About the Bioinformatics Centre

BIF (Bioinformatics Infrastructure Facility) of NIPER is created to support research and teaching efforts in the Pharmacoinformatics department of NIPER. The main focus of BIF is  Computer Aided Drug Design,  Computer Aided Drug Delivery.  Integration of Bioinformatics and Chemoinformatics so as to deliver effective tools and protocols for Pharmacoinformatics research and training is the main  objective of the BIF centre.  The main focus areas are anti-diabetics, anti-malarial, anti-cancer research. Drug metabolism using computational methods, metabolom informatics, metabolism drug databases, metabolite database, research on the oxidation reactions by drug metabolizing enzymes, etc. are extensively being taken up for research at the centre. Drug Delivery Science which incorporates Pharmaceutical Technology, Biotechnology, Information Technology and Nanotechnology are also in active research area at BIF-NIPER.

Area of Specialization:
  • Pharmacoinformatics
  • Computer Aided Drug Design
  • Computer Aided Drug Metabolism
  • Computer Aided Drug Toxicity
  • Computer Aided Drug Delivery
  • Molecular Modeling
  • Quantum Medicinal Chemistry
  • Pharmacoinformatic software tool development
  • Toning up the level of pharmaceutical education and research by training the future teachers, research scientists and managers for the industry and profession.
  • Continuing education programmes
  • Creation of National Centers to cater to the needs of pharmaceutical industries and other research and teaching institutes
  • Collaboration with Indian industries to meet the global challenges
  • National/International collaborative research
  • Curriculum and media development
  • Study of sociological aspects of drug 'use and abuse', and rural pharmacy, etc
  • Conducting programmes on drug surveillance, community pharmacy and pharmaceutical management
Current area of research

Design of Anti-malarial, Anti-cancer, Anti-diabetic and anti-tubercular agent design is the major thrust area.  Computer aided lead identification and lead optimization for all possible disease areas is in progress. Computer aidedDrug delivery and toxicity.

Databases/applications developed

Dendrimer Building Toolkit
It is a pharmacoinformatic software tool developed in house in NIPER for the generation and building of dendrimer, in AMBER Suite.
It is a pharmacoinformatic software tool developed in house in NIPER for estimation of quantity of protein in the medium sample.
Q2 Method Validator
It is a pharmacoinformatic software tool developed in house in NIPER for the validation of the method developed for analysis as per the standards given in ICH Q2 guidline.
Dendrimer Property Calculator
It is a pharmacoinformatic software tool developed in house in NIPER for the calculation of physio-chemical properties of dendrimer.
It is a pharmacoinformatic software tool developed in house in NIPER for the analysis of the active site residues in protein-ligand interactions.
The expanded form of the in house devloped tool is Docked Pose Selector in CYP-450, which analyzes the results of protein-ligand molecular docking, carried out in the Glide module of Maestro of Schrödinger
ChemClean is a specifically designed in house  software tool for 2-D structure sketch and optimization as structure with proper geometry reveals many chemical and physical properties of molecule itself
Dendrimer Builder Toolkit
Dendrimeric nano particles are important class of compounds, the 3D structure of these should be built without tangling problems.  For this purpose, the commercially available tools are also not quite satisfactory.  At NIPER we have developed an innovative method of building these complicated molecular structure and made it available for free.  ( J. Comput. Chem.  2012, 33, 1997). This software is freely downloadable from NIPER, Mohali and IISc, Bangalore webstites.

Infrastructure facilities

Personal Computers : 15
GPU : 2
Servers : 1
Xerox  machine: 1
Printer : 1
Network : NIPER (LAN)

Inter Institutional collaboration

Developed strong collaboration with PU, IISER, IMTECH, Delhi University, etc.. Such groups are headed by

  • Prof. S.V. Kessar, Panjab University, Chandigarh.
  • Prof. A.K. Chakraborti, NIPER, Mohali
  • Prof. P. Rama Rao, NIPER, Mohali
  • Prof. M.P. Mahajan, G.N.D. Univ., Amritsar
  • Prof. A.K. Madan, Guru Jhambeswar University, Rohtak
  • Dr. Damanjit Kaur, Guru Nanak Dev University, Amritsar
  • Dr. S.K. Guchhait, NIPER, Mohali
  • Dr. Vibha Tandon, Delhi University, Delhi
  • Dr. A.K. Verma, Delhi University, Delhi

OSDD-CSIR MPDS Collabration :
Collaboration with CSIR (Council of Scientific and Industrial Research, Govt. of India) intiative OSDD (Open Source Drug Discovery) and contribute and participate in the development of MPDS (Molecular Property Diagnostic Suite), a software toolset that rationally diagnoses (druggable) molecules to provide state-of-the-art Chemoinformatics support to Indian researchers working on myriad aspects of Chemoinformatic sand Drug discovery.

