Saikat Chakrabarti , Ph.D.

Senior Principal Scientist & Deputy Head
Structural Biology & Bioinformatics
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Research Interest

We are actively involved in identification and subsequent analysis of important bio-molecular interactions involving proteins, DNA and other macro-molecules in systemic diseases like Cancer and Infectious diseases, like malaria, leishmaniasis, etc.  Primary objectives and/or contributions of our research group are to develop robust and efficient approaches to understand the hidden properties of protein-protein interactions (PPI) systems leading to infection/systemic disease by a) integrating large scale “multi-omics” data through network biology/graph theoretical algorithms, mathematical modelling and machine learning techniques, b) in-depth analysis of molecular interaction patterns using state-of-the-art molecular modeling, docking and dynamics strategies, and c) experimental characterization/verification of the identified bio-markers and/or therapeutic targets. 

We utilize large-scale genomics, transcriptomics, proteomics, and metabolomics data to construct disease or context specific bio-molecular interaction networks and further study them to understand and decipher their biological significance using meta-interactome analysis. Our group also develops various computational tools, techniques and web servers, which are freely available for users and are beneficial to the scientific community throughout the world. 

Recently, we have also ventured into developing image processing and machine learning / deep learning based software packages to process and analyze brain MRI and CT images for detection of early features of Alzheimer’s disease and stroke, respectively.  

Please visit our lab website (http://www.hpppi.iicb.res.in/saikatlab/) for more detailed overview and description of the previous and ongoing projects and to use various tools (servers and databases) that we have developed over the years.

Credentials

  1. Senior Principal Scientist, CSIR-IICB
  2. Deputy Head, Structural Biology and Bioinformatics Division
  3. Professor of Academy of Scientific and Innovative Research (AcSIR)
  4. Ramalingaswamy Fellow
  5. Staff Scientist @ NCBI/NLM/NIH, 2009
  6. Postdoctoral Fellow @ NCBI/NLM/NIH, 2004-2009
  7. PhD @ NCBS, TIFR, Bangalore, India, 1999-2004

Patents & Publications

Publications

Follow our publications also at Google Scholar and ResearchGate

Recent publications...

84. Kulavi S, Dhar D, Kamal IM, Chakrabarti S, Bandyopadhyay J. EIF4A3 targeted therapeutic intervention in glioblastoma multiforme using phytochemicals from Indian medicinal plants - an integration of phytotherapy into precision onco-medicine. Journal of Biomolecular Structure and Dynamics. 2024 Feb 12:1-21. Impact Factor: 5.235. doi: 10.1080/07391102.2024.2314257. PMID: 38345073.

83. Das R, Maity S, Das P, Kamal IM, Chakrabarti S, Chakrabarti O. CMT2A-linked MFN2 mutation, T206I promotes mitochondrial hyperfusion and predisposes cells towards mitophagy. Mitochondrion. 2023 Jan; 74:101825. Impact Factor: 4.534. doi: 10.1016/j.mito.2023.101825. PMID: 38092249.

82. Kamal IM, Das A, Datta S, Paul K, Chakrabarti S, Chakrabarti S, Bhattacharjee P. A Novel spice-antioxidant based nano-vehicle as a putative green alternative of synthetic AChE inhibitor drugs. Journal of Biomolecular Structure and Dynamics. 2023 Aug 28:1-18. Impact Factor: 5.235. doi: 10.1080/07391102.2023.2248274. PMID: 37639732.

81. Bandopadhyay S, Kamal IM, Padmanaban E, Ghosh DD, Chakrabarti S, Roy SS. Oncogene‐mediated nuclear accumulation of lactate promotes epigenetic alterations to induce cancer cell proliferation. Journal of Cellular Biochemistry. 2023 Apr;124(4):495-519. Impact Factor:4.481. doi: 10.1002/jcb.30381. PMID: 36999756.

 

80. Kamal IM and Chakrabarti S. MetaDOCK: A Combinatorial Molecular Docking Approach. ACS Omega. 2023 Jan 31;8(6):5850-5860. Impact Factor:4.132. doi: 10.1021/acsomega.2c07619. PMID: 36816658.

