About the Bioinformatics Centre

The Distributed Information Sub-Centre (Bioinformatics Centre) at RGCB, setup and funded by DBT, GOI under the National Bioinformatics Network program started functioning from May 2002 with a view to catering the needs of the scientific community and to augmenting their research activities through information inputs. The main function of the Centre is to act as a member of Bioinformatics Network System for providing information to the interested users on topics pertaining to the relevant areas of Biotechnology specially genomics and proteomics.

Area of Specialization:
  • Database and Software development in biotechnology
  • Sequence Analysis and Molecular Modeling
  • To provide a national bio-information network designed to bridge the inter disciplinary gaps in biotechnology information and to establish link among scientists in organizations involved in R&D and manufacturing activities in biotechnology.
  • To build up information resources, prepare databases on biotechnology and to develop relevant information handling tools and techniques.
  • To evolve and implement program on education of users and training of information scientists responsible for handling of biotechnology information and its applications to biotechnology research and development.
  • To develop, support and enhance public information resources for biotechnology e.g. Gene banks, molecular biology data and related research information resources.
Achievements at a glance
  • Research in the following above mentioned 3 areas is in progress and several research papers have been published.
  • Acquired additional infrastructure facilities including hardware’s, software’s and database.
  • To provide services for the analysis of biological data, bibliographic references to published literature in science and technology (including databases and patents).
  • Training programmes held in Bioinformatics.
  • The PG course (M.Tech) in Bioinformatics specialization has been introduced this year; however this is an independent activity of the university.
Recent publications

Nisha E Thomas, Reshma Thamkachy, KC Sivakumar, KJ Sreedevi, Xavier Lieben, Sannu A Thomas, Rohith Kumar, Kallikat N Rajasekharan, Lynne Cassimeris, Suparna Sengupta., Reversible Action of Diaminothiazoles in Cancer Cells is Implicated by the Induction of a Fast Conformational Change of Tubulin and Suppression of Microtubule Dynamics., Mol Cancer Ther 2013(accepted).

Nimmy Augustine, A.K. Goel,  KC Sivakumar,  R. Ajay Kumar,  Sabu Thomas., Resveratrol - A potential inhibitor of biofilm formation in Vibrio cholera., Phytomedicine 2013.(Available online)

Mithun V Varghese, Annapoorna K, Sivakumar KC, Sathish Mundayoor, GS Vinodkumar., Dry powder cationic lipopolymeric nanomicelle inhalation for targeted delivery of antitubercular drug to alveolar macrophage., Int J Nanomedicine. 2013; 8: 2871–2885.

Thasni KA, Ratheeshkumar T, Rojini G, Sivakumar KC, Rakesh Sathish N, Srinivas G, Asoke B, Veena S, Priya S., Structure activity relationship of plumbagin in BRCA1 related cancer cells., Mol Carcinog. 2013 May;52(5):392-403.

Mani T, Sivakumar KC, Manjula S. Expression and Functional Analysis of Two Osmotin(PR5) Isoforms with Differential Antifungal Activity from Piper colubrinum: Prediction of Structure-Function Relationship by Bioinformatics Approach. Mol Biotechnol., 2012 Nov;52(3):251-61.

Sivakumar KC, Dhanesh SB, Shobana S, James J, Mundayoor S. A systems biology approach to model neural stem cell regulation by notch, shh, wnt, and EGF signaling pathways., OMICS. 2011 Oct; 15(10):729-37.

Mallika V, Sivakumar KC, Soniya EV. Evolutionary Implications and Physicochemical Analyses of Selected Proteins of Type III Polyketide Synthase Family., Evol Bioinform. 2011; 7:41-53.

V. Mallika, KC Sivakumar, E. V. Soniya., PKSIIIexplorer: TSVM approach for predicting Type III polyketide synthase proteins.,Bioinformation. 2011 Apr 22;6(3):125-7.

Aswati Nair R, Kiran AG,  Sivakumar KC, and George Thomas., Molecular characterization of an oomycete-responsive PR-5 protein gene from Zingiber zerumbet., Plant Mol Biol Rep (2010) 28:128–135.

Soman SS,  Sivakumar KC, Sreekumar E. Molecular dynamics simulation studies and in vitro site directed mutagenesis of avian beta-defensin Apl_AvBD2.,  BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S7.

Mallika V,  Sivakumar KC, Soniya EV., A novel system for predicting plant protein kinase superfamily by using machine learning methodology., ACM Digital Library, 2010, http://doi.acm.org/10.1145/1722024.1722064.

Mallika V,  Sivakumar KC, S Jaichand and E V Soniya., Kernel based machine learning algorithm for the efficient prediction of type III polyketide synthase family of proteins., Journal of Integrative Bioinformatics, 2010, 7(1):143.

