I support NIAID research projects by performing computer modeling of protein structures. My main areas of expertise include drug discovery applications such as ligand-protein docking and QSAR, structural modeling including molecular dynamics simulations, and advanced visualization techniques such as Virtual Reality and Augmented Reality.
Selected Publications
Kern, O., Leon, P.C.V., Gittis, A., Bonilla, B., Cruz, P., Chagas, A.C., Ganesan, S., Ribeiro, D., Martin-Martin, I., and Calvo, E. The structures of two salivary proteins from the West Nile vector Culex quinquefasciatus reveal a beta-trefoil fold with putative sugar binding properties
, Current Research in Structural Biology, 3, 95-105 (2021).
Remcho, T., Guggilapu, S., Cruz, P., Nardone, G., Heffernan, G., O'Connor, R., Bewley, C., Wellems, T., and Lan, K. Isomerization of antimalarial drug WR99210 explains its inactivity in a commercial stock
, Antimicrobial Agents and Chemotherapy, 65(1), e01385-20 (2020).
Pan, M., Neilson, M.P., Grunfeld, A.M., Cruz, P., Wen, X., Insall, R.H., Jin, T. A G-protein-coupled chemoattractant receptor recognizes lipopolysaccharide for bacterial phagocytosis
, PLOS Biology, 5/25/2018, PLoS Biol 16(5): e2005754 (2018).
Sampaio, E.P., Ding, L., Rose, S.R., Cruz, P., Hsu, A.P., Kashyap, A., Rosen, L.B., Smelkinson, M., Tavella, T.A., Ferre, E.M.N., Wierman, M.K., Zerbe, C.S., Lionakis, M.S., and Holland, S.M. Novel STAT1 Mutation Disrupts Small Ubiquitin-Releated Modifier (SUMO) Conjugation Causing Gain of Function
, The Journal of Allergy and Clinical Immunology, 141(5), 1844-1853 (2018).
Pirtskhalava, M., Gabrielian, A., Cruz, P., Griggs, H.L., Squires, R.B., Hurt, D.E., Grigolava, M. Chubinidze, M., Gogoladze, G., Vishnepolsky, B., Alekseev, V., Rosenthal A., and Tartakovsky M. DBAASP v.2: an enhanced database of structure and antimicrobial/cytotoxic activity of natural and synthetic peptides
, Nucleic Acids Research, 44(D1): D1104-D1112 (2016).
Cramer, R.D., Cruz, P., Stahl, G., Curtiss, W.C., Campbell, B., Masek, B., and Soltanshahi, F. Virtual Screening for R-Groups, including Predicted pIC50 Contributions, within Large Structural Databases, Using Topomer CoMFA
, J. Chem. Inf. Model. 48, 2180-2195 (2008).
Arnold, F.H., Wolk, S., Cruz, P., and Tinoco, I., Jr. Structure, Dynamics, and Thermodynamics of Mismatched DNA Oligonucleotide Duplexes d(CCCAGGG) and d(CCCTGGG)
, Biochemistry 26, 4068-4075 (1987).
Hall, K., Cruz, P., Tinoco, I., Jr., Jovin, T.M., and van de Sande, J.H. Z-RNA- a Left-Handed RNA Double Helix
, Nature 311, 584-586 (1984).
Cruz, P., Bubienko, E., and Borer, P.N. A Model for Base Overlap in RNA
, Nature 298, 198-200 (1982).
| Group Publications |