@article{wagoner_cheon_chang_hall_2014, title={Impact of sequence on the molecular assembly of short amyloid peptides}, volume={82}, ISSN={["1097-0134"]}, DOI={10.1002/prot.24515}, abstractNote={ABSTRACT}, number={7}, journal={PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS}, author={Wagoner, Victoria A. and Cheon, Mookyung and Chang, Iksoo and Hall, Carol K.}, year={2014}, month={Jul}, pages={1469–1483} }
 @article{wagoner_cheon_chang_hall_2012, title={Fibrillization Propensity for Short Designed Hexapeptides Predicted by Computer Simulation}, volume={416}, ISSN={["0022-2836"]}, DOI={10.1016/j.jmb.2011.12.038}, abstractNote={Assembly of normally soluble proteins into ordered aggregates, known as amyloid fibrils, is a cause or associated symptom of numerous human disorders, including Alzheimer's and the prion diseases. Here, we test the ability of discontinuous molecular dynamics (DMD) simulations based on PRIME20, a new intermediate-resolution protein force field, to predict which designed hexapeptide sequences will form fibrils, which will not, and how this depends on temperature and concentration. Simulations were performed on 48-peptide systems containing STVIIE, STVIFE, STVIVE, STAIIE, STVIAE, STVIGE, and STVIEE starting from random-coil configurations. By the end of the simulations, STVIIE and STVIFE (which form fibrils in vitro) form fibrils over a range of temperatures, STVIEE (which does not form fibrils in vitro) does not form fibrils, and STVIVE, STAIIE, STVIAE, and STVIGE (which do not form fibrils in vitro) form fibrils at lower temperatures but stop forming fibrils at higher temperatures. At the highest temperatures simulated, the results on the fibrillization propensity of the seven short de novo designed peptides all agree with the experiments of López de la Paz and Serrano. Our results suggest that the fibrillization temperature (temperature above which fibrils cease to form) is a measure of fibril stability and that by rank ordering the fibrillization temperatures of various sequences, PRIME20/DMD simulations could be used to ascertain their relative fibrillization propensities. A phase diagram showing regions in the temperature-concentration plane where fibrils are formed in our simulations is presented.}, number={4}, journal={JOURNAL OF MOLECULAR BIOLOGY}, author={Wagoner, Victoria A. and Cheon, Mookyung and Chang, Iksoo and Hall, Carol K.}, year={2012}, month={Mar}, pages={598–609} }
 @article{wagoner_cheon_chang_hall_2011, title={Computer simulation study of amyloid fibril formation by palindromic sequences in prion peptides}, volume={79}, ISSN={["0887-3585"]}, DOI={10.1002/prot.23034}, abstractNote={Abstract}, number={7}, journal={PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS}, author={Wagoner, Victoria A. and Cheon, Mookyung and Chang, Iksoo and Hall, Carol K.}, year={2011}, month={Jul}, pages={2132–2145} }
 @article{hall_waggner_2006, title={Computational approaches to fibril structure and formation}, volume={412}, ISBN={["0-12-182817-4"]}, ISSN={["0076-6879"]}, DOI={10.1016/s0076-6879(06)12020-0}, abstractNote={Assembly of normally soluble proteins into amyloid fibrils is a cause or associated symptom of numerous human disorders. Although some progress toward understanding the molecular‐level details of fibril structure has been made through in vitro experiments, the insoluble nature of fibrils make them difficult to study experimentally. We describe two computational approaches used to investigate fibril formation and structure: intermediate‐resolution discontinuous molecular dynamics simulations and atomistic molecular dynamics simulations. Each method has its strengths and weaknesses, but taken together the two approaches provide a useful molecular‐level picture of fibril structure and formation.}, journal={AMYLOID, PRIONS, AND OTHER PROTEIN AGGREGATES, PT B}, publisher={Elsevier/Academic}, author={Hall, Carol K. and Waggner, Vcroria A.}, year={2006}, pages={338–365} }