79. SomChaudhury S, Nandi M, Kumar K, Ruidas B, Sur TK, Prasad P, Chakrabarti S, De P, Sil J, Das Mukhopadhyay C. Rodent Model Preclinical Assessment of PEGylated Block Copolymer Targeting Cognition and Oxidative Stress Insults of Alzheimer's Disease. MolNeurobiol.2023 Jan 4.Impact Factor: 5.59. doi: 10.1007/s12035-022-03194-7. PMID: 36598649

78. Sarkar P, Banerjee S, Chakrabarti S, Chakrabarti P, Bandyopadhyay A, Mitra AG, Saha S, Roy A, Sarkar S. Genome characterization, phylogenomic assessment and spatio-temporal dynamics study of highly mutated BA variants from India. Indian J Med Microbiol. 2022 Nov 15:S0255-0857(22)00232-8. Impact Factor: 0.988.  doi: 10.1016/j.ijmmb.2022.10.006. PMID: 36400646

77.Saha G, Sarkar S, Mohanta PS, Kumar K, Chakrabarti S, Basu M, Ghosh MK. USP7 targets XIAP for cancer progression: Establishment of a p53-independent therapeutic avenue for glioma. Oncogene. 2022 Nov;41(47):5061-5075.Impact Factor: 8.756.  doi: 10.1038/s41388-022-02486-5. PMID: 36243803

76. Das R, Das S, Chakrabarti S, Chakrabarti O. CMT2A-linked mitochondrial hyperfusion-driving mutant MFN2 perturbs ER-mitochondrial associations and Ca2+ homeostasis. Biol Cell. 2022 Nov;114(11):309-319. Impact Factor: 3.506.  doi: 10.1111/boc.202100098. PMID: 35924634

75. Chatterjee S, Mukherjee I, Bhattacharjee S, Bose M, Chakrabarti S, Bhattacharyya SN. Target-Dependent Coordinated Biogenesis of Secondary MicroRNAs by miR-146a Balances Macrophage Activation Processes. Mol Cell Biol. 2022 Apr 21;42(4):e0045221. Impact Factor: 5.069. doi: 10.1128/mcb.00452-21. PMID: 35311564. 

74. Garg A, Goel N, Abhinav N, Varma T, Achari A, Bhattacharjee P, Kamal IM, Chakrabarti S, Ravichandiran V, Reddy AM, Gupta S, Jaisankar P. Virtual screening of natural products inspired in-house library to discover potential lead molecules against the SARS-CoV-2 main protease. J Biomol Struct Dyn. 2022 Jan 19:1-13. Impact Factor: 4.15. doi: 10.1080/07391102.2022.2027271. PMID: 35043750.

73. Mallick P, Maity S, Chakrabarti O, Chakrabarti S. Role of systems biology and multi-omics analyses in delineating spatial interconnectivity and temporal dynamicity of ER stress mediated cellular responses. Biochim Biophys Acta Mol Cell Res. 2022 Apr;1869(4):119210. Impact Factor: 5.011. doi: 10.1016/j.bbamcr.2022.119210. PMID: 35032474.

72. Das R, Kamal IM, Das S, Chakrabarti S, Chakrabarti O.MITOL-mediated DRP1 ubiquitylation and degradation promotes mitochondrial hyperfusion in a CMT2A-linked MFN2 mutant.Journal of Cell Science 2022. Impact Factor: 5.282.doi

71. Khatun M, Kumar K, Baidya A, Mondal RK, Baszczyňski O, Kalčic F, Banerjee S, Dhali GK, Das K, Chowdhury A, Janeba Z Chakrabarti S, Datta S. Variability in the response of HBV D-subgenotypes to antiviral therapy: designing pan D-subgenotypic reverse transcriptase inhibitors.Journal of Virology 2021. Impact Factor: 5.103. doi

70. Das A, Basu S, Bandyopadhyay D, Mukherjee K, Datta D, Chakraborty S, Jana S, Adak M, Bose S, Chakrabarti S, Swarnakar S, Chakrabarti P, Bhattacharyya SN. Inhibition of extracellular vesicle-associated MMP2 abrogates intercellular hepatic miR-122 transfer to liver macrophages and curtails inflammation iScience 2021. Impact Factor: 5.48. doi

69. Kumar K, Bose S, Chakrabarti S. Identification of Cross-Pathway Connections via Protein-Protein Interactions Linked to Altered States of Metabolic Enzymes in Cervical Cancer. Frontiers in Medicine 2021. Impact Factor: 5.091. doi

68. Das S, Panigrahi P, Chakrabarti S. Corpus Callosum Atrophy in Detection of Mild and Moderate Alzheimer's Disease Using Brain Magnetic Resonance Image Processing and Machine Learning Techniques. Journal of Alzheimer's disease reports 2021. Impact Factor: 4.472 doi

67. Biswas N, Mallick P,Maity SK,Bhowmik D,Mitra AG,Saha S,Roy A,Chakrabarti P,Paul S,Chakrabarti S. Genomic Surveillance and Phylodynamic Analyses Reveal the Emergence of Novel Mutations and Co-mutation Patterns Within SARS-CoV-2 Variants Prevalent in India. Front Microbiol. 2021. Impact Factor: 5.640 doi:

66. Sarraf NR, Mukhopadhyay S, Banerjee A, Das AK, Roy S, Chakrabarti S , Manna M, Saha P. Genome wide comparison of Leishmania donovani strains from Indian visceral leishmaniasis and para-Kala azar dermal leishmaniasis patients. Acta Trop. 2021. Impact Factor: 3.112. doi: https://doi.org/10.1016/j.actatropica.2021.106086

