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PROTEIN STRUCTURE PREDICTIONS

Protein Structure Predictions

We have created a protein structure prediction pipeline (PSPP) that uses state-of-the-art software deployed on DoD high-performance computing assets to predict the three-dimensional (3-D) structure of a protein from its amino acid sequence. We aim to utilize this pipeline to rapidly screen drugs in silico, assess vaccine development, understand enzymatic reactions, and model protein interactions, all of which require access to the 3-D structure of novel protein sequences.

Software

Publications

Chaudhury, S., D. R. Ripoll, and A. Wallqvist. Structure-based pKa prediction provides a thermodynamic basis for the role of histidines in pH-induced conformational transitions in dengue virus. Biochemistry and Biophysics Reports. 2015; 4:375-385. [PDF]

Koehler, J. W., J. M. Smith, D. R. Ripoll, K. W. Spik, S. L. Taylor, C. V. Badger, R. J. Grant, M. M. Ogg, A. Wallqvist, M. C. Guttieri, R. F. Garry, and C. S. Schmaljohn. A fusion-inhibiting peptide against Rift Valley fever virus inhibits multiple, diverse viruses. PLOS Neglected Tropical Diseases. 2013 September 12; 7(9):e2430. [PDF]

Bergmann-Leitner, E. S., S. Chaudhury, N. J. Steers, M. Sabato, V. Delvecchio, A. S. Wallqvist, C. F. Ockenhouse, and E. Angov. Computational and experimental validation of B and T-cell epitopes of the in vivo immune response to a novel malarial antigen. PLOS ONE. 2013 August 16; 8(8):e71610. [PDF]

Chaudhury, S., M. D. AbdulHameed, N. Singh, G. Tawa, P. M. D'haeseleer, A. T. Zemla, A. Navid, C. E. Zhou, M. C. Franklin, J. Cheung, M. J. Rudolph, J. Love, J. F. Graf, D. A. Rozack, J. L. Dankmeyer, K. Amemiya, S. Daefler, and A. Wallqvist. Rapid countermeasure discovery against Francisella tularensis based on a metabolic network reconstruction. PLOS ONE. 2013 May 21; 8(5):e63369. [PDF]

Chaudhury, S., M. A. Olson, G. Tawa, A. Wallqvist, and M. S. Lee. Efficient conformational sampling in explicit solvent using a hybrid replica exchange molecular dynamics method. Journal of Chemical Theory and Computation. 2012 February; 8(2):677-687. [PDF]

Bondugula, R., A. Wallqvist, and M. S. Lee. Can computationally designed protein sequences improve secondary structure prediction? Protein Engineering Design & Selection. 2011 May; 24(5):455-461. [PDF]

Lee, M., and M. Olson. Protein folding simulations combining self-guided Langevin dynamics and temperature-based replica exchange. Journal Chemical Theory and Computation. 2010 July 26; 6(8):2477-2487. [PDF]

Lee, M. S., R. Bondugula, V. Desai, N. Zavaljevski, I.-C. Yeh, A. Wallqvist, and J. Reifman. PSPP: a protein structure prediction pipeline for computing clusters. PLOS ONE. 2009 July 16; 4(7):e6254. [PDF]

Lee, M. S., R. Bondugula, V. Desai, N. Zavaljevski, I.-C. Yeh, A. Wallqvist, and J. Reifman. A web-accessible protein structure prediction pipeline. Proceedings of the HPCMP Users Group Conference. San Diego, CA. 2009 June 15-19; 169-174. [PDF]

Hu, X., X. Jiang, D. E. Lenz, D. M. Cerasoli, and A. Wallqvist. In silico analyses of substrate interactions with human serum paraoxonase 1. Proteins. 2009 May 1; 75(2):486-498. [PDF]

Bondugula, R., M. S. Lee, and A. Wallqvist. FIEFDom: a transparent domain boundary recognition system using a fuzzy mean operator. Nucleic Acids Research. 2009 February; 37(2):452-462. [PDF]

Olson, M. A., I.-C. Yeh, and M. S. Lee. Coarse-grained lattice model simulations of sequence-structure fitness of a ribosome-inactivating protein. Biopolymers. 2008 February; 89(2):153-159. [PDF]

Lee, M. S., I.-C. Yeh, N. Zavaljevski, P. Wilson, and J. Reifman. A software pipeline for protein structure prediction. Proceedings of the 25th Army Science Conference. Orlando, FL. 2006 November 17-21; 423-430. [PDF]