The goal of this application is to enhance the computational capabilities at Virginia Commonwealth University (VCU), and benefit the researchers and students on the MCV Campus of VCU, who are interested in using advanced computational methods to investigate the relationship between structure and function of macromolecules at the atomic level. We wish to acquire a new High Performance Computing Cluster (HPCC) to meet a rapidly growing demand for tasks such as molecular modeling and simulation, computational structural biology, bioinformatics, NMR, and X-ray crystallography. By using this state-of-the-art computational facility, scientists can dramatically accelerate their research, reduce the costs for wet-lab experiments, and shorten the period of drug discovery for diseases. By developing and sharing this computational facility a team of investigators will build an environment to nurture collaborations between members and enhance an interdisciplinary research effort at VCU. This facility could also become a resource to attract new investigators to enrich biomedical research at VCU.

Public Health Relevance

Modern biomedical research strongly depends on high-performance computing and powerful computational resources. Advanced computational simulations will help scientists explore the relationship between structure and function of macromolecules at the atomic level, and accelerate the process of structure-based drug discovery for prevention or cure of human diseases.

National Institute of Health (NIH)
National Center for Research Resources (NCRR)
Biomedical Research Support Shared Instrumentation Grants (S10)
Project #
Application #
Study Section
Special Emphasis Panel (ZRG1-BST-M (30))
Program Officer
Levy, Abraham
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
Virginia Commonwealth University
Schools of Medicine
United States
Zip Code
Gangji, Rahaman Navaz; Sankaranarayanan, Nehru Viji; Elste, James et al. (2018) Inhibition of Herpes Simplex Virus-1 Entry into Human Cells by Nonsaccharide Glycosaminoglycan Mimetics. ACS Med Chem Lett 9:797-802
Kummarapurugu, Apparao B; Afosah, Daniel K; Sankaranarayanan, Nehru Viji et al. (2018) Molecular principles for heparin oligosaccharide-based inhibition of neutrophil elastase in cystic fibrosis. J Biol Chem 293:12480-12490
Wang, Huiqun; Kellogg, Glen E; Xu, Ping et al. (2018) Exploring the binding mechanisms of diaminopimelic acid analogs to meso-diaminopimelate dehydrogenase by molecular modeling. J Mol Graph Model 83:100-111
Marmolejo-Murillo, Leticia G; Aréchiga-Figueroa, Iván A; Cui, Meng et al. (2017) Inhibition of Kir4.1 potassium channels by quinacrine. Brain Res 1663:87-94
Sankarayanarayanan, Nehru Viji; Strebel, Tamara R; Boothello, Rio S et al. (2017) A Hexasaccharide Containing Rare 2-O-Sulfate-Glucuronic Acid Residues Selectively Activates Heparin Cofactor II. Angew Chem Int Ed Engl 56:2312-2317
Zheng, Shuo; Kummarapurugu, Apparao B; Afosah, Daniel K et al. (2017) 2-O, 3-O Desulfated Heparin Blocks High Mobility Group Box 1 Release by Inhibition of p300 Acetyltransferase Activity. Am J Respir Cell Mol Biol 56:90-98
Patel, Nirmita J; Sharon, Chetna; Baranwal, Somesh et al. (2016) Heparan sulfate hexasaccharide selectively inhibits cancer stem cells self-renewal by activating p38 MAP kinase. Oncotarget 7:84608-84622
Mosier, Philip D; Chiang, Meng-Jung; Lin, Zhengshi et al. (2016) Broad Spectrum Anti-Influenza Agents by Inhibiting Self-Association of Matrix Protein 1. Sci Rep 6:32340
Sarkar, Aurijit; Yu, Wenbo; Desai, Umesh R et al. (2016) Estimating glycosaminoglycan-protein interaction affinity: water dominates the specific antithrombin-heparin interaction. Glycobiology 26:1041-1047
Moreno, José L; Miranda-Azpiazu, Patricia; García-Bea, Aintzane et al. (2016) Allosteric signaling through an mGlu2 and 5-HT2A heteromeric receptor complex and its potential contribution to schizophrenia. Sci Signal 9:ra5

Showing the most recent 10 out of 32 publications