Tools

Molecular Graphics Tools and Resources

TOOLS DESCRIPTIONS WEB SITES REFERENCES
The RCSB Protein Data Bank The Protein Data Bank is the single worldwide repository for the processing and distribution of 3-D biological macromolecular structure data. PDB Berman, H. M., J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne. "The Protein Data Bank." Nucleic Acids Research 28 (2002): 235-242.
Deep View Swiss PDB Viewer The Deep View Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyze several proteins at the same time. Deep Viewer Guex, N., and M. C. Peitsch. "SWISS-MODEL and the Swiss-Pdb Viewer: An Environment for Comparative Protein Modeling." Electrophoresis 18 (1997): 2714-2723.
National Center for Biotechnology Information Established in 1988 as a national resource for molecular biology information, NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information - all for the better understanding of molecular processes affecting human health and disease.

This Web site provides access to a myriad of biological sequence databases, structural databases, bioinformatics tools, and literature search tools.

NCBI
Basic Local Alignment Search Tool BLAST provides a method for rapid searching of nucleotide and protein databases. It is a sequence comparison algorithm optimized for speed used to search sequence databases for optimal local alignments to a query. BLAST

Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. "Basic Local Alignment Search Tool." J. Mol. Biol. 215 (1990): 403-410.

ClustalW Alignment ClustalW is a general purpose multiple sequence alignment program for DNA or proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. ClustalW Alignment

Higgins, D., J. Thompson, T. Gibson, J. D. Thompson, D. G. Higgins, and T. J. Gibson. "CLUSTAL W: Improving the Sensitivity of Progressive Multiple Sequence Alignment through Sequence Weighting, Position-specific Gap Penalties and Weight Matrix Choice." Nucleic Acids Res. 22 (1994): 4673-4680.

RASMOL RasMol is a molecular graphics program intended for the visualization of proteins, nucleic acids and small molecules. The program reads in molecular co-ordinate files and interactively displays the molecule on the screen in a variety of representations and colour schemes. Supported input file formats include Brookhaven Protein Databank (PDB), Tripos Associates' Alchemy and Sybyl Mol2 formats, Molecular Design Limited's (MDL) Mol file format, Minnesota Supercomputer Centre's (MSC) XYZ (XMol) format and CHARMm format files. Different parts of the molecule may be represented and coloured independently of the rest of the molecule or displayed in several representations simultaneously. RasMol can read a prepared list of commands from a 'script' file (with a *.spt extension) to allow a given image or viewpoint to be regenerated quickly. RASMOL

Sayle, Roger, and E. James Milner-White. "RasMol: Biomolecular Graphics for all." Trends in Biochemical Sciences (TIBS) 20, no. 9 (September 1995): 374.