65. Bose S, Kumar K and Chakrabarti S. System Biology and Network Analysis Approaches on Oxidative Stress in Cancer.In: Chakraborti S., Ray B.K., Roychowdhury S. (eds) Handbook of Oxidative Stress in Cancer. Mechanistic Aspects. Springer, Singapore. 2021. Impact Factor: NA https://doi.org/10.1007/978-981-15-4501-6_158-1

64. Mukherjee I and Chakrabarti S. Co-evolutionary Landscape at the Interface and Non-Interface Regions of Protein-Protein Interaction Complexes. Comput Struct Biotechnol J. 2021. Impact Factor: 7.271. doi: https://doi.org/10.1016/j.csbj.2021.06.039

63. Biswas N , Kumar K, Mallick P, Das S, Kamal IM, Bose S, Choudhury A and Chakrabarti S. Structural and drug screening analysis of the non-structural proteins of SARS-CoV2 virus extracted from Indian COVID-19 patients. Frontiers in Genetics. 2021. Impact Factor: 4.599. doi: https://doi.org/10.1016/j.csbj.2021.06.039

62. D De, Mukherjee I, Guha S,et.al. Rheb-mTOR Activation Rescues Amyloid Beta-Induced Cognitive Impairment and Memory Function by Restoring miR-146 Activity in Glial Cells. Mol Ther Nucleic Acids. 2021. Impact Factor: 8.886. doi: https://doi.org/10.1016/j.omtn.2021.04.008

61. Das S, Chakrabarti S. Classification and prediction of protein–protein interaction interface using machine learning algorithm. Sci Rep. 2021. Impact Factor: 4.379. doi: https://doi.org/10.1038/s41598-020-80900-2

60. Biswas N, Kumar K, Bose S, Bera R and Chakrabarti S. Analysis of Pan-Omics Data in Human Interactome Network (APODHIN) Front Genet. 2020. Impact Factor :3.258
https://doi.org/10.3389/fgene.2020.589231

59. Das MR,Banerjee A, Sarkar S, Majumder J, Chakrabarti S. and Jana SS Amino-alcohol Bio-conjugate of Naproxen Exhibits Anti-inflammatory Activity through NF-κB Signaling Pathway. bioRxiv. 2020. https://doi.org/10.1101/2020.01.10.901223.

58. Bhattacharya M, De S, Chakrabarti S. Origin and Evolution of DNA methyltransferases (DNMT) along the tree of life: A multi-genome survey. bioRxiv. 2020. https://doi.org/10.1101/2020.04.09.033167

57.Kumari N, Karmakar A, Chakrabarti S. and Kumar S Integrative computational approach revealed crucial genes associated with different stages of diabetic retinopathy. Front Genet. 2020. Impact Factor :3.258
https://doi.org/10.3389/fgene.2020.576442

56. Biswas N and Chakrabarti S. Artificial Intelligence (AI)-Based Systems Biology Approaches in Multi-Omics Data Analysis of Cancer. Front Oncol. 2020. Impact Factor :4.84
https://doi.org/10.3389/fonc.2020.588221

55. Sanga S, Ghosh A, Kumar K, Polavarapu K, Kumar VP, Vengalil S, Nashi S, Bardhan M, Arunachal G, Raju S, Gayathri N, Biswas NK, Chakrabarti S, Nalini A, Roy S, Acharya M.Whole Exome Analyses of Congenital Muscular Dystrophy and Congenital Myopathy Patients from India Reveal a Wide Spectrum of Known and Novel Mutations. Eur J Neurol 2020 Impact Factor : 4.516
doi: https://doi.org/10.1111/ene.14616

54. Kumar K , Chakraborty A and Chakrabarti S*PresRAT: a server for identification of bacterial small-RNA sequences and their targets with probable binding region. RNA Biology 2020 Impact Factor : 5.35
doi: https://doi.org/10.1080/15476286.2020.1836455

53. Paul K, Chakraborty S, Mallick P, Bhattacharjee P, Pal TK, Chatterjee N and Chakrabarti S. Supercritical carbon dioxide extracts of small cardamom and yellow mustard seeds have fasting hypoglycemic effects: Diabetic rat, predictive iHOMA2 models and molecular docking study. British Journal of Nutrition. 2020 Impact Factor : 3.5
doi:

52. Das A, Biswas N, and Chakrabarti S. Leish-ExP: A Database Of Exclusive Proteins From Leishmania Parasite. Br. J Bio. Med. Res. 04, 03, 1253-1269. 2020. Impact Factor :4.7

51. Mookherjee D, Das S, Mukherjee R, Bera M, Jana SC, Chakrabarti S, Chakrabarti O. RETREG1/FAM134B mediated autophagosomal degradation of AMFR/GP78 and OPA1 -a dual organellar turnover mechanism. Autophagy. 2020 Impact Factor :11.13
doi:10.1080/15548627.2020.1783118.

