Software

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

GMAP: A 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. sites 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.

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.

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 affinity 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

Misscellaneous

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.