@inproceedings{b5face857dee429fa9702d1cd188f424,
title = "Sampling in in silico biomolecular studies: single-stage experiments vs multiscale approaches",
abstract = "In silico studies of biological molecules face the problem of sampling quality due to the systems size (in atom numbers), the time scale of the investigated processes and the admissible computational time step. Advances in hardware alone are incapable of resolving this problem and the efforts are oriented towards sampling techniques enhancements, multilevel system representations and development of multistage and multiscale methods through synergistic protocols from complementary approaches. We combine a mean field approach with all atom molecular dynamics (MD), to develop a multistage algorithm that can model protein folding and dynamics over very long time periods with atomic-level precision. We compare the quality of conformation-space sampling for villin headpiece (PDB ID 2F4K) with a 125 μ s long folding simulation performed on the dedicated supercomputer ANTON.",
keywords = "Biological molecules, Mean field theory, Molecular dynamics, Molecular modeling, Numerical simulations, Protein folding",
author = "Nevena Ilieva and Jiaojiao Liu and Xubiao Peng and Jianfeng He and Antti Niemi and Peicho Petkov and Leandar Litov",
note = "Publisher Copyright: {\textcopyright} Springer International Publishing AG 2018.; 11th International Conference on Large-Scale Scientific Computations, LSSC 2017 ; Conference date: 11-09-2017 Through 15-09-2017",
year = "2018",
doi = "10.1007/978-3-319-73441-5_56",
language = "English",
isbn = "9783319734408",
series = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",
publisher = "Springer Verlag",
pages = "507--515",
editor = "Ivan Lirkov and Svetozar Margenov",
booktitle = "Large-Scale Scientific Computing - 11th International Conference, LSSC 2017, Revised Selected Papers",
address = "Germany",
}