Top

UNIVERSITY OF KALYANI, WEST BANGAL


About the Bioinformatics Centre
 

The Bioinformatics Infrastructure Facility (BIF) Centre housed at dept. of Biochemistry & Biophysics of University of Kalyani was established under the Biotechnology Information System Network (BTIS) program of Department of Biotechnology (DBT), Ministry of Science & Technology in March, 2007. This centre was initially aimed for providing a computational biology platform to the students, research scholars and faculty members of all the Life Science Departments of this University, as well as, the neighboring institutes near Kalyani. The initial set up was made with 10 desktop computers and 2 servers with both windows and Linux operating system connected through LAN. From 2012, a new laboratory has been built up with two powerful workstations and three desktops. Scientific commercial software packages like GCG, DS Suite, Geneious Pro, Matlab, AMBER, GOLD, CSD and other scientific program packages free for academicians are always accessible to the users. The Centre carries out frontline research & development in the broad areas of computational biology like creation and development of programmes and databases, protein-ligand interaction studies, Molecular Modeling & dynamics of macromolecules. This centre is the only facility in this remote locality and it creates a coherence among the academic and research community around this area. To popularize the bioinformatics among students, total ten national workshops have been organized on various fields of bioinformatics since its inception and more than 200 pupils have been trained in all these workshops. Twelve students completed their dissertation, among them 5 enjoyed DBT funded studentship and 6 traineeship. Total 13 research papers have been published in various international journals.

Area of Specialization:
  • Computational & Structural Bioinformatics, Protein-ligand interaction, macromolecular modeling & simulation, database designing.
 
Objectives
  • To establish this centre as the main Bioinformatics infrastructure resource in this locality with the collaborative research work among other institutions for enriching human resources and accelerating research in bioinformatics.
  • Development of more databases & bioinformatics tools.
  • Human resource development by organizing National Workshops & Training Programs.
  • Improvising the biology teaching using Bioinformatics Infrastructure Facility.
  • Carrying the frontier Research on Protein – Ligand interactions, modeling studies of membrane system, Structural Bioinformatics to develop novel drug molecules, Cluster and self assembly study.
 
Current area of research
Database on enzyme Dehydrogenase

Homepage of dehydrogenase database (http://www.bifku.in/DBD/)

BIF, KU, regularly maintains the completely web-based structural database named DB Dehydrogenase, covering almost all dehydrogenases [150 enzyme classes, 1200 entries from 160 organisms] whose structures are available. It was created by extracting and integrating various online resources (such as NCBI, UniProt, BRENDA, PDBsum, KEGG, IUBMB, MetaCyc, SYSTERS, PRIAM, InterPro, published literatures etc) to provide the true and reliable data and implemented by MySQL relational database through user friendly web interfaces using CGI Perl. This database contains brief pathway, co-enzyme, co-factor information, disease association, sequences, taxonomic characteristics, structural details, inhibitor details, references and links to other resources of all entries. The database is well equipped with flexible search options for data extraction and exploration. Thus DB Dehydrogenase is an effort from BIF, KU to bring sequential, structural and functional information of all dehydrogenases in one place.
Modeling the cystatin super family and study its inhibition against cysteine proteases

Papain-cystatin S inhibition

Cystatins are extensively studied cysteine protease inhibitors (CPIs) long known for their traditional inhibitory activity towards C1 and C13 family of cysteine proteases (CP). We have tried to put some light on the molecular mechanisms behind the differential inhibitory affinity of family 2 human cystatins for CPs through computational approaches. Despite rigorous conservation of structural pattern and amino acid sequence, how cystatins are able to manage their specificity profile towards CPs and varies their enzymatic affinity drastically by minute alteration of inhibitory site composition is the matter of our study. At the same time in silico studies are designed / ongoing for domain swapping and recognition of additional binding sites of human family two cystatins.
 
Roles of Cytochrome p450 enzymes in anticancer drug

Cytochrome P450 are mainly responsible for the metabolism of commonly used chemotherapeutic agents by forming active or inactive metabolites. P450 enzymes are mainly located in the liver. A clear understanding of these metabolic pathways involved will allow us to predict the efficacy and safety of novel anticancer molecules and help us to: (1) Design new chemotherapeutic agent which retains anticancer properties. Such drugs will also help in reduction of drug–drug interactions in patients undergoing multiple therapies. (2) Develop inhibitors or substrates of CYP responsible for the metabolism of anticancer agents can be co-administered to increase the half-life of drug and thus reduce dosing in patients. (3) CYP metabolism of inactive pro-drug into cytotoxic drug can be explored in designing safer potent anticancer agents.

