The DBT funded Bioinformatics Infrastructure Facility (BIF) Center at University of Kalyani has been providing scientific supports to the researchers throughout the world. The Center has created a commendable platform to both research and education to the faculty members, research scholars and students of all the life science departments of this University as well as nearby institutes. The center is strengthened with some powerful workstations and various scientific commercial software packages, as well as many free-for-academics scientific programs.
Workshops and Training Programs are being conducted regularly from the Center. More than 400 students have so far been trained through these endeavours.
By the assessment of DBT, the BIF Center of University of Kalyani secured the 5th position among all the BIF Centers present in Universities at 29th BTISnet Coordinators Meet in 2018.
Till now, more than ten research scholars have completed their scientific works and received their Ph.D degrees by using the facilities of this center.
The Center caters to the needs of the students outside the University, both at the national and International levels.
The main focus of this center is to create awareness among Biological Science disciplines and to encourage them for interdisciplinary research. The BIF center of University of Kalyani is the only center in this part of West Bengal. The center caters to the different needs of the various Biological Science disciplines. The center organizes workshops regularly each year and through the workshops many students are being trained.
Different research projects are being carried out using the facilities of the center. The main theme areas of research are:
a) Structural Bioinformatics: In this domain, protein-protein, protein-ligand and protein-macromolecular interactions are being studied. Molecular mechanics and molecular dynamics simulations are constantly being carried out. High throughput studies pertaining to building of new drug like compounds are also being performed. A few recent publications are:
Analysis of the structural dynamics of the mutations in the kinase domain of PINK1 protein associated with Parkinson’s disease.
Sima Biswas, and Angshuman Bagchi (Corresponding author)
Gene (2023) Jan 6:147183. doi: 10.1016/j.gene.2023.147183. Online ahead of print. PMID: 36623675; ISSN: 0378-1119
A drug repurposing endeavor to discover a multi‑targeting ligand against RhlR and LasR proteins from opportunistic human pathogen Pseudomonas aeruginosa
Nilkanta Chowdhury, and Angshuman Bagchi (Corresponding author)
Journal of Molecular Modeling (2022) 28:295 doi: https://doi.org/10.1007/s00894-022-05301-w PMID: 33555486. ISSN: 1610-2940 (print version), 0948-5023 (electronic version)
b) Study of NGS data: With the financial support from DBT, we have already extended our research work to the analysis of Next Generation Sequencing Data. The preliminary works published from such fields were aimed at analyzing the structure function relationships of circular RNAs. A few relevant publications are:
Unusual nature of long non-coding RNAs coding for “unusual peptides”
Angshuman Bagchi
Gene (2020), Volume 729, 1 March 2020, 144298, ISSN: 0378-1119
Different roles of circular RNAs with protein coding potentials.
Angshuman Bagchi
Biochemical and Biophysical Research Communications (2018) Jun 12; 500(4):, 2018; 907-909. doi: 10.1016/j.bbrc.2018.04.190. Epub 2018 Apr 30.
c) Statistical Bioinformatics: We are also working on the predictions of protein-protein interactions using machine learning techniques. We are also trying to analyse the various aspects of the effects of the mutations and single nucleotide polymorphisms in protein functions. The relevant publications are:
Disease Probability Index (DPI, χ): A new alignment-free scoring method to evaluate the
propensities of polypeptide sequences leading to disease onset
Ananya Ali and Angshuman Bagchi (Corresponding author)
BioSystems (2018), 172, 1-8, ISSN: 0303-2647
Structural study of the effects of mutations in proteins to identify the molecular basis of the loss of local structural fluidity leading to the onset of autoimmune diseases
Ananya Ali, Semanti Ghosh and Angshuman Bagchi (Corresponding author)
Biochemical and Biophysical Research Communications (2017), Vol. 484, Pg. no. 165170,
ISSN: 0006-291X
A few relevant publications arising out of fruitful collaborations of the Coordinator, Prof. Angshuman Bagchi with different laboratories worldwide
International
With the lab of Prof. Luigia Grazia FRESU, Department of Health Sciences, School of Medicine, University of Piemonte Orientale, Via Solaroli, 17, 28100 Novara, Italy.
Design, synthesis and biological evaluation of vortioxetine derivatives as new COX-1/2 inhibitors in human monocytes.
Talmon M, Chaudhari RD, Suryavanshi H, Chowdhury N, Quaregna M, Pin A, Bagchi A, Biswas G, Fresu LG.