Faculty members
Prof. Prasad V. Bharatam  
Prof. Bharatam, FRSC (PhD,University of Hyderabad) hails from an Indian rural environment and a highly traditional family background. His research expertise is in the design (CADD) and synthesis of computationally designed compounds. He introduced the concepts like ‘additivity of molecular fields’ and ‘nitreones’. His work also deals with the computational analysis of drug metabolism, drug toxicity and drug delivery. He has published 150 original research articles. Various recognitions received by Prof. Bharatam include the Alexander von Humboldt (AvH) fellowship (2002), the Chemical Research Society of India (CRSI) medal (2008), IBM Faculty award (2007), the Ranbaxy Research Award (2008) and the OPPI Scientist award (2009).  
Dr. M. Elizabeth Sobhia  
Dr. M. E. Sobhia is currently working as Assistant Professor in Department of Pharmacoinformatics, at NIPER, S.A.S. Nagar. She completed her master and Ph.D from Department of Crystallography and Biophysics, University of Madras.Her research expertise is in Rational drug design using CADD methods including 3D-QSAR, Molecular Docking, Receptor based and ligand based pharmacophore Mapping, Virtual Screening, and Molecular Dynamics simulations. She has publised around 70 research articles in peer reviewed national and international journals  
Dr. Abhay T. Sangamwar  
He is an Assistant Professor, Dept of Pharmacoinformatics, NIPER, S.A.S. Nagar. He previously held the positions from 2000-2009 as a Senior Lecturer and Head, Dept. of Pharmaceutics, NPC, Nanded, MS, India and previously from 1995-2000 as a Quality Control and Production Executive with a reputed Pharma Industry. His areas of interest include, Lead discovery by Bioinformatics and cheminformatics approaches; Lead optimization by Pharmacoinformatics approach; Model based drug development in translational research in Computer Aided Molecular Design - PK/PD modeling of CYP & p38 MAP kinase and Investigations ofsolid state properties of pharmaceutical solids by in silico approaches. He has got around 30 research publications to hiscredit and research fundings from UGC and DST.  


Name of the Coordinator

Dr. Veena Pande

Postal Address

Depatment of Biotechnology, KumaunUniversityBhimtalCampus, BhimtalUttrakhand- 263136

Phone Number

(05942) 248042

Fax No.

(05942) 248042



About the Institution

National Institute of Pharmaceutical Education and Research (NIPER) is the first national level institute in pharmaceutical sciences with a proclaimed objective of becoming a center of excellence for advanced studies and research in pharmaceutical sciences. The Government of India has declared NIPER as an 'Institute of National Importance'.  It is an autonomous body set up under the aegis of Department of Pharmaceuticals, Ministry of Chemicals and Fertilizers, Government of India.  The Institute is conceived to provide leadership in pharmaceutical sciences and related areas not only within the country, but also to the countries in South East Asia, South Asia and Africa. NIPER is a member of the Association of Indian Universities and Association of Commonwealth Universities.
The Institute is located about 250 Km north of Delhi at S.A.S. Nagar (Mohali), Punjab on a total area of 130 acres.
NIPER Vision
"To become a globally recognized brand in the areas of education and research in pharmaceutical sciences for the benefit of people of India and other countries and the growth of the pharmaceutical industry."
NIPER Mission

  • Imparting quality education in the areas of Pharmaceutical Sciences..
  • Promotion of innovative and translation research.
  • National/ international collaborative research and linkages.
  • Study of national/ international pharmaceutical policy issues.
  • Collaboration with pharma industries to meet the global challenges.
  • Creation of specialized centres to cater to the needs of pharmaceutical industries and other research and teaching institutes.
  • Conducting programmes on drug surveillance, including study of sociological aspects of drug 'use and abuse'.
  • Community pharmacy and pharmaceutical management.
  • Continuing education programme.
Achievements at a glance
  • Training several students of M.S. Pham. Pharmacoinformatics of NIPER Molahi
  • Development of several Pharmacoinformatics tools.
  • Performing lead identification and lead optimization research for anti-diabetic, anti-malarial and anci-cancer agents.
Recent Publications

Vaibhav Jain, P.V.  Bharatam Nanoscale, 2014, DOI - 10.1039/C3NR05400D(accepted)

Detour Matrix based Adjacent Path Eccentric Distance Sum Indices for QSAR/QSPR Part I: Development and Evaluation.Monika Singh, Harish Jangra, P.V. Bharatam and Anil K. Madan. Int. J. Comput. Biol. Drug Design, 2014, (accepted)

Importance of hydrophobic parameters in identifying appropriate pose of CYP substrate in cytochromes. Ramesh M., P.V. Bharatam, Eur. J. Med. Chem. 2014, 71, 15-23

Mechanism-Based Inactivation of Cytochromes by Furan Epoxide: Unravelling the Molecular Mechanism". N. Taxak, S. Kalra, P.V. Bharatam, Inorg. Chem. 2013, 52, 13496-13508.

