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 as required for drug discovery This facility will be instrumental in assisting with the research conducted in the newly proposed FAMU-RCMI Cancer and Neuroscience Cores
At present Molecular Modeling Facility is supported by a perpetual license for Sybyl-X 2.0 software suite, annual academic licenses for 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.
- 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, which include conformation generation and clustering, filtering, molecular mechanics and dynamics.
- Macromolecular modeling and simulations which include protein crystal structure refinement methods, homology modeling and molecular dynamics.
- Lead discovery methodologies which include ligand based and structure based methods. The structure based methods consists of docking, virtual screening work flow, receptor based core hopping, protein structure alignment etc.
The molecular modeling facility will be operated by Dr. Suresh Eyunni, (firstname.lastname@example.org) under the supervision of Prof. Ken Redda (email@example.com). Dr. Suresh Eyunni would be responsible for conducting individual and group training sessions and providing technical assistance.
Hands on training on the software and methodologies would be provided to students and staff in the College of Pharmacy and Pharmaceutical Sciences either personally or in group upon request.
Graduates are anticipated to learn valuable modeling principles and techniques for application in their individual scientific projects. They can also utilize the facility’s resources and personnel expertise to enhance their insight into modeling as a research tool. Most of the modeling software comes with Application Programming Interface (API) to customize their modules. Our facility will support their endeavors.
At present, the facility would not charge any fee for their services. The facility staff, however strongly encourage the students and faculty gain valuable experience in using the software for their research purposes. The facility staff is responsible for training, trouble shooting, obtaining licenses and implementation of the requested software. If a particular staff of the facility is involved in more than 50 % of the computational work in a student/PI s research, he is expected to be included as an author in the student/PI s publication/patent or conference abstract/poster. If the contribution of the staff is less than 50 % he and the facility would be expected to be acknowledged in the abstracts/posters/publications as appropriate for their services.