50. Das S, Banerjee A, Kamran M, Ejazi SA, Asad M, Ali N, Chakrabarti S A chemical inhibitor of heat shock protein 78 (HSP78) from Leishmania donovani represents a potential anti-leishmanial drug candidate JBC. 2020 Impact Factor :4.106
doi:10.1074/jbc.RA120.014587.

49. Kaul Z, Mookherjee D, Das S, Chatterjee D, Chakrabarti S, Chakrabarti O. Loss of tumor susceptibility gene 101 (TSG101) perturbs endoplasmic reticulum structure and function.BBA Mol Cell Res. 2020 Impact Factor :4.739
doi:10.1016/j.bbamcr.2020.118741.

48. Ganguly S, Mukherjee I, Chakrabarti S, Roy S, Sundar S, Chattopadhyay K and Bhattacharyya SN MicroRNA Exporter HuR Clears Internalized Pathogens by Promoting Pro-inflammatory Response in Infected Macrophages EMBO Molecular Medicine 2020. Impact factor: 10.293
doi:

47.Tania Luthra, VenkannaBanothu, Uma Adepally, Krishna Kumar , Swathi M, Chakrabarti S , Maddi SR, Sen S. Discovery of novel pyrido-pyrrolidine hybrid compounds as alphaglucosidase inhibitors and alternative agent for control of type 1 diabetes. European Journal of Medicinal Chemistry 2020. Impact factor: 4.816
doi:

46.Chakraborty J, Kanungo A, Mahata T, Kumar K, Sharma G, Pal R, Ahammed KS, Patra D, Majhi B, Chakrabarti S, Das S and Dutta S. Quinoxaline derivatives disrupt the base stacking of hepatitis C virus-internal ribosome entry site RNA: reduce translation and replication. ChemCommun 2019. Impact factor: 5.996
doi:

45. Chakraborty S, Paul K, Mallick P, Pradhan S, Das K, Chakrabarti S, Nandi DK, Bhattacharjee P Consortia of bioactives in supercritical carbon dioxide extracts of mustard and small cardamom seeds lower serum cholesterol levels in rats: new leads for hypocholesterolaemic supplements from spices. J Nutr Sci. 2019. Impact factor: *.*
doi: 10.1017/jns.2019.28

44. Chatterjee D, Kaul Z Das S, Sougrat R, Chakrabarti S, Chakrabarti O. Cytosolic aggregates in presence of non-translocated proteins perturb endoplasmic reticulum structure and dynamics. Traffic 2019. Impact factor: 4.4
doi: 10.1111/tra.12694

43. Bag AK, Mandloi S, Jarmalavicius S, Mondal S, Kumar K, Mandal C, Walden P, Chakrabarti S, Mandal C. Connecting signaling and metabolic pathways in EGF receptor-mediated oncogenesis of glioblastoma. PLos Computational Biology 2019. Impact factor: 4.428
doi:

42. Luthra T, Nayak AK, Bose S, Chakrabarti S, Gupta A, Sen S. Indole based antimalarial compounds targeting the melatonin pathway: Their design, synthesis and biological evaluation. European Journal of Medicinal Chemistry 2019. Impact factor: 4.816
doi:https://doi.org/10.1016/j.ejmech.2019.02.019

41. Shadab M, Banerjee A, Sinha R, Das S, Asad M, Kamran M, Maji M, Deepthi M, Jha B, Kumar M, Tripathi A, Kumar B, Chakrabarti S, ALI N. RNA-seq revealed expression of many novel genes associated with Leishmania donovani persistence and clearance in the host macrophage. Front. Cell. Infect Microb 2019. Impact factor: 4.3
doi:https://doi.org/

40. Mukherjee I, Roy S, Chakrabarti S. Identification of important effector proteins in the FOXJ1 transcriptional network associated with ciliogenesis and ciliary function. Front. Genet. 2019. Impact factor: 4.151
doi:https://doi.org/10.3389/fgene.2019.00023

39. Mukherjee R, Bhattacharya A, Sau A, Basu S, Chakrabarti S, Chakrabarti O. Calmodulin regulates MGRN1-GP78 interaction mediated ubiqitin proteasomal degradation system. FASEB Journal. 2018. Impact factor: 5.498
doi:https://doi.org/10.1096/fj.201701413RRR