Comparative modeling of pivotal enzymes, MurA / MurZ, of the peptidoglycan machinery and identification of potential inhibitors by computational methods.                M. Khokhar, N. Kaur, V. Jain, R. Tewari, R. Sandhir, P.V. Bharatam. Med. Chem. Res. 2014, 23, 1819-1828.

Study  of Electronic Structure Analysis, Isomeric Preferences and  Zwitterionicbehaviour of Lornoxicam. Z. Nathewad, S. Bhatia, D. Dhaked, P.V. Bharatam. Computational and Theoretical Chemistry, 2013, 1023, 51-58.

Structural elaboration of a natural product: Identification of 3,3’–diindolylmethane–aminophosphonate and urea derivatives as potent apoptotic anticancer agents which downregulate NF–kB (p65)". S.K. Guchhait, S. Kandekar, R. Preet, M. Kashyap,  M.U., Renu Prasad; P. Mohapatra, D. Das, S.R. Satapathy, R. Shakti, S. Siddharth, V. Jain, M. Choudhuri, C. Kundu, P.V. Bharatam. ChemMedChem. 2013, 8, 1873-1884.

3-Formylchromone based topoisomerase IIa inhibitors: discovery of potent leads. S. Singh, A. T. Bhaviskar, V. Jain,  N. Mishra,  U.C. Banerjee, P.V. Bharatam, K. Tikoo, M.P.S. Ishar. MedChemComm 2013,  4, 1257-1266.

Identification of druggable targets for Acinetobacterbaumannii via subtractive genomics and plausible Inbibitors for MurA and MurB. N. Kaur, M. Khokhar, V. Jain, P.V. Bharatam, R. Sandhir, R. Tewari. Appl. Biochem. Biotech. 2013, 171, 417-436.

Molecular dynamic simulations on PPI dendrimer-drug complexes. V. Jain, V. Maingi, P.K Maiti, P.V. Bharatam.Soft Matter, 2013, 9, 6492-6496.

Rationalizing formation and fate of toxic metabolites from general anesthetics : A DFT study.  V.A. Dixit, S. Bhatia, H. Jangra, P.V. Bharatam. Drug Metabolism Letters, 2013, 6, 221-234.

Importance of C−H∙∙∙O Intramolecular Hydrogen-bonding Across a  Non-proteinogenic γ-aminobenzoic acid residue: Stabilization of a Flat β-Strand-like Template". M. Ramesh,  P.V. Bharatam, P. Venugopalan, R. Kishore, Crystal Growth Design, 2013, 13, 2004-2012.

Synthesis, biological evaluation and molecular modeling studies of novel heterocyclic compounds as anti-proliferative agents. A. Chaudhary, P. P. Sharma, G. Bhardwaj, V. Jain, P. V. Bharatam, B. Shrivastav, R. K. Roy. Medicinal Chemistry Research, 2013, 21, 5654-5669.

Dendrimer Building ToolKit: Model Building and Characterization of Various Dendrimer Architectures V. Maingi; V. Jain; P.V. Bharatam; P. K. Maiti. J. Comp. Chem. 2012, 33, 1997–2011

Metabolic-intermediate Complex Formation with Cytochrome P450: Theoretical Studies in Elucidating the Reaction Pathway for the Generation of Reactive Nitroso Intermediate. N. Taxak, B. Patel,P. V. Desai,M. Mohutsky,V. J. Klimkowski, V. Gombar, P.V. Bharatam. J. Comp. Chem. 2012, 33, 1740-1747

Conformational and Synthon Polymorphism in Bicalutamide: A Quantum Chemical Study. D. K. Dhaked, V.Jain, Y. Kasetti, P.V. Bharatam. Structural Chem. 2012, 23, 1857-1866.

Fourth generation detour matrix based topological indices for QSAR/QSPR part-1: development and evaluation. R.K. Marwaha, H. Jangra, P.V.Bharatam, K. C. Das, A. K. Madan. Int. J. Comp. Biol. Drug Des.

