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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 structure of a protein from its amino acid sequence. The methods included in the pipeline include homology modeling and ab initio prediction algorithms. Access to three-dimensional structures of novel protein sequences is crucial for rapid in silico drug screening, assessment of vaccine development, understanding enzymatic reactions, and modeling protein interactions.

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 2223 KB]

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 2822 KB]

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 1460 KB]

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 609 KB]

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 2887 KB]

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 255 KB]

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 3326 KB]

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 919 KB]

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 572 KB]

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 594 KB]

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 2111 KB]

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 240 KB]

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 321 KB]