38. Chauhan J, Dasgupta M, Luthra T, Awasthi A, Tripathi S, Banerjee A, Pausl S, Nag D, Chakrabarti S, Chakrabarti G, Sen S. Design, Synthesis and biological evaluation of antimitotic C2-aroyl/arylimino tryptamine derivatives that are also potent inhibitors of indoleamine-2,3-dioxygenase(IDO) European J. of Pharma Sc. 2018. Impact factor: 3.088
doi:https://doi.org/10.1016/j.ejps.2018.08.033

37. Palit S, Mukherjee S, Niyogi S, Banerjee A, Patra D, Chakraborty A, Chakrabarti S, Chakrabarti P, Dutta S. Quinoline‐glycomimetic conjugates reducing lipogenesis and lipid accumulation in hepatocytes. Chem Bio Chem 2018. Impact factor: 3.088
doi:https://doi.org/10.1002/cbic.201800271

36. Roy NS, Debnath S, Chakraborty A, Chakraborty P, Bera I, Ghosh R, Ghoshal N, Chakrabarti S, Roy S. Enhanced basepair dynamics pre-disposes protein-assisted flips of key bases in DNA strand separation during transcription initiation. Phys ChemChem Phys 2018. Impact factor: 4.123
doi:https://doi.org/10.1039/C8CP01119B.

35. Ahmad B, Banerjee A, Tiwari H, Jana S, Bose S, Chakrabarti S Structural and functional characterization of the Vindoline biosynthesis pathway enzymes of Catharanthus roseus. J. of mol Mod 2018. Impact factor: 1.425
doi:https://doi.org/10.1007/s00894-018-3590-2

34. Khatra H, Khan P P, Pattanayak S, Bhadra J, Rather B, Chakrabarti S, Saha T, Sinha S Hedgehog antagonist pyrimidine-indole-hybrid molecule inhibits ciliogenesis through microtubule destabilization. ChemBioChem 2018. Impact factor: 3.088
doi:

33. Ayyub S A, Dobriyal D, Shah R A, Lahry K, Bhattacharyya M, Bhattacharyya S, ChakrabartiS &Varshney U Coevolution of the translational machinery optimizes initiation with unusual initiator tRNAs and initiation codons in mycoplasmas. RNA Biology 2017. Impact Factor: 5.3
doi:10.1080/15476286.2017.1377879

32. Nargis T, Kumar K, Ghosh AR, Sharma A, Rudra D, Sen D, Chakrabarti S, Mukhopadhyay S, Ganguly D, Chakrabarti P, KLK5 induces shedding of DPP4 from circulatory Th17 cells in Type 2 Diabetes. Molecular Metabolism 2017;6:453. Impact Factor: 6.799
doi:10.1016/j.molmet.2017.09.004.

31. Mandloi S. and Chakrabarti S. Protein sites with more coevolutionary connections tend to evolve slower, while more variable protein families acquire higher coevolutionary connections. F1000 Research 2017;6:453. Impact Factor: 1.13
doi:10.12688/f1000research.11251.2

30. Banerjee P, Chakraborty A, Mondal RK, Khatun M, Datta S, Das K, Pandit P, Mukherjee S, Banerjee S, Ghosh S, Chakrabarti S, Chowdhury A, Datta S. HBV quasispecies composition in Lamivudine-failed chronic hepatitis B patients and its influence on virological response to Tenofovir-based rescue therapy. Sci Rep., 2017, 7, 44742 Impact Factor : 5.228
doi: 10.1038/srep44742. PMID: 28303969

29. Mukherjee R, Das A, Chakrabarti S, Chakrabarti O. Calcium dependent regulation of protein ubiquitination – interplay between E3 ligases and calcium binding proteins. BBA - Molecular Cell Research., 2017. Impact Factor : 5.12
doi: 10.1016/j.bbamcr.2017.03.001 PMID: 28285986

28. Bathula C, Ghosh S, Hati S, Tripathy S, Singh S, Chakrabarti S, Sen S. Bioisosteric modification of known fucosidase inhibitors to discover a novel inhibitor of a-L-fucosidase. RSC Adv., 2017, 7, 3563-3572. Impact Factor : 3.289
doi: 10.1039/C6RA24939F.

27. Roychowdhury A, Samadder S, Das P, Mandloi S, Addya S, Chakraborty C, Basu PS, Mondal R, Roy A, Chakrabarti S, Roychoudhury S, Panda CK. Integrative genomic and network analysis identified novel genes associated with the development of advanced cervical squamous cell carcinoma. BiochimBiophysActa. 2016;1861:2899-2911. Impact Factor : 5.083
doi: 10.1016/j.bbagen.2016.09.014. PMID: 27641506

26. Mukherjee I, Chakraborty A, Chakrabarti S. Identification of internalin-A-like virulent proteins in Leishmania donovani. Parasit Vectors. 2016;9(1):557. Impact Factor : 3.234
doi: 10.1186/s13071-016-1842-5. PMID: 27765050

