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HIV Databases 3D Macromolecular Structure
Tools and Introduction

 

3D Structure Viewing Programs

User-Maintained Database of Commercial Molecular Visualization and Modeling Software:
A database of commercial software.
User-Maintained Database of Free Molecular Visualization and Modeling Software:
A database of freeware and shareware software.
The molvisindex.org World Index of Molecular Visualization Resources
A listing of the above two databases, plus many more tools, image galleries, etc.
MDL CHIME:
MDLŽ Information Systems CHIME is a free "plug-in" that works with Netscape versions 4.x (best) and Internet Explorer (with some bugs) for visualizing the three-dimensional structures of macromolecules. The CHIME/Protein Explorer pair and similar tools have essentially superseded RasMol as the tool for quick and easy viewing (rotation, zoom, coloring, etc.) of macromolecular structures obtained via the WWW. Eric Martz has built a nice description of CHIME, its uses, and advantages over RasMol.
Protein Explorer:
Protein Explorer is free software for visualizing the three-dimensional structures of macromolecules. It is arguably the easiest-to-use software of its kind. It is suitable for high school and college students (ages 16 years and older), yet it is also widely used by graduate students and researchers.
DeepView:
DeepView (known until year 2000 as Swiss-PDBViewer) is a powerful visualization and modeling freeware program. It supports mutation, alignment, energy minimization, homology modeling, and more.
Cn3D:
Cn3D is a helper application for your web browser that allows you to view 3-dimensional structures. Cn3D runs on Windows, Macintosh, and Unix-based operating systems. Cn3D simultaneously displays structure, sequence, and alignment, and now has powerful annotation and alignment editing features. Cn3D does not read the Protein Databank structure files s(.PDB format), it reads ASN.1 format files of structures available from the ENTREZ STRUCTURES database at NCBI. Cn3D is an open-source code visualization tool for biomolecular structures, What sets Cn3D apart from other software is its ability to correlate structure and sequence information: for example, a scientist can quickly find the residues in a crystal structure that correspond to known disease mutations, or conserved active site residues from a family of sequence homologs. Cn3D displays structure-structure alignments along with their structure-based sequence alignments, to emphasize what regions of a group of related proteins are most conserved in structure and sequence. Also included are custom labeling features, high-quality OpenGL graphics, and a variety of file exports that together make Cn3D a powerful tool for literature annotation. Cn3D is typically run from a WWW browser as a helper application for NCBI's Entrez system, but it can also be used as a standalone application.
RasMol:
RasMol is free software for visualizing the three-dimensional structures of macromolecules. It is essentially the foundation upon which CHIME and Protein Explorer were built. Anyone who is familiar with RasMol scripting commands, will transition easily to the use of CHIME and PE. RasMol itself remains a viable tool which has the advantages of open source and compatibility with a wider range of computing platforms (whereas CHIME/PE are currently restricted to the NetScape and IE www browsers. The rasmol.org site has the latest enhancements, but for beginners, the U. Mass site has an enormous amount of documentation that is not duplicated at rasmol.org. Reading RasMol documentation is useful for many of the other tools (such as Protein Explorer and CHIME), because they are based on the RasMol foundation, and use similar or identical scripting commands.
Visual Molecular Dymanics ( VM D ):
VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS-X, Unix, or Windows, is distributed free of charge, and includes source code. VMD has much greater power than RasMol, CHIME or Protein Explorer, but also greater complexity and thus more time is required to master its use. VMD scripting commands are not identical to RasMol, so scripts developed on one tool are not portable to the other. VMD produces higher-quality graphical images than CHIME/RasMol/PE.
Software for Kinemages (MAGE, Java-MAGE, KiNG, PreKin, etc.):
Kinemages are 3D-rendered images including but not restricted to chemical/molecular data. Advantages over CHIME-based images are greater platform portability (the only requirement is a www browser with JAVA enabled. Disadvantages are a less easy to use scripting language and lack of the equivalent of Protein Explorer for providing a "front end" to the basic "engine". Kinemages can be rotated by the user, using the mouse, but cannot be manipulated by the user to change colors, views (ball-stick vs. cartoon or spacefill for example), while CHIME images can be.
STING:
STING is a PDB Viewer and Interactive WWW TOOL with emphasis on bi-directional coupling of sequence and 3D information. STING offers a simple and easy way to map single amino acid letter code information in a sequence to its position in 3D and vice versa! Special attention in STING is given to MacroMolecular INTERFACE analysis.


