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Protein explorer

The ideal procedure would find the global minimum in the interaction energy between the substrate and the target protein, exploring all variable degrees of freedom for the system. To meet these demands a number of docking techniques simplify the procedure and the user will choose the ones closest to the topic being studied. [Pg.203]

Visualization software allows the user to display molecular structures imported from databases or other software programs. Chime, RasMol, and Protein Explorer programs are available at the websites listed below for Windows operating PCs and Macintosh PowerPC computers. [Pg.149]

Protein Explorer, a free RasMol and Chime derivative with extended capabilities, is available at http //www.umass.edu/microbio/chime/explorer/. The program allows the user to visualize macromolecular structure in relation to function. [Pg.151]

Protein explorer This program is the expanded version of Rasmol and works very well. It is available at http //proteinexplorer.org and has better mouse control than Rasmol. [Pg.476]

Lysozyme and Antibodies To fully appreciate how proteins function in a cell, it is helpful to have a three-dimensional view of how proteins interact with other cellular components. Fortunately, this is possible using on-line protein databases and the three-dimensional molecular viewing utilities Chime and Protein Explorer. If you have not yet installed the Chime plug-in on your computer, go to www.mdlchime.com/chime and follow the instructions for your operating system and browser. Once chime is installed, go to the Protein Data Bank (www.rcsb.org/pdb). [Pg.189]

In this exercise you will examine the interactions between the enzyme lysozyme (Chapter 4) and the Fab portion of the anti-lysozyme antibody. Use the PDB identifier 1FDL to explore the structure of the IgGl Fab fragment-lysozyme complex (antibody-antigen complex). View the structure using Protein Explorer, and also use the information in the PDBsum summary of the structure to answer the following questions. [Pg.189]

Protein Explorer is free software for visualizing the 3D structures of protein, DNA, and RNA macromolecules, and their interactions and binding of ligands, inhibitors, and drugs found at the URL http //molvis.sdsc.edu/protexpl/frntdoor.htm. [Pg.419]

Protein Explorer is a knowledge base with introductory information on many topics about protein structure, such as the origins and limitations of 3D protein structure data, specific oligomers vs. crystal contacts, hydrogen bonds, cahon-pl interactions, etc. Protein Explorer is more user-friendly than the comparable software RASMOL, also available on servers such as ExPASy. [Pg.419]

I. RasMol and Protein Explorer http //www.umass.edu/microbio/rasmoE and http //molvis.sdsc.edu/protexpEfrntdoor.htm, respectively. [Pg.211]

Protein explorer is one of the most widely used visualization tools for protein structures. Protein Explorer is free software for visualizing the three-dimensional structures of protein, DNA, and RNA macromolecules, and their interactions and binding of ligands, inhibitors, and drugs. Protein explorer is easy to use, free, and widely used. It can be used be novice users as well as experts. The RasMol website has been visited by over 250,000people from 115 countries. [Pg.213]

Q Finding and Viewing Your Favorite Molecules In Protein Explorer -... [Pg.214]

Juick-Start Protein Explorer o explore DNA complexed with a protein... [Pg.214]


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See also in sourсe #XX -- [ Pg.211 ]




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