25. Ghosh M, Niyogi S, Bhattacharyya M, Adak M, Nayak DK, Chakrabarti S, Chakrabarti P. Ubiquitin Ligase COP1 Controls Hepatic Fat Metabolism by Targeting ATGL for Degradation.Diabetes. 2016. pii: db160506. Impact Factor : 8.784
doi: 10.2337/db16-0506. PMID:27658392

24. Bhattacharyya D, Hazra S, Banerjee A, Datta R, Kumar D, Chakrabarti S, and Chattopadhyay S. Transcriptome-wide identification and characterization of CAD isoforms specific for podophyllotoxin biosynthesis from Podophyllum hexandrum. Plant Mol Biol. 2016;92(1-2):1-23. Impact Factor: 3.905
doi: 10.1007/s11103-016-0492-5. PMID:27387305

23. Banerjee A,Chakraborty S, Chakraborty A, Chakrabarti S , and Ray K. Functional and Structural Analyses of CYP1B1 Variants Linked to Congenital and Adult-Onset Glaucoma to Investigate the Molecular Basis of These Diseases. PLoS ONE. 2016;11(5):e0156252. Impact Factor: 3.057
doi: 10.1371/journal.pone.0156252. PMID: 27243976

22. Alam SK, Yadav VK, Bajaj S, Datta A, Dutta SK, Bhattacharyya M , Bhattacharya S, Debnath S, Roy S, Boardman LA, Smyrk TC, Molina JR, Chakrabarti S, Chowdhury S, Mukhopadhyay D, Roychoudhury S. DNA damage-induced ephrin-B2 reverse signaling promotes chemoresistance and drives EMT in colorectal carcinoma harboring mutant p53. Cell Death and Differentiation. 2016;23(4):707-22. Impact Factor : 8.218
doi: 10.1038/cdd.2015.133. PMID: 26494468

21. Das MR, Bag AK, Saha S, Ghosh A, Dey SK, Das P, Mandal C, Ray S, Chakrabarti S, Ray M, Jana SS Molecular association of glucose-6-phosphate isomerase and pyruvate kinase M2 with glyceraldehyde-3-phosphate dehydrogenase in cancer cells. BMC Cancer. 2016;16:152. Impact Factor: 3.265
doi: 10.1186/s12885-016-2172-x. PMID: 26911935

20. Ghosh RD, Ghuwalewala S, Das P, Mandloi S, Alam SK, Chakraborty J, Sarkar S, Chakrabarti S, Panda CK, Roychoudhury S. MicroRNA profiling of cisplatin-resistant oral squamous cell carcinoma cell lines enriched with cancer-stem-cell-like and epithelial-mesenchymal transition-type features. Sci Rep. 2016;6:23932. Impact Factor : 5.228
doi: 10.1038/srep23932. PMID: 27045798

19. Roy K, Mandloi S, Chakrabarti S, Roy S. Cholesterol Corrects Altered Conformation of MHC-II Protein in Leishmania donovani Infected Macrophages: Implication in Therapy. PLoSNegl Trop Dis. 2016;10(5):e0004710. Impact Factor: 3.948
doi:10.1371/journal.pntd.0004710.PMID: 27214205

18. Jain CK, Pradhan BS, Banerjee S, Mondal NB, Majumder SS, Bhattacharyya M, Chakrabarti S, Roychoudhury S, Majumder HK. Sulfonoquinovosyldiacylglyceride selectively targets acute lymphoblastic leukemia cells and exerts potent anti-leukemic effects in vivo. Sci Rep. 2015;5:12082. Impact Factor : 5.228
doi: 10.1038/srep12082. PMID: 26189912

17. Chanda SD, Banerjee A, Nandi S, Chakrabarti S, Sarkar MC Cordycepin an Adenosine Analogue Executes Anti Rotaviral Effect by Stimulating Induction of Type I Interferon. J VirolAntivir Res 2015;4:2. Impact Factor : 0.8
doi: http://dx.doi.org/10.4172/2324-8955.1000138
16. Khan MW, Biswas D, Ghosh M, Mandloi S, Chakrabarti S and Chakrabarti P. mTORC2 controls cancer cell survival by modulating gluconeogenesis. Cell Death Discov. 2015;1:15016. Impact Factor : 4.114
doi: 10.1038/cddiscovery.2015.16 PMID:27551450

15. Mandloi S. and Chakrabarti S. PALM-IST: Pathway Assembly from Literature Mining--an Information Search Tool. Sci Rep. 2015;5:10021. Impact Factor: 5.228
doi:10.1038/srep10021 PMID: 25989388

14. Bhattacharyya M. and Chakrabarti S. Identification of important interacting proteins (IIPs) in Plasmodium falciparum using large-scale interaction network analysis and in-silico knock-out studies. Malaria journal. 2015;14:70. Impact Factor : 3.079
doi: 10.1186/s12936-015-0562-1. PMID:2587964

