Replica exchange molecular dynamics simulations of amyloid peptide aggregation

@misc{citeulike:2520323, abstract = {The replica exchange molecular dynamics (REMD) approach is applied to four oligomeric peptide systems. At physiologically relevant temperature values REMD samples conformation space and aggregation transitions more efficiently than constant temperature molecular dynamics (CTMD). During the aggregation process the energetic and structural properties are essentially the same in REMD and CTMD. A condensation stage toward disordered aggregates precedes the \$\beta\$-sheet formation. Two order parameters, borrowed from anisotropic fluid analysis, are used to monitor the aggregation process. The order parameters do not depend on the peptide sequence and length and therefore allow to compare the amyloidogenic propensity of different peptides.}, author = {Cecchini, M. and Rao, F. and Seeber, M. and Caflisch, A. }, citeulike-article-id = {2520323}, eprint = {q-bio.BM/0409021}, keywords = {aggregation, computation}, month = {Sep}, posted-at = {2008-03-12 13:51:28}, priority = {2}, title = {Replica exchange molecular dynamics simulations of amyloid peptide aggregation}, url = {http://arxiv.org/abs/q-bio.BM/0409021}, year = {2004} }

TY - ELEC ID - citeulike:2520323 L3 - citeulike-article-id:2520323 TI - Replica exchange molecular dynamics simulations of amyloid peptide aggregation N2 - The replica exchange molecular dynamics (REMD) approach is applied to four oligomeric peptide systems. At physiologically relevant temperature values REMD samples conformation space and aggregation transitions more efficiently than constant temperature molecular dynamics (CTMD). During the aggregation process the energetic and structural properties are essentially the same in REMD and CTMD. A condensation stage toward disordered aggregates precedes the $\beta$-sheet formation. Two order parameters, borrowed from anisotropic fluid analysis, are used to monitor the aggregation process. The order parameters do not depend on the peptide sequence and length and therefore allow to compare the amyloidogenic propensity of different peptides. KW - aggregation KW - computation AU - Cecchini, M AU - Rao, F AU - Seeber, M AU - Caflisch, A PY - 2004/Sep/17/ UR - http://arxiv.org/abs/q-bio.BM/0409021 ER -