Radhakrishnan EK, Sivakumar KC, Soniya EV Molecular Characterization of Novel form of Type III Polyketide Synthase from Zingiber Officinale Rosc. and its Analysis using Bioinformatics Method. J Proteomics Bioinform, 2009; 2: 310-315.

Majumder Syamantak, Rajaram Megha, Muley Ajit, Seerapu Himabindu Reddy, Tamilarasan KP, Kolluru Gopi Krishna, Sinha Swaraj, Siamwala Jamila, Gupta Ravi, Ilavarasan R, Venkataraman S, Sivakumar KC, Anishetty Sharmila, Kumar Pradeep G, Chatterjee Suvro., Thalidomide attenuates nitric oxide driven angiogenesis by interplaying with soluble guanylate cyclase., British Journal of Pharmacology, 2009, 158(7): 1720 - 1734.

Sivakumar, KC, Thomas, B. and Karunagaran, D. ‘Three dimensional structure of the closed conformation (active) of human merlin reveals masking of actin binding site in the FERM domain’, International Journal of Bioinformatics Research and Applications 2009; 5(5): 516 – 524.

About the Institution

Rajiv Gandhi Centre for Biotechnology (RGCB) is a premier research institute in India, exclusive devoted to research in Molecular Biology and Biotechnology. It is located at Thiruvananthapuram (Trivandrum), the capital city of the state of Kerala in India. This centre is an autonomous institute under the Department of Biotechnology of the Govt. of India. Previously, it was an R&D centre under Kerala State Council for Science, Technology and Environment.

The Centre was inaugurated on November 18, 2002 by then President of India, Dr. APJ Abdul Kalam. The institute has highly focused research departments working on medical biotechnology (Molecular Medicine, Molecular Reproduction, Molecular Microbiology, Cancer Biology & Neurobiology) and plant genetic engineering. The Center has a regional facility for Genetic Fingerprinting, which provides DNA analysis services for forensic & criminal investigations, paternity disputes, identification of wildlife remains, authentication of plants and seeds besides a battery of molecular diagnostics for genetic and infectious diseases. RGCB is also a major provider of laboratory and infrastructure services to other academic and research institutions.
National Seminars and Workshops

Organizing periodic training programs and seminars has been an integral part of the centre. The centre has been successful in creating awareness among scientists, researchers, students and those interested in the field of bioinformatics. For the last several years, Centre was contributing significantly for the manpower development by organizing workshops and seminars in the field of bioinformatics funded by DBT. Details of various seminars and workshops conducted by DISC are given below:

  • National Seminar on Bioinformatics (NSB’03), 23rd July 2003.
  • National Seminar on Bioinformatics (NSB’04), 14th – 16th December 2004.
  • National Conference and Workshop on Molecular Modeling (NCWMM’06), 21st - 24th March 2006.
  • "Workshop on Molecular Modeling using InsightII – Molecular Visualization and Homology Modeling", 15th - 19th November 2007.
  • "Workshop on Computer Aided Drug Design", 1st - 2nd August 2008
Databases/applications developed

The Centre is actively involved in creating softwares and integrated knowledgebase for those who are working in the areas of plant bioinformatics. Some of the databases and webservers developed at the centre are:

  • PKSIIIexplorer[http://type3pks.in/tsvm/pks3/]
  • PKSIIIpred [http://type3pks.in/prediction/]
  • TypeIII Polyketide Synthase Database [http://type3pks.in]
Infrastructure facilities

To keep pace with the development in the bioinformatics field, impetus is given to set up the necessary computational infrastructure and resources for the research community. The Centre has access to online CDAC Tera-scale Supercomputing Facility (CTSF) on Param Padma Super Computer situated at CDAC-Bangalore. The center has upgraded its computational resources by setting up high performance computing facility. Twelve Intel Core-i7 Desktop PC’s (customized for parallel computing), Three Dell PowerEdge T300 Workstations and Five Dell Vostro 400 PC. The molecular modeling package Accelrys Discovery Studio 2.0 purchased on DBT grant is used for a molecular modeling, docking and simulation studies. Apart from commercial package Discovery Studio2.0, the centre have popular Open bioinformatics softwares such as :- EMBOSS, Autodock, WHATIF, MODELLER ClustalW, Phylip, Cn3D, Rasmol, HMMR, MEGA4, XMGRACE, GROMACS, FTDOCK, PyMol, Jackal, Patchdock, Z-dock etc.


Faculty Members:

Coordinator           Dr. Sathish Mundayoor
Technical Officer      Mr. K. C. Sivakumar
Phone (O)          +91-0471-2342315   ext: 425
Fax      +91-0471-2348096
Email   disc@rgcb.res.in,   sivakumar@rgcb.res.in
Coordinator    Dr. Sathish Mundayoor
Technical Officer    Mr. K. C. Sivakumar
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