Bioorg Med Chem. (I.F: 2.572) 2020 Dec 1;28(23):115760. doi: 10.1016/j.bmc.2020.115760. Epub 2020 Sep 11.PMID: 32992247, ISSN: 0960-894X
With the lab of Prof. Anny Slama-Schwok, Virologie et Immunologie Moléculaires INRA UR892, Domaine de Vilvert, 78352 Jouy-en-Josas, France
Identification of a novel complex between the nucleoprotein and PA(1-27) of influenza A virus polymerase
Jasmina Vidic, Magali Noiray, Angshuman Bagchi and Anny SLAMA-SCHWOK
Biochemistry (I.F: 2.876), Vol. 55, Pg. no. 4259-4262, ISSN: 0006-2960 (print version), ISSN: 1520-4995 (electronic version
National
With the lab of Prof. Parames Chandra Sil, Bose Institute, Kolkata
Amelioration of oxidative stress mediated inflammation and apoptosis in pancreatic islets by Lupeol in STZ-induced hyperglycaemic mice
Abhishek Kumar Das, Uday Hossain, Sumit Ghosh, Sima Biswas, Mullicka Mandal, Bhagirath Mandal, Goutam Brahmachari, Angshuman Bagchi, Parames C. Sil
Life Sciences (I.F: 6.78) 2022; Jul 2:120769. doi: 10.1016/j.lfs.2022.120769. Online ahead of print. PMID: 35792182; ISSN: 0024-3205
With the lab of Prof. Subrata Sau, Bose Institute, Kolkata
Dimerization ability, denaturation mechanism, and the stability of a staphylococcal phage repressor and its two domains
Anindya Biswas, Semanti Ghosh, Debabrata Sinha, Anindya Dutta, Soham Seal, Angshuman Bagchi(Corresponding author), Subrata Sau
International Journal of Biological Macromolecule (I.F: 3.671), 2019 Mar 1; 124:903-914. doi:
10.1016/j.ijbiomac.2018.11.263. Epub 2018 Dec 2. ISSN: 0141-8130 (print version), 1879-0003 (electronic version)
Alanine substitution mutations in the DNA binding region of a global staphylococcal virulence regulator affect its structure, function, and stability
Sukhendu Mandal, Semanti Ghosh, Debabrata Sinha, Avisek Mahapa, Soumitra Polley, Deeya Saha, Keya Sau, Angshuman Bagchi (Corresponding author), Subrata Sau
International Journal of Biological Macromolecule (I.F: 3.671), 2019, ISSN: 0141-8130 (print version), 1879-0003 (electronic version) Mar12; 113:1221-1232. doi: 10.1016/j.ijbiomac.2018.03.045. [Epub ahead of print]
With the lab of Prof. Snehasikta Swarnakar, IICB, Kolkata
Omeprazole prevents stress induced gastric ulcer by direct inhibition of MMP-2/TIMP-3 interactions
Deep Sankar Rudra, Uttam Pal, Nilkanta Chowdhury, Nakul Chandra Maiti, Angshuman Bagchi ,Snehasikta Swarnakar
Free Radical Biology and Medicine (I.F: 7.376), 2022 Mar; 181:221-234. doi: 10.1016/j.freeradbiomed.2022.02.007. ISSN: 0891-5849 (print); 1873-4596 (web)
For a detailed list, you are requested to visit:
https://pubmed.ncbi.nlm.nih.gov/?term=angshuman+bagchi&sort=date
Hardware :
P(IV) Lenovo desktop Computers with 17” TFT monitors (10), High-end (X236) and medium (x226) IBM server (2), Canon black & white copier cum printer(1), HP colour laser printer (1), HP scanner (1), APC Smart RT-5000 UPS with 16 batteries (1), Sony L.C.D. projector (1)
Operating System Software :
Windows XP Professional, Red Hat Linux 6 Enterprise Edition.
Scientific Sortware Packages :
Acclerys GCG pack, Shelex-97 package, Accelrys DS suite (will be available shortly), Genious Pro (will be available shortly), Microsoft Visual Studio 2005, Microsoft SQL Server 2005 Standard Edition.
Internet Connection :
This Centre is intra connected and has BSNL Broadband (2 MBPS) connection.
Databases :
Cambridge Structural Database will be available soon. One database on the enzyme dehydrogenase developed by a graduate student of this department will be linked shortly.
The center conducts regular workshops.
An overview of the workshops conducted during the last couple of years
2017-2018
DBT Sponsored National Workshop on “Structural applications on high throughput data analysis” during 20th to 21st of February, 2018
Total number of participants: 21
2018-2019
DBT Sponsored National Workshop on “Bioinformatics from sequence and structural perspective” during 11th to 13th of March, 2019
Total number of participants: 33
2019-2020
21 Day Summer Training on Bioinformatics during 2nd to 22nd July, 2019
Total number of participants: 33
DBT Sponsored National Workshop on “Introduction to Bioinformatics from a students’ perspective” on 2nd of March, 2020
Total number of participants: 30
2020-2021
National Webinar on “Latest Trends in Bioinformatics” during 10th to 11th of June, 2020
Total number of participants: 30