LIST

OF IMP SOFTWARES AND THEIR

USE

Name of the software

followed by Use

1) Chem office / chem. Draw ultra (version no. 10) -- used to draw the structures of drug molecules in 2D and then to convert them in 3 D , to find the IUPAC name of the unknown compound, to find the structure of the drug from its IUPAC name,to give NMR spectrum (approx) of unknown drug. also provide MASS data of compound Give data like
COOH NH 2 N H 2N N N N HOOC N CH3 NH O

Chemical Formula: C20H22N8O5 Exact Mass: 454.17 Molecular Weight: 454.44 m/z: 454.17 (100.0%), 455.17 (24.6%), 456.18 (3.3%) Elemental Analysis: C, 52.86; H, 4.88; N, 24.66; O, 17.60

Boiling Point: 1566.5 [K] Melting Point: 1407.8 [K] Critical Temp: 1309.2 [K] Critical Pres: 28.3 [Bar] Critical Vol: 1203.5 [cm3/mol] Gibbs Energy: 213 [kJ/mol] Log P: 0.9 MR: Henry's Law: 37.5 Heat of Form: -389.6 [kJ/mol] tPSA: 208.42 CLogP: -0.529219 CMR: 11.6419

2)Pymol,Rasmol.Jmol,Molmol , VMD(Visual Molecular Dynamics) ----all these softwares r used to visualize the protein / peptide 3 d structure ---all these softwares r used to visualize the protein / peptide 3 d structure..

VMD 1.8.6 screen shot:

Mole facture structure editing The Theoretical and Computational Biophysics Group is pleased to announce VMD version 1.8.6. VMD provides exciting new capabilities for exporting molecular graphics to 3-D PDF files, high dynamic range images, and eerily "three dimensional" renderings using ambient occlusion lighting with production quality renderers. The MacOS X and Unix versions of VMD now benefit from far more extensive use of multiprocessor (and multicore) acceleration, greatly improving performance for several common structure analysis operations. By default VMD will now use all available processor cores to accelerate parallelized portions of the code which currently include several structure analysis routines, interactive molecular dynamics, and ray tracing. Many new and updated structure building and analysis tools have been added in this release, easing the process of setting up, running, and analyzing computer simulations of biomolecules. This release also contains many performance and efficiency improvements benefiting those loading, displaying, and analyzing large structures with millions of atoms, as well as thousands of medium sized molecules.

MOLMOL (MOLecule analysis and MOLecule display)

MOLMOL is a molecular graphics program for displaying, analyzing, and manipulating the three-dimensional structure of biological macromolecules, with special emphasis on the study of protein or DNA structures determined by NMR. The program runs on UNIX and Windows NT/95/98/2000 and is freely available.

RasMol
RasMol is a program for molecular graphics visualisation originally developed by Roger Sayle. RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images. RasMol runs on wide range of architectures and operating systems including Microsoft Windows, Apple Macintosh, UNIX and VMS systems. UNIX and VMS versions require an 8, 24 or 32 bit colour X Windows display (X11R4 or later). The X Windows version of RasMol provides optional support for a hardware dials box and accelerated shared memory communication (via the XInput and MIT-SHM extensions) if available on the current X Server. The program reads in a molecule coordinate file and interactively displays the molecule on the screen in a variety of colour schemes and molecule representations. Currently available representations include depth-cued wireframes, 'Dreiding' sticks, spacefilling (CPK) spheres, ball and stick, solid and strand biomolecular ribbons, atom labels and dot surfaces.

3)Discovery studio gate --- used for molecular modeling and docking

Discovery Studio http://accelrys.com/products/datasheets/ds-overview-20.pdf

4) Endnote ---used to give reference @ the end of ur project.. 5)Lhasa LPS ( Derek) ---for toxicity prediction of the drug.. 6)modeller 9V3 ---for homology modeling MODELLER is used for homology or comparative modeling of protein three-dimensional structures. The user provides an alignment of a sequence to be modeled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms. MODELLER implements comparative protein structure modeling by satisfaction of spatial restraints, and can perform many additional tasks, including de novo modeling of loops in protein structures, optimization of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison of protein structures, etc. 7)2D QSAR, 3D QSAR, CoMFA,CoMSIA ---for finding the structure activity relationship (CoMSIA ) stand for Comparative Molecular Similarity Indices Analysis CoMFA (Comparative Molecular Field Analysis) 8)BLAST,FASTA,PROSPECTUS,COPIA ---for sequence alignment of proteins.. and nucleic acids..

9)Genscan, Glimmer ---gene finding and sequence analysis 10)CLUSTAL W ,CLUSTAL X ---for sequence alignment of proteins.. 11)AMBER,CHARMM,chem2 pac,GROMOS,GROMACS,MOE,SCHRODINGER ---3 D structure visualization,molecular dynamics,energy minimixation.. 12)MM2,MOPAC, AM1, PM3 ---molecular dynamics 13)Gaussian ---for quantum chemistry calculations 14)Sigmastat ---used for statistical calculations.. 15)Alchemi,cache,SYBYL ---structure drawing, 3 D visualization of drugs and proteins 16)EMBOSS(European Molecular Biology Open Software Suite) ,GCG ---clusture of many softwares used mainly for homology modeling 17)Autodock ---for docking studies (checking drug molecular fitting into receptor) 18)Topkat ---used for toxicity prediction 19)Tripose --mainly used for molecular design and drug design