 
Studies of drug targets of Plasmodium falciparum

IspH along with its substrate (PDB ID: 3KE8)

Malaria is one of the most common vector-borne diseases with the highest impact on the world's human population due to ever evolving virulence of its parasites in response to medical interventions. 17 novel drug targets were identified in Plasmodium falciparum using computational approaches, which can further lead to design drugs against malaria. We have studied an enzyme ispH and its catalytic activities which is very essential for isoprenoids biosynthesis pathway of Plasmodium. Comparative modeling and MD simulation has been used to generate a highly reliable structure of Plasmodium ispH. Applying virtual screening based molecular docking and considering the mode of binding and affinities, we have screened 12 potential leads which carry all the properties of any “approved drugs”. The knowledge of Plasmodium LytB inhibitory mechanism from this study can provide valuable support for the antimalarial inhibitor design in future. Our research in this field will be continued with other drug targets of Plasmodium falciparum.

 
Computational studies on voltage gated potassium channel

Voltage gated potassium channels are the transmembrane proteins that sense the voltage difference across the cell and allow rapid & selective flow of K+ ions across the membrane. Hence these channels are the key components in generation and propagation of electrical impulses in nervous system.  During repolarization, these channels undergo a drastic conformational change to come in its active form and allow passive flow of K+ ions from the cell to restore the membrane potential. A few number of crystal structures are available till date to understand the relationship between their molecular structure and physiological function. So using computational approaches, several progresses have been made in this regard to generate different alternative conformations of these proteins as well as to study their functional mechanisms. In this centre, we model these proteins in both open and close state conformations and try to unravel their several functions like gating mechanisms, ion conduction, effects of mutations and their inhibition in atomic level using molecular simulation.

 


About the Institution
 

University of Kalyani was established by the chief architect of Modern Bengal, the great philanthropist and physician Dr. Bidhan Chandra Roy in the year 1960. The University of Kalyani is a State- University and its activities are guided by the Kalyani University Act, 1981 (amended up to 2001), enacted by the Govt. of West Bengal. The university is situated in very natural surroundings close to mother earth covering an area of 400 acres in Kalyani town of West Bengal with national highway (N.H.34) on one side and the river Ganges on the other.
It has completed its five decades of commendable service to the development of Higher Education in all fields. The University is presently offering thirty-two postgraduate programmes under four faculties namely, Science, Arts & Commerce, Education and Engineering, Technology & Management. Two more faculties, the Faculty of law and the Faculty of Music & Fine Arts have been introduced recently.

tr>
Achievements at a glance
 
  • A database on Enzyme Dehydrogenase has been developed and implemented on web. It is also maintained and updated on regular basis. (http://www.bifku.in/DBD/).
  • Total ten national workshops have been organized successfully by this centre and more than 200 students have been trained.
  • 13 research papers have been published in various international journals and 5 papers have been published various conference proceedings using this centre.
  • This centre is being used by around 100 users of this University and other institutions.
 
Databases/applications developed

One database on enzyme dehydrogenase has been developed which is available online at http://www.bifku.in/DBD.

 
Infrastructure facilities
 

Name with Brand

Quantity

P(IV) Lenovo desktop Computers with 17” TFT monitors

12

High-end (X236) and medium (X226) IBM server  

2

Lenovo D30 Thinkstations

2

Lenovo D10 Thinkstation

1

Lenovo Thinkpad

1

APC Smart RT-5000 UPS with 16 batteries

2

Canon black & white copier cum printer 

1

HP colour laser printer

1

HP scanner 

1

Sony L.C.D. projector

1

 

Scientific commercial software packages: Accelrys GCG, Accelrys DS Suite, Geneious Pro, Matlab, AMBER, GOLD, CSD and other scientific program packages free for academicians are always accessible to the users.
Databases: Cambridge Structural Database, SQL Server 2005 Standard Edition, MySQL.
Connectivites: This Centre is intra connected and opted the University leased line internet connection (Service provider : BSNL)

Recent Publications

Anindita Roy Chowdhury (Chakravarty), H.G. Nagendra, Alpana Seal. Correlation among Contribution of Hydrophobic Aromatic and Aliphatic Residues in six Enzyme classes. (Communicated)

Angshuman Bagchi. Structural analyses of the permease like protein SoxT: a member of the sulfur compound metabolizing sox operon. Gene, Vol. 521, Pg. no. 207-210.

