,4-Diamine Endows Herbicidal Activity Against Phalaris Minor a Weed of Wheat Crop Field: An in-Silico and Experimental Approaches of Herbicide Discovery" Journal of molecular modeling 2021 (Accepted)

  2020

  5. An in silico approach to identify potential medicinal plants for treating Alzheimer disease: a case study with acetylcholinesterase, AM Potshangbam, A Nandeibam, T Amom, N Potshangbam, H Rahaman, RS Rathore, Journal of Biomolecular Structure and Dynamics, 1-13 (2020) in press
  6. Fifteen 4-(2-methoxyphenyl) piperazin-1-ium salts containing organic anions: supramolecular assembly in zero, one, two and three dimensions, C Harish Chinthal, CN Kavitha, HS Yathirajan, S, RS Rathore, C.G. Glidewell, Acta Crystallographica Section E: Crystallographic Communications 76 (11) 2020.
  7. K Kumar Reddy, R S Rathore , P Srujana, R R Burri, C Ravikumar Reddy, M Sumakanth, Pallu Reddanna, M Rami Reddy, Mini Rev Med Chem. 2020;20, 1179-1187. Performance Evaluation of Docking Programs- Glide, GOLD, AutoDock & SurflexDock, Using Free Energy Perturbation Reference Data: A Case Study of Fructose-1, 6-bisphosphatase-AMP Analogs. doi: 10.2174/1389557520666200526183353.
  8. Kiran Kumar, H. S. Yathirajan, Asma, N. Manju, B. Kalluraya, R. S. Rathore and C. Glidewell (2020) Acta Crystallographica E (Wiley/IUCr). E76, 683-691. Functionalized 3-(5-ar­yloxy-3-methyl-1-phenyl-1H-pyrazol-4-yl)-1-(4-substituted-phen­yl)prop-2-en-1-ones: synthetic pathway, and the structures of six examples. https://doi.org/10.1107/S2056989020005113
  9. Naresh Damuka, K. Kurumurty, P. Angamba Meetei, R.S. Rathore, A.K. Kondapi and V. Vindal, (2020) Pharmacological Reports (Springer Nature). In press. Discovery of Dual Cation-π Inhibitors of Acetylcholinesterase: Design, Synthesis and Biological Evaluation. https://doi.org/10.1007/s43440-020-00086-2
  10. Angamba Meetei, R.S. Rathore, P. Nongdam, (2020) Heliyon (Cell Press) 6(2), e033782019. Discovery of sulfone-resistant dihydropteroate synthase (DHPS) as a target enzyme for kaempferol, a natural flavonoid. https://doi.org/10.1016/j.heliyon.2020.e03378
  11. A.E. Shaibah, H.S. Yathirajan, N. Manju, B. Kalluraya, R.S. Rathore, C. Glidewell (2020) Acta Crystallographica E (Wiley/IUCr) E76, 48-52. Two isostructural 3-(5-ar­yloxy-3-methyl-1-phenyl-1H-pyrazol-4-yl)-1-(thio­phen-2-yl)prop-2-en-1-ones: disorder and supra­molecular assembly. https://doi.org/10.1107/S205698901901658X
  12. A. E. Shaibah, H. S. Yathirajan, Asma, N. Manju, B. Kalluraya, R. S. Rathore and C. Glidewell, (2020) Acta Crystallographica E (Wiley/IUCr) E76, 360-365. Conversion of di­aryl­chalcones into 4,5-di­hydro­pyrazole-1-carbo­thio­amides: mol­ecular and supra­molecular structures of two precursors and three products. https://doi.org/10.1107/S2056989020001735
  13. Jayaswal PK, Shanker A, Singh NK (2020) Genome wide annotation and characterization of young, intact long terminal repeat retrotransposons (In-LTR-RTs) of seven legume species. Genetica 148: 253-268.
  14. Kumar S, Kumari S, Shanker A (2020) In silico mining of simple sequence repeats in mitochondrial genomes of genus Orthotrichum. Journal of Scientific Research 64: 179-182.
  15. Kumar S, Shanker A (2020) Length variation of chloroplast simple sequence repeats in the genus Eucalyptus L’Hér. Plant Science Today 7(3): 353-359
  16. Jayaswal PK, Shanker A, Singh NK (2020) Genome-wide comparative and evolutionary analysis of transposable elements in eight different legume plants Indian Journal of Agricultural Sciences 90: 1025-1031.
  17. Kumar S, Shanker A (2020) In silico comparative analysis of simple sequence repeats in chloroplast genomes of genus Nymphaea. Journal of Scientific Research 64: 186-192.
  18. Suchitra Singh & AK Singh (2020) Mutated USP9X-Associated TRIM33 Inhibition in the Metastasis of Gingivobuccal Oral Squamous Cell Carcinoma EJMO. 2020; 4(4): 309-318
  19. Kamboj M., Jain K., Singh D.P., Singh A.K. Chaturvedi D^e., Molecular modeling, in-silico docking and antibacterial studies of novel template wangled macrocyclic complexes involving isatin moiety. Journal of Molecular Structure, Elsevier, 2020 (1207) Volume 1207, 5 May 2020, 127602 (Impact Factor 2.120).
  20. Rani, S., Singh, A.K., Paswan, R.R. et al. Preparation, Characterization and Antibacterial Evaluation of Soy Protein Isolate Biopolymeric Films Loaded with Nalidixic Acid. J Polym Environ (2020). 28, 1841–1850(2020). [Impact Factor 2.896].
  21. Tiwari S.K., Singh A.K., Singh A (2020). In-silico primer designing and PCR for detection of novel coronavirus-19, Journal of Infection and Public Health, (2020) 13(12), 1885-1886. Elsevier. (Impact factor : 2.447)
  22. Chandra G., Patel S., Panchal M., Singh D.V. (2020) S-Adenosyl-L-homocysteine hydrolase: Its Inhibitory Activity against Plasmodium falciparum and Development of Malaria Drugs. Mini Rev Med Chem . doi: 10.2174/1389557521666201218155321. (I.F.-3.0
  23. Singh, P., Khan, A., Kumar, R., Kumar, R., Singh, V. K., & Srivastava, A. (2020). Recent developments in siderotyping: procedure and application. World Journal of Microbiology and Biotechnology, 36(12), 1-15. (IF - 2.44).
  24. Rai, N. K., Mathur, S., Singh, S. K., Tiwari, M., Singh, V. K., Haque, R.,Tiwari, S., & Sharma, L. K. (2020). Differential regulation of mitochondrial complex I and oxidative stress based on metastatic potential of colorectal cancer cells. Oncology letters, 20(6), 1-1.
  25. Kumar R, Ojha KK, Kushwaha P, Singh VK. Muscle biopsies differ in relation to expression of fiber‐type specific genes. J Diabetol 2020;11:198‐203

  Patent

  26. Title:6-ethoxy-4-n-(2-morpholin-4-ylethyl)-2-n-propan-2-yl-1,3,5-triazine-2,4-diamine endowed with herbicidal activity against susceptible and resistant biotypes of Phalaris minor. Inventor: Durg Vijay Singh et.al., (2020). Field of Invention: Pharmaceuticals

E-Resources for Courses

Course Assessment Design - MSc

1. Semester –I


2. Semester –II


3. Semester –III


4. Semester-IV

In-house Developed Softwares and Databases

 1. Event Management System

 2. MedPServer: Natural Product based Database and Target Identifications

Gallery