Galleries and Examples

These links provide examples of the usefulness of the above tools. Most of these examples are just .GIF or .JPEG static images taken from 3D-rendered views, so they can be viewed without JAVA or CHIME.
An Accurate Look into HIV:
Teresa Larsen, a guest scientist in Art Olson's Molecular Graphics Laboratory at The Scripps Research Institute (TSRI), has been assembling HIV Macromolecular structure and other evidence into a computer-rendered video of HIV, its life cycle, and the key enzymes that drug designers have targeted. She has also been making a 3D model of HIV-1 in plastic.
HIV-1 RT by Kaylan Das:
Kaylan Das of Rutgers University has been modeling HIV-1 Reverse Transcriptase, and has produced graphical images of RT bound to many RT-inhibiting drugs.
HIV-1 Reverse Transcriptase:
Reverse Transcriptase was "Molecule of the Month" for September, 2002 at the Protein DataBank (PDB)
HIV Reverse Transcriptase Review in Science:
Huang H, Chopra R, Verdine GL, Harrison SC.
Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance.
Science. 1998 Nov 27;282(5394):1669-75.
PMID: 9831551 or (PDF file download)
molvisindex.org galleries list:
The molvisindex.org index of galleries contains galleries of many proteins including some HIV proteins.


CHIME-based Tutorials

(Please CHECK to make sure you have installed the CHIME plug-in into your browser and that it is functioning, before proceeding)
A troubleshooting guide is available.
The Online Macromolecular Museum:
The Online Macromolecular Museum has a gallery of exhibits as noted below. These exhibits are a very good introduction to the power and utility of CHIME-based tutorials. They were created by undergraduate students with the supervision (and editorial corrections) of their professor, David Marcey, and this should serve as inspiration to researchers and graduate students who are not "experts" at macromolecular modeling.
The MHC Complex:
Eric Martz with support from the Division of Undergraduate Education of the National Science Foundation, has created a tutorial on the Major Histocompatibility Complex.
The Consurf Gallery also contains an MHC exhibit, and an exhibit influenza virus hemagglutinin fusion domain, which can be compared to HIV-1 env gp120.
HIV-1 Integrase:
Matthew Bok Walsh and David Marcey have created a HIV-1 integrase tutorial for the On-Line Macromolecular Museum.
HIV-1 Protease Tutorial:
Miyeko Mana and David Marcey have created a HIV-1 Protease tutorial for the On-Line Macromolecular Museum.
HIV-1 Reverse Transcriptase Tutorial:
Matthew Goldman and David Marcey have created a HIV-1 Reverse Transcriptase tutorial for the On-Line Macromolecular Museum.
HIV-1 Nef Protein Tutorial:
Maggie Somple, Nathan Silva, and David Marcey have created a HIV-1 Nef tutorial for the On-Line Macromolecular Museum.
HIV-1 Env and Influenza Hemagglutinin Tutorial:
Erik Mazur and David Marcey have created a tutorial illustrating similarities between the HIV-1 Env protein and Influenza Hemagglutinin for the On-Line Macromolecular Museum.
Index of CHIME-based tutorials:
The molvisindex.org World Macromolecular Visualization Index contains a user-maintained database of CHIME-based tutorials, including some that are HIV-1 proteins. It is a very useful resource for finding examples of tutorials from which ideas can be borrowed for HIV work.


Computational Tools

These links provide some examples of tools that use 3D structure information and/or multiple sequence alignments to and perform computational analyses such as energy minimization.
Incremental combinatorial extension for 3D Structure Alignment:
Shindyalov IN, Bourne PE (1998)
Protein structure alignment by incremental combinatorial extension (CE) of the optimal path.
Protein Engineering 11(9) 739-747.

Combinatorial extension is one of several methods for comparing two protein structures. For example, one may wish to compare the structure of HIV-1 RT with and without an inhibitor bound.
ConSurf:
Consurf is useful for identification of functional regions in proteins by surface-mapping of phylogenetic information. The ConSurf server provides tools to score the site-specific evolutionary conservation within a protein family, and the means to map the scores onto the 3D-structure of a member of this family. The server also provides various intermediate results used in the calculations, such as the multiple alignment of the homologous sequences and the phylogenetic tree describing their relations. The ConSeq server also calculates evolutionary conservation of amino acid sequence, but does not map the results onto a 3D structure.
The PDB Software List:
The PDB software list is similar to the molvisindex.org database of resources. A notable difference is that the molvisindex.org site does not have a good listing of computational tools.
The Predict Protein Server:
PredictProtein is a service for sequence analysis, and structure prediction. You submit any protein sequence and PredictProtein retrieves similar sequences in the database and predicts aspects of protein structure.


Links

DRUMS a set of color codes useful for displaying macromolecular structures
Los Alamos Drug Resistance Database contains information about anti-HIV drugs and drug-resistance-conferring mutations
Other HIV/AIDS sites for more software and information on HIV/AIDS


last modified: Tue May 27 11:35 2008


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