13. Anshu A, Mannan MA, Chakraborty A, Chakrabarti S. and Dey M. A novel role for protein kinase Kin2 in regulating HAC1 mRNA translocation, splicing, and translation. Mol. Cell. Biol. 2015;35(1):199-210. Impact Factor : 4.427
doi:10.1128/MCB.00981-14. PMID: 25348718

12. Theeya N, Ta A, Das S, Mandal RS, Chakrabarti O, Chakrabarti S, Ghosh AN, Das S. An inducible and secreted eukaryote-like serine/threonine kinase of Salmonella enterica serovar Typhi promotes intracellular survival and pathogenesis. Infect Immun. 2015;83(2):522-33. Impact Factor : 3.603
doi: 10.1128/IAI.02521-14. PMID: 25404028

11. Paul A, Samaddar S, Bhattacharya A, Banerjee A, Das A, Chakrabarti S, DasGupta M. Gatekeeper tyrosine phosphorylation is autoinhibitory for Symbiosis Receptor Kinase. FEBS Lett. 2014;588(17):2881-9. Impact Factor : 3.519
doi: 10.1016/j.febslet.2014.06.056. PMID: 24996184

10. Banerjee A, Dey S, Chakraborty A, Datta A, Basu A, Chakrabarti S and Datta S. Binding mode analysis of a major T3SS translocator protein PopB with its chaperone PcrH from Pseudomonas aeruginosa. Proteins. 2014;82(12):3273-85. Impact Factor : 2.499
doi: 10.1002/prot.24666. PMID: 25116453

9. Nayak MK, Agrawal AS, Bose S, Naskar S, Bhowmick R, Chakrabarti S, Sarkar S and Chawla-Sarkar M. Antiviral activity of baicalin against influenza virus H1N1-pdm09 is due to modulation of NS1-mediated cellular innate immune responses. J AntimicrobChemother. 2014;69(5):1298-310. Impact Factor : 4.919
doi: https://doi.org/10.1093/jac/dkt534 PMID: 24458510

8. Chakraborty A, Mukherjee S, Chattopadhyay R, Roy S and Chakrabarti S. Conformational Adaptation in the E. coli Sigma 32 Protein in Response to Heat Shock. J Phys Chem B. 2014;118(18):4793-802. Impact Factor : 3.187
doi: 10.1021/jp501272n PMID: 24766146

7. Chakraborty A and Chakrabarti S. A survey on prediction of specificity-determining sites in proteins. Brief Bioinform. 2014;16(1):71-88. Impact Factor : 8.399
doi: 10.1093/bib/bbt092 PMID: 24413183

6. Roy K, Ghosh M, Pal TK, Chakrabarti S and Roy S. Cholesterol lowering drug may influence cellular immune response by altering MHC II function. J Lipid Res. 2014;16(1):71-88. Impact Factor : 4.368
doi: 10.1194/jlr.M041954. PMID: 24038316

5. Mazumder A, Bose M, Chakraborty A, Chakrabarti S and Bhattacharyya SN. A transient reversal of miRNA-mediated repression controls macrophage activation. EMBO Rep. 2013;14(11):1008-16. Impact Factor : 7.739
doi: 10.1038/embor.2013.149. PMID: 24030283

4. De D, Datta Chakraborty P, Mitra J, Sharma K, Mandal S, Das A, Chakrabarti S, Bhattacharyya D. Ubiquitin-Like Protein from Human Placental Extract Exhibits Collagenase Activity. PLoS ONE. 2013;8(3):e59585. Impact factor : 3.057
doi: 10.1371/journal.pone.0059585 PMID: 23555718

3. Chakraborty A, Mandloi S, Lanczycki CJ, Panchenko AR, Chakrabarti S. SPEER-SERVER: a web server for prediction of protein specificity determining sites. Nucleic Acids Res. 2012;40(Web Server issue):W242-8. Impact Factor : 9.202
doi: 10.1093/nar/gks559. PMID: 22689646

2. Chakraborty A , Ghosh S, Chowdhary G, Maulik U, Chakrabarti S. DBETH: A Database of Bacterial Exotoxins for Human Nucleic Acids Res. 2012;40(Database issue):D615-20. Impact Factor : 9.202
doi: 10.1093/nar/gkr942 PMID: 22102573

1.Goyal M, Alam A, Iqbal MS, Dey S, Bindu S, Pal C, Banerjee A, Chakrabarti S, Bandyopadhyay U. Identification and molecular characterization of an Alba-family protein from human malaria parasite Plasmodium falciparum. Nucleic Acids Res. 2012;40(3):1174-90. Impact Factor : 9.202
doi: 10.1093/nar/gkr821 PMID: 22006844

 
Other publications...
 