Semanti Ghosh and Angshuman Bagchi. Mutation study of DsrM from Allochromatium vinosum using the amino acid sequences. Meta Gene (Elsevier), Vol.1, Pg. no. 33-42.

Simanti Bhattachrya, Amit Das, Rakhi Dasgupta and Angshuman Bagchi. Hypoglycosylation of dystroglycan due to T192M mutation: A molecular insight behind the fact. (Accepted in Gene)

Semanti Ghosh and Angshuman Bagchi. Characterization of DsrK and DsrO from Allochromatium vinosum and other proteobacteria using the amino acid sequences. Research and Reviews: Journal of material Sciences, Vol.1, Pg. no. 31-38.

Roy SS, Patra M, Nandy SK, Banik M, Dasgupta R, Basu T. In vitro holdase activity of E. coli small heat-shock proteins IbpA, IbpB and IbpAB: a biophysical study with some unconventional techniques. (Accepted in Protein & Peptide Letters)

Suman K. Nandy, Rajabrata Bhuyan, Alpana Seal. Modeling Family 2 Cystatins and their interaction with Papain. Journal of Biomolecular Structure and Dynamics, 2012, (in Press). DOI:10.1080/07391102.2012.706403.

Suman K. Nandy, Rajabrata Bhuyan, Alpana Seal. DB Dehydrogenase: an online integrated structural database on enzyme dehydrogenase. Bioinformation, Volume 8(20): Bioinformation 8(20): 1000-1002 (2012).

Bagchi A., Structural insight into the mode of interactions of SoxL from Allochromatium vinosum in the global sulfur oxidation cycle. Mol Biol Rep. 2012 Dec; 39(12):10243-8. doi: 10.1007/s11033-012-1900-9.

Sourav Singha Roy, Monobesh Patra, Rakhi Dasgupta & Angshuman Bagchi. A structural insight into the prokaryotic heat shock transcription regulatory protein s32: an implication of s32-DnaK interaction. Bioinformation 8(21): 1026-1029 (2012).

Roy, S.S., Patra M., Basu T., Dasgupta, R., Bagchi, A. Evolutionary analysis of prokaryotic heat shock transcription regulatory protein σ32. Gene (2012). doi:10.1016/j.gene.2011.12.043.

Anindita Roy Chowdhury (Chakravarty), H. G. Nagendra, and Alpana Seal. Computational analysis of hydrophobicity across six enzyme classes revealing relative contribution of aliphatic and aromatic residues. Biotechnol. Bioinf. Bioeng. 2011, 1(1):83-91.

Bagchi, A., Structural modeling of SoxF protein from Chlorobium tepidium: an approach to understand the molecular basis of thiosulfate oxidation. Biochemical Biophysical Research Communication. 10/2011; 414(2):409-11. DOI:10.1016/j.bbrc.2011.09.101

Rita Ghosh, Dipanjan Guha, Sudipta Bhowmik and Angshuman Bagchi, Possible role of 2, 2’- (Diazinodimethylidyne) di - (ophenylene) dibenzoate, a novel hydrazine as an anti - HIV agent. Journal of Biophysics and Structural Biology Vol. 2(4), pp.

 
Contacts
 

Dr. Alpana Seal
Coordinator, BIF Centre
Department of Biochemistry and Biophysics
University of Kalyani, Kalyani - 741235, West Bengal.                                              
Phone Number: 033 2582 3405(O), 9830795655(M)  
Email: btis_ku@yahoo.co.in, kalyaniuniv.btisnet@mail.nic.in
Website: http://www.bifku.in/

 

 

 
Contact us Site map Archive   Last updated on: 23 October 2017
© 2012 BTISNet Inc. All rights reserved                                   Created and maintained jointly by JNTBGRI, Apex Centre and NIC Cell, DBT