Computational study on the conformational preferences in Nateglinide. V. Jain, D. Kumar Dhaked, Y. Kasetti, P. V. Bharatam. J. Phys. Org. Chem. 2012, 25,649-657

CytochromeP450 Isoenzyme Specificity in the Metabolism of Anti-malarial Biguanides: Molecular Docking and Molecular Dynamics Analyses. D. S. Patel, Ramesh M. and P.V. Bharatam. Med. Chem. Res., 2012, 21, 4274-4289

CYP Isoform specificity towards drug metabolism: Analysis using common feature hypothesis. M. Ramesh, P.V. Bharatam. J. Mol. Mod. , 2012, 18, 709-720

Entrapment and Kinetic Resolution of Stabilized Axial and Equatorial Conformers of Spiro-β-Lactams. N. Anand, B.A. Shah, M. Kapoor, R. Parshad, R.L. Sharma, M. S. Hundal, A.P.S. Pannu, P.V. Bharatam,   S.C. Taneja. J. Org. Chem. 2011, 76, 5999-6006 

N-Fused imidazoles as novel anticancer agents that inhibit catalytic activity of topoisomerase IIα and induced apoptosis in G1/S phase.A.T. Baviskar, C. Madaan, R. Preet, P. Mohapatra, V. Jain, S.K. Guchhait, C. N. Kundu, U.C. Banerjee, P. V. Bharatam. J. Med. Chem. 2011, 54, 5013-5030.

S-Oxidation of thiazolidinedione with hydrogen peroxide, peroxynitrous acid, and C4a-hydroperoxyflavin: A theoretical study. N. Taxak, V. Parmar, D.S. Patel, A. Kotasthane,  P.V. Bharatam. J. Phys. Chem. A, 2011,  115,   891-898.

Computer-aided molecular design of 1H-imidazole-2,4-Diamine derivatives as potential inhibitors of plasmodium falciparum  DHFR enzyme. L. Adane, P.V. Bharatam. J. Mol. Mod., 2011, 17, 657-667. 

A new colorimetric chemodosimeter for Hg2+ based on charge-transfer compound of N-methylpyrrole with TCNQ. P. Kaur, S. Kaur, Y. Kasetti, P.V. Bharatam, K. Singh. Talanta, 2010, 83, 644-650. 

Intramoleculardihydrogen bond: A new perspective in Lewis acid catalyzed nucleophilic epoxide ring opening reaction. V.A. Dixit, P.C. Rathi, P.V. Bharatam. Theochem, 2010, 962, 97-100. 

Comparative 3D QSAR study on β1-, β2-, and β3-adrenoceptor agonists. P. S. Kumar, P.V. Bharatam. Med. Chem. Res., 2010, 19, 1121-1140.

Chiral solvating agents for cyanohydrins and carboxylic acids. L.S. Moon, M. Pal, Y. Kasetti, P.V. Bharatam, R S. Jolly. J. Org. Chem., 2010, 75, 5487-5498. 

Thioureacatalyzedaminolysis of epoxides under solvent free conditions. Electronic control of regioselective ring opening.S.S. Chimni, N. Bala, V.A. Dixit, P.V. Bharatam. Tetrahedron, 2010, 66, 3042-3049. 

A simple, mild and regioselective method for the benzylation of carbohydrate derivatives promoted bysilver carbonate. S. Malik, V.A. Dixit, P.V. Bharatam, K.R.P. Kartha. Carbohydrate Research, 2010, 345, 559-564. 

Electronic structure and reactivity of guanylthiourea: A quantum chemical study. A. Mehdi, L. Adane, D.S. Patel, P.V. Bharatam. J. Comput. Chem., 2010, 31, 1259-1267. 

Inclusion complexes of noscapine in β-cyclodextrin offer better solubility and improved pharmacokinetics. J. Madan, N. Dhiman, V.K. Parmar, S. Sardana, P.V. Bharatam, R. Aneja, R. Chandra,

Importance of selenium in antioxidant behavior of ebselen: A theoretical study.               D. Kaur, P. Sharma, P. V. Bharatam. Theochem, 2010, 939, 118-123.

Shape- and chemical feature-based 3D-pharmacophore model generation and virtual screening: Identification of Potential Leads for P. falciparum DHFR Enzyme Inhibition.L. Adane, D.S. Patel, P.V. Bharatam. Chem. Biol. Drug Design, 2010, 75, 115-126. 

A DFT and CASSCF Study of photocycloaddition reactions of biradicals from 6-Amino-2-(3-Thienoyl)-1,4-benzoquinone. G. Sharma, I. Abraham, R. Pardasani, P.V. Bharatam, T. Mukherjee. Bull. Chem. Soc. Jpn., 2009, 82, 1477-1488.

3D-QSAR analysis of cycloguanil derivatives as inhibitors of A16V + S108T mutant Plasmodium falciparumdihydrofolate reductase enzyme.L. Adane, P.V. Bharatam. J. Mol. Graph. Mod., 2009, 28, 357-367. 

A New chiral shift reagent for determination of enantiomeric excess and absolute configuration of cyanohydrins. L.S. Moon, R.S. Jolly, Y. Kasetti, P.V. Bharatam.     Chem. Commun., 2009, 1067-1069. 


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