1. Chakrabarti S and Panchenko AR. Structural and functional roles of coevolved sites in proteins; PLoS ONE. 2010;5(1):e8591; Impact Factor : 3.057

2. Pugalenthi G, Tank K, Suganthan PN, Lanczycki CJ and Chakrabarti S. Prediction of functionally important sites of proteins using neural network ensemble approach. BiochemBiophys Res Commun. 2009;384:155-159; Impact Factor : 2.371

3. Chakrabarti S and Panchenko AR. Ensemble approach to predict specificity determinants: benchmarking and validation. BMC Bioinformatics 2009;10:207; Impact Factor : 2.435

4. Pugalenthi G, Tank K, Suganthan PN and, ChakrabartiS.Identification of structurally conserved residues of proteins in absence of structural homologs using neural network ensemble. Bioinformatics 2009; (Epub ahead of print); Impact Factor : 5.766

5. Chakrabarti S and Panchenko AR. Coevolution in defining the functional specificity. Proteins 2009;75:231-240; Impact Factor : 2.499

6. Lanczycki CJ and Chakrabarti S. A tool for the prediction of functionally important sites in proteins using a library of functional templates. Bioinformation 2008; 2(7):279-83; Impact Factor : 0.80

7. Pugalenthi G, Suganthan PN, Sowdhamini R and Chakrabarti S. MegaMotifBase: a database of structural motifs in protein families and superfamilies. Nucleic Acids Research 2008;36 (database issue); Impact Factor : 9.202

8. Chakrabarti S, Bryant SH and Panchenko AR. Functional specificity lies within the properties and evolutionary changes of amino acids. J Mol Biol. 2007;373(3):801-10; Impact Factor : 4.517

9. Pugalenthi G, Suganthan PN, Sowdhamini R and Chakrabarti S. SMotif: A server for structural motifs in proteins. Bioinformatic 2007;23, 637-638; Impact Factor : 5.766

10. Chakrabarti S and Lanczycki CJ.Analysis and Prediction of Functionally Important Sites in Proteins. Protein Science 2007;16, 4-13; Impact Factor : 3.039

11. Chakrabarti S, Lanczycki CJ, Panchenko AR, Przytycka TM, Thiessen PA and Bryant SH. State of the art: refinement of multiple sequence alignments. BMC Bioinformatics 2006;7, 499; Impact Factor : 2.435

12. Chakrabarti S, Manohari G, Pugalenthi G and R. Sowdhamini.SSToSS - Sequence-Structural Templates of Single-member Superfamilies. InSilico Biology 2006;6, 0029; Impact Factor : 1.67

13. Chakrabarti S, LanczyckiCJ,Panchenko AR, Przytycka TM, Thiessen PA and Bryant SH. Refining multiple sequence alignments with conserved core regions. Nucleic Acid Res. 2006;34, 2598-606; Impact Factor : 9.202

14. Bhadra R, Sandhya S, Abhinandan KR, Chakrabarti S, Sowdhamini R, Srinivasan N. Cascade PSI-BLAST web server: a remote homology search tool for relating protein domains. Nucleic Acids Res. 2006;34:W143-6; Impact Factor : 9.202

15. Sandhya S, Chakrabarti S, Abhinandan KR, Sowdhamini R and Srinivasan N. Detection of remote similarities between proteins by cascading PSI-BLAST. Journal of Biomolecular Structure and Dynamics 2005;23(3):283-98; Impact Factor : 2.3

16. Chakrabarti S, Prem AA, Bhardwaj N, and Sowdhamini R. SCANMOT: search for protein homologues in sequence databases using simultaneous restraints of multiple motifs. Nucleic Acid Research 2004;33:W274-6; Impact Factor : 9.202

17. Chakrabarti S, Bhardwaj N, Prem AA, and Sowdhamini R. Improvement of Alignment Accuracy Utilizing Sequentially Conserved Motifs. BMC Bioinformatics 2004;5;(1):167; Impact Factor : 5.766

18. Chakrabarti S, Jaisurya J, and Sowdhamini R. Improvement of Comparative Modeling: application of spatial orientation of motifs as additional restraints. Journal of Molecular Modeling 2004;10, 69-75; Impact Factor : 1.438

19. Chakrabarti S and Sowdhamini R. Regions of minimal structural variation among members of protein domain superfamilies: Application to remote homology detection and modeling using distant relationships;FEBS Letters 2003;569, 31-6; Impact Factor : 3.519

20. Chakrabarti S, Venkataramanan K, and Sowdhamini R. SMoS: A database of Structural Motifs of Superfamily. Protein Eng 2003;16, 791-3; Impact Factor : 2.364

21. Chakrabarti S and Sowdhamini R. Functional sites and evolutionary connections of Acyl Homoserine Lactone synthases. Protein Eng 2003;16, 271-278; Impact Factor : 2.364

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