NCSI: Molecular Dynamics Simulation of Alanine Racemase in Pathogen Pseudomonas Aeruginosa for Drug Design Purposes

Status	Completed
Mentor Name	Hung-Chung Huang
Mentor's XSEDE Affiliation	XSEDE Empower program mentor during 2020 Spring.
Mentor Has Been in XSEDE Community	4-5 years
Project Title	Molecular Dynamics Simulation of Alanine Racemase in Pathogen Pseudomonas Aeruginosa for Drug Design Purposes
Summary	Pseudomonas aeruginosa is an opportunistic pathogen and associated with serious cross-infections in the hospitals and clinics; the D-alanine produced by alanine racemase (AlaR) is used for peptidoglycan biosynthesis in bacteria, so AlaR is a good drug design target on P. aeruginosa. Limited X-ray structure for the AlaR from P. aeruginosa, so ten AlaR high-resolution structures from Geobacillus stearothermophilus would be studied and compared to Molecular Dynamics (MD) simulation trajectory of the AlaR from P. aeruginosa (with PDB ID: 6a2f) for drug design purposes.
Job Description	Students will learn how to set up the Alanine Racemase 3D structure (PDB ID: 6a2f) with ligand(s) and cofactor PLP in a water box based on the CHARMM force field, then do the MD simulation with UIUC/NAMD in a supercomputer in XSEDE resources. Students will learn how to resume job, collect, and transfer data to our Bioinformatics Lab where the MD trajectory data will be further processed and analyzed.
Computational Resources	We need the supercomputing power in XSEDE resources for the parallel supercomputing with UIUC/NAMD program. The mentor Dr. Huang has obtained XSEDE startup computing resources on April 2020 that include SDSC Comet GPU Nodes (Comet GPU) with 2,500.0 GPU Hours and PSC GPU (Bridges GPU) with 2,500.0 GPU Hours. We will use "Comet GPU" and/or "Bridges GPU" in XSEDE with the CUDA GPU version of UIUC/NAMD program to run our MD simulations.
Contribution to Community
Position Type	Learner
Training Plan	The expected level of student effort for semester participation is 12 weeks at 8 ~10 hours per week. Planned trainings are shown as listed below. 1. Unix basics and commonly used Unix (Linux) commands in order to navigate the system in XSEDE and the Linux servers in Dr. Huang's Lab. 2. charmm program and CHARMM force field basics 3. UIUC/NAMD set up and running basics 4. MD data collection and transfer basics 5. MD data analyses with UIUC/VMD program
Student Prerequisites/Conditions/Qualifications	The PI Dr. Hung-Chung Huang have been familiar with MD simulation work with a MD paper featured in the cover of Biopolymers Journal (March 2008 issue) as seen in the link below. https://onlinelibrary.wiley.com/doi/abs/10.1002/bip.20893
Duration	Semester
Start Date	09/15/2020
End Date	12/15/2020