Research Facilities and Services

The Molecular Modeling facility provides the modern modeling software suites on Windows and Linux platforms and technical assistance in performing QSAR, Protein receptor-ligand docking, Virtual screening, Cheminformatics, Molecular Dynamics, and other functions required for drug discovery. This facility will be instrumental in assisting with the research conducted in the FAMU-RCMI Cancer and Neuroscience Cores.

EQUIPMENT:
The Molecular Modeling facility supports a perpetual license for Sybyl-X 2.0 software suite and annual academic licenses for the following software.

1. Cresset Computational Chemistry Software.
2. Open Eye Scientific Software.
3. Scalable Molecular Dynamics Software (Desmond, NAMD).

For teaching purposes, we have two dedicated Linux machines in Laboratory for Molecular Modeling, New Pharmacy Building, and for research purposes, dedicated Windows/Linux dual operating system work stations in all Medicinal Chemistry laboratories in CoPPS, IPH.

SPECIFIC SERVICES:

• Lead optimization by QSAR Analysis for a dataset containing the activity values using CoMFA, Topomer CoMFA, CoMSIA, Pharmacophore based hypothesis generation, and receptor-ligand docking analysis.
• Small molecule modeling and simulation include conformation generation and clustering, filtering, molecular mechanics, and dynamics.
• Macromolecular modeling and simulations include protein crystal structure refinement methods, homology modeling, and molecular dynamics.
• Lead discovery methodologies include ligand-based and structure-based methods. The structure-based methods consist of docking, virtual screening workflow, receptor-based core hopping, protein structure alignment, etc.

STAFF:
Dr. Suresh Eyunni (suresh.eyunni@famu.edu), under the supervision of Dr. Kinfe Redda (kinfe.redda@famu.edu), operates the facility. Dr. Eyunni is responsible for conducting individual and group training sessions and providing technical assistance. Hands-on training of the software and methodologies would be provided to learners and staff in the College either personally or in a group upon request. Graduate learners are anticipated to learn valuable modeling principles and techniques for application in their scientific projects.  They can also utilize the facility's resources and personnel expertise to enhance their insight into modeling research tools. Most of the modeling software comes with Application Programming Interface (API) to customize their modules. Our facility will support their endeavors.

FEE STRUCTURE: 
At present, the facility would not charge any fee for its services. However, the facility staff strongly encourages the learners and faculty to gain valuable experience using the software for their research purposes. The facility staff is responsible for training, troubleshooting, obtaining licenses, and implementing the requested software. If a staff member of the facility is involved in more than 50% of the computational work in a learner/PI's research, they are expected to be included as an author in the learner/PI's publication/patent or conference abstract/poster. If the staff member's contribution is less than 50%, the staff member and the facility would be acknowledged in the abstracts/posters/publications as appropriate for their services.

The Nuclear Magnetic Resonance Facility (NMR) provides instrumentation and technical assistance for obtaining NMR spectra for liquid samples. This facility supports drug discovery research and other chemicals, biochemical research to monitor chemical reactions, identify/elucidate chemical structures, and determine the purity of synthetic products. This facility also provides basic training for graduate and undergraduate learners in the CoPPS, IPH, and chemistry departments on how to use the instrument to meet their research / experimental needs and the requirements for medicinal chemistry or medicinal chemistry organic chemistry courses.

SPECIFIC SERVICES:

1. Standard1-D Hydrogen spectra, liquid samples;
2. Standard 1-D Carbon spectra, including APT, DEPT, liquid samples;
3. Homo 2-D experiments, COSY, etc.;
4. Hetero 2-D experiments, HETCOR, etc.;
5. Special observation of ¹⁵N, ³¹P, ¹⁹F spectrum (with advance schedule).
6. Special experiments under temperature from -80 ^oC to 200 ^oC (with advance schedule).

EQUIPMENT:  
The facility has one Varian NMR Spectrometer system, Mercury plus 300 MHz Spectrometer system, with ATB (Automation Triple-Resonance Broadband) PFG (Pulsed Field Gradient) probe, Carousel autosampler, and software VNMRJ 2.2D.

The facility has the Bruker Avance III HD 600 high-performance digital NMR system with SmartProbe, which can observe ¹⁵N, ³¹P, ¹⁹F, ¹H, and ¹³C and BSVT, which allows experiments at temperatures from -80 ^oC to 200 ^oC.

STAFF:
The NMR facility will be operated by Dr. Wang Zhang, the facility manager (wang.zhang@famu.edu) (850-412-5356). He is responsible for maintenances and coordination of the routine usage of the instrument among individuals and providing technical assistance to requested operators.

FEES:
We charge $7.50 for each hydrogen spectrum; $15.00 for each carbon spectrum ($20 to $30 for diluting sample, which requires an extended scan). Special experiments with other nuclear or under non-room temperature will charge extra fees determined by the time required for the service.

The Proteomics facility provides various proteomic services, including protein molecular weight determination, identification, and analysis.  This facility will enable FAMU biomedical researchers to answer pressing biological questions about the functions and roles of proteins in diseases impacting the underserved and minority populations.  With sample preparation, separations, mass spectrometry, and informatics, we will be able to provide information that drives knowledge about disease pathology, and target-based drug discovery will be realized.

EQUIPMENT:

• ABSciex 4800 MALDI TOF-TOF Mass Spectrometer
• Protean IEF System
• TM-Sprayer
• Bio-Rad VersaDoc 4000 Imager
• Phospho Imager
• Creiterion Dodeca Cell and Criterion Cell

SPECIFIC SERVICES:

• Protein separation using either 2D-Gel electrophoresis
• Gel imaging using Bio-Rad VersaDoc Imager
• Archiving and retrieval of proteomics data for protein informatics analysis
• Sample preparation
• Provide consultation on experimental design
• Provide individual/group proteomics training
• Digest samples were analyzed using ABSciex 4800 MALDI-TOF-TOF
• Gel spot cutting, trypsin digestion, and peptide extraction

STAFF:
The Proteomics facility will be managed and operated by Dr. Equar Taka (equar.taka@famu.edu) and Dr. Tracy Womble (tracy.womble@famu.edu) under the supervision of Dr. Selina Darling-Reed (Selina.darling@famu.edu).

FEE STRUCTURE:
Regarding fees, please contact either facility managers, Dr. Tracy Womble (850-561-2466) or Dr. Equar Taka (850-599-3127). At present, the facility does not charge any fee to FAMU RCMI or non-RCMI faculty members for the services provided. However, this is subject to change. The facility staff strongly encourages the learners and faculty to gain valuable experience using the software for prospective research projects. The facility staff is responsible for training, troubleshooting, obtaining licenses, and implementing the requested software. If a staff member of the facility is involved in more than 50% of the computational work in a learner/PI’s research, the staff member is expected to be included as an author in the learners/PI’s publication/patent or conference abstract/poster. If the staff member's contribution is less than 50%, the staff member and the facility would be acknowledged in the abstracts/posters/publications as appropriate for their services.