Software and Services: Molecular Modeling

The Molecular Modeling Center supports various molecular visualization programs, homology modeling and threading programs, and collaborative support in structure evaluation.

 

Molecular Modeling Center - MMC Subscription:

SYBYL and All other Linux/SGI served programs (includes data backup).
Use of MMC Linux/SGI workstations (graphics and computational time)
Access to Ingenuity Pathways Analysis software
Access to On-line Current Protocols
2 registrants in any MMC basic class or 1 registrant MMC advanced class.
4 hours personnel support (consultation, programming, sys-admin, etc).

• Graphical Display (SYBYL)
• Protein Analysis
• Homology Modelling (Modeller, Threader)
• Interactive Protein Design
• Docking and Drugs  (in collaboration with Emerson Center)

 

Sybyl

Sybyl, molecular structure and visualization software, is available to BimCore subscribers. Sybyl is accessible on the Linux workstations in the BimCore computer lab, Room B28, 1462 Bldg. Current Sybyl licenses include: Sybyl Base, Biopolymer, Dynamics, Molcad. To request consultation or training, please contact Kim Gernert by email or phone at 404-727-3501.

Additional Sybyl modules (Advanced Computing, FlexX, QSAR, Unity) are available through Emerson Center or Dr. Jim Snyder.

Modeller

Modeller is used for homology or comparative modeling of protein three-dimensional structures. A. Sali (ref); A. Sali lab.

Modeller can be accessed through collaboration with BimCore staff (email K Gernert), through a BimCore Web Interface, through on-line tutorials, or past in-class lab tutorials (GMB790r, K Gernert). See A. Sali manual.

Threader

Threader, optimal sequence threading, is a fold recognition program used for sequence to structure alignment where no sequence homology is found.

Threader can be accessed through collaboration with BimCore staff (email K Gernert), through a BimCore Web Interface, or past in-class lab tutorials (GMB790r, K Gernert).

On-line Protocols

BimCore has licensed OnLine Protocol content from Wiley Publishing and it is now available to BimCore subscribers. This agreement provides limited access to various protocols. The terms of our agreement require users to login to the Current Protocols page from an Emory IP or through the Emory VPN.

Emory Protocols include: Bioinformatics, Cell Biology, Cytometry, Human Genetics, Immunology, Magentic Resonance Imaging, Neuroscience, Nucleic Acid Chemistry, Pharmacology, Protein Science, Toxicology, Molecular Biology, Microbiology

Bioinformatic Tutorials

Bioinformatic Tutorials are multi-step tutorials including step-by-step directions, hints and interpretations, which walk you through the steps of homology modelling listed below. Contact K Gernert for access and additional support.

1. sequence analysis (predictions, annotations, Expasy: sprot)
2. blast searches
3. selection of homologs
4. evaluation through: prodom, pfam, interpro
5. homologous protein families
6. evaluation of known protein structures
7. sequence to structure alignment (Dali)
8. model building
9. model evaluation
10. optimization.

Contact K Gernert for additional support.