Services

Are You Ready to Request a Consultation or Service?

All requests can be made via e-mail or by submitting a Service Request Form. Please indicate all of the project's MMS specific aims and objectives. New customers should include in their request, background information, and literature data.

Services Provided

Modeling of proteins and nucleic acids structures
Once a new target protein or nucleic acid is identified, its three-dimensional structure can provide valuable information about the target. The MMS can build, model, and study different protein and nucleic acid structures.

Protein–protein and protein–nucleic acid interactions
Many biochemical pathways in the human body (particularly cancer signaling pathways) involve an interaction between two proteins and/or a protein and nucleic acids. Using modeling techniques, such interactions can be studied.

Interaction of proteins/nucleic acids with small molecules
Interactions of small molecules with the target proteins and nucleic acids can be studied. Understanding such interactions helps to prioritize the small molecules for actual synthesis and minimize the synthetic efforts.

Virtual screening of small molecule databases
The MMS has a large database of small molecules. This database can be searched for potential inhibitors of target proteins. Since most of the small molecules are commercially available, these can be purchased and then tested for activity.

Structure-activity relationship (SAR) studies
Quantitative SAR studies are useful in cases when the structure of a target protein is not known. In such cases, using SAR studies on a series of molecules with similar activity, pharmacophore requirements can be derived.

Software Resources Available through MMS

Insight II programs; Accelrys

Biopolymer: Protein and DNA modeling

Discover/Discover 3: Molecular mechanics and dynamics program

Affinity Docking: Small molecule docking for protein and nucleic acids

Sybyl; Tripos Inc.

Biopolymer with Site ID: Protein modeling with identification of sites on protein

FlexiDock and FlexX/FlexS: Docking and superimposition programs for small molecules

Unity 4.4 databases: Virtual databases of small molecules with pharmacophore searching facility

DISCOtech: Pharmacophore mapping program

2006 Collaborations

^{*Cancer Metastasis and Signaling and Molecular and Genetics joined together in 2009 to form the Cancer Biology and Genetics Program as the basic science arm of the Arizona Cancer Center.}  

Fees

Fees and charges for the use of Molecular Modeling Service are based upon the total annual budget and total usage. Usually customers are billed every three months for on-going projects. Short duration projects are billed at the end of the project.

For any accounting questions, please contact David Bishop, the MMS Program Coordinator.