Softwares developed by BIC group

 

    Protein Modelling

  • CPSSD

    • (Compact Protein secondary structure Database): allows one to extract protein secondary structure information from DSSP files to create protein secondary structure database in compact and user friendly format.

  • ASSP

    • (Assessment of secondary structure prediction): has been develop ed for evaluating the quality of protein secondary structure prediction and for appraising the secondary structure prediction methods.

  • ONNM

    • (Optimized Nearest Neighbour Method): was developed to predict the protein secondary structure from their amino acid sequence. It first predicts the secondary structure by combining netural network and nearest neghbour approach.

  • PSSPR

    • (Prediction of Protein Conformational States): A 64 conformational states prediction method has been developed to predict the dihedral angle of protein backbone.

  • CATSP

    • (Computer Aided Tertiary Structure Prediction): This program used the dihedral angles of protein backbone and s econdary structure information and generate the Cartesian coordinate of tertiary structure of protein. This program also allow to use the rotamer library (Dunbark and Karplus) to compute the sidechain angles.

     

    Molecular Biology

  • DNASIZE

    • This computer program has been developed for computing the size of DNA fragments from their electrophoretic mobilities using a graphical method. This program can also be used to compute the size of proteins or polypeptides from SDS-PAGE. In addition to computing the size of DNA fragments and protein size the program also allows one to present the comparison of standard curves obtained from gel electrophoresis (or SDS-PAGE). The program is written in C and can be run on IBM PC or a compatible computer under MS-DOS version 2.0 or higher, and requires a CGA, EGA or VGA card. Click to down load this program.

    Reference: Raghava, G.P.S. (1994) Improved estimation of DNA fragment lengths from gel electrophoresis. Biotechniques 17: 100-104.

    This package is also avilable from ftp site (dnasize.$exe) of EBI

  • GMAP

    • comprehensive computer program GMAP, has been developed for mapping the potential restriction endonuclease (R. E.) sites in non-ambiguous DNA sequence, predicting the number and type of mutations required to introduce unique R.E. sites in the non-ambiguous, searching all R.E. s ites in ambiguous DNA sequence obtained by reverse translation of a given amino acid sequence; iv) searching R.E. sites in DNA sequence obtained from reverse translation of amino acid sequence employing user-defined codon usage. These facilities allow the program to be employed for the design of synthetic genes as well as the modular redesign of gene. Click to down load this program.

    Reference: Raghava, G.P.S. and Sahni, G. (1994) GMAP: a multipurpose computer program to aid synthetic gene design, cassette mutagenesis and introduction of potential restriction sites into DNA sequences. Biotechniques 16: 1116-1123. (Compact Protein secondary structure Database): allows one to extract protein secondary structure information from DSSP files to create protein secondary structure database in compact and user friendly format.

    The vax/vms version of this package is avilable from EBI ft p site. The DOS version is also avilable from ftp site (gmap$.exe) of EBI.

  • DNAOPT

    • DNAOPT computer program has been developed to assist the users in optimizing the conditions of gel electrophoresis and SDS-PAGE. Click to down load this program.

    Reference: Raghava, G. P. S. DNAOPT : A computer program to aid optimization of gel conditions of DNA gel electrophoresis and SDS-PAGE. Biotechniques 18: 274-81.

     

    Immunology

  • ELISAeq

    • A computer program is developed which utilizes a graphical method for determining the concentration of either the antibody or the antigen from ELISA data. This computer program also calculate essential parameter the signal, capacity and flatness (constants used in hyperbolic regression), for ELISA optimization.This program is develoed in GW-BASIC at IBM-PC under DOS. Click to down load this program.

    Reference: Raghava, G.P.S., Joshi, A.K. and Agrewala, J.N. (1992) Calculation of antibody and antigen concentrations from ELISA data using a graphical method. J. Immunol. Methods 153, 263-264.

  • Ab-Affi

    • A simple and reliable method based upon law of mass action for calculating affi nity of a monoclonal antibody using non-competitive ELISA, has been developed. This program is develoed in GW-BASIC at IBM-PC under DOS. Click to down load this program.

    Reference: Raghava, G.P.S. and Agrewala, J.N. (1994) Method for determining the affinity of monoclonal antibody using non-competitive ELISA : A computer program. Journal of Immunoassay 15: 115-128.

  • IL4IFNG

    • A computer program for computing of murine interleukin-4 and interferon-gamma by exploiting the unique abilities of these lymphokines to induce the secretion of IgG1 AND IgG2a has been developed.This program is develoed in GW-BASIC at IBM-PC under DOS. Click to down load this program.

    Reference: Agrewala, J.N., Raghava, G.P.S., Mishra, G.C. (1993) Measurement and computation of murine interleukine-4 and interfron-gamma by exploiting the unique abilities of these lymphokines to induce the secretion of IgG1 and IgG2a. Journal of Immunoassay 14, 83-97.

     

    Miscellaneous

  • Hemo

    • A computer program which facilitates the feeding of OD data directly from ELISA reader by interfacing it to the computer for computing parameters like C50, C100 and beta and representing hemolytic pattern of drugs graphically has been developed. The program, for analysis and calculation of the data is written in Q-BASIC.This program is develoed at IBM-PC under DOS. Click to down load this program.

    Reference: Raghava, G.P.S., Goel, A., Singh, A. M., and Varshney, G. (1994) A Simple Microassay for Computing the Hemolytic Potency of Drugs. Biotechniques it 17: 1148-53.

 

Bioinformatics Centre has procured several software from general purpose to specific use with commercial and/or academic licenses. Some of the software at BIC are:

 
  • Molecular Modelling

    • AMBER, GROMOS, CHARMM, BiomedCache, MODELER, Hex, AutoDock, Babel and Insight II.

  • Sequence and Structure Analysis

    • Wisconsin package, BLAST, CLUSTAL-W, PHYLIP, DSSP, CE and SSAP.

  • Statistical Analysis

    • SPSS, Stastica and R.

  • Molecular Graphics

    • Rasmol, Midas Plus, Swiss PDB viewer, MOLMOL and MOLSCRIPT.

  • Artificial Intelligence

    • SNNS and Support Vector Machine.

  • Database

    • Oracle and PostgreSQL.

  • Graphs and Graphics

    • Sigma Plot, GNU Plot, Corel Draw and Adobe PhotoShop.

  • Document Publishing and Presentation

    • Adobe Suite, MS Office, Reference Manager and Star Office.

  • Hindi Publishing

    • Hindi Software Tools, Akshar for Windows and LeapOffice 2000.

  • Web Designing

    • Adobe Illustrator, Front Page, Page Maker, MS Publisher and Macromedia Dreamweaver.

  • Anti-virus software

    • Norton AntiVirus, MacAfee Virus Scan and Kaspersky.

  • Operating Systems

    • Microsoft Windows: Advance server 2003, 2000 Professional, XP, Vista, windows-7. Red Hat Enterprise Edition Advanced Server, SGI IRIX, Solaris 10, Suse Enterprise and Cent OS and Darwin XServe2.

 

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