Determination of reaction coordinates via locally scaled diffusion map

Journal of Chemical Physics - Tập 134 Số 12 - 2011
Mary A. Rohrdanz1, Wenwei Zheng1, Mauro Maggioni2, Cecilia Clementi1
1Rice University 1 , Department of Chemistry, Houston, Texas 77005, USA
2Duke University 2 , Department of Mathematics, Durham, North Carolina 27708, USA

Tóm tắt

We present a multiscale method for the determination of collective reaction coordinates for macromolecular dynamics based on two recently developed mathematical techniques: diffusion map and the determination of local intrinsic dimensionality of large datasets. Our method accounts for the local variation of molecular configuration space, and the resulting global coordinates are correlated with the time scales of the molecular motion. To illustrate the approach, we present results for two model systems: all-atom alanine dipeptide and coarse-grained src homology 3 protein domain. We provide clear physical interpretation for the emerging coordinates and use them to calculate transition rates. The technique is general enough to be applied to any system for which a Boltzmann-sampled set of molecular configurations is available.

Từ khóa


Tài liệu tham khảo

2010, J. Phys. Chem. B, 114, 6979, 10.1021/jp101476g

2010, Proc. Natl. Acad. Sci. U.S.A., 107, 1088, 10.1073/pnas.0910390107

2006, J. Chem. Phys., 125, 054910, 10.1063/1.2229206

2005, J. Chem. Phys., 122, 014503, 10.1063/1.1818091

1998, J. Chem. Phys., 108, 334, 10.1063/1.475393

2005, J. Phys. Chem. B, 109, 6769, 10.1021/jp045546c

2005, Proc. Natl. Acad. Sci. U.S.A., 102, 6732, 10.1073/pnas.0408098102

2007, J. Chem. Phys., 126, 164103, 10.1063/1.2720838

2007, Chem. Phys. Lett., 446, 182, 10.1016/j.cplett.2007.08.017

1998, J. Chem. Phys., 108, 1964, 10.1063/1.475562

2004, J. Chem. Phys., 120, 10880, 10.1063/1.1738640

1986, Principal Components Analysis

2006, Proteins, 65, 898, 10.1002/prot.21185

2005, Proteins, 58, 45, 10.1002/prot.20310

2000, Science, 290, 2323, 10.1126/science.290.5500.2323

2000, Science, 290, 2319, 10.1126/science.290.5500.2319

2006, Proc. Natl. Acad. Sci. U.S.A., 103, 9885, 10.1073/pnas.0603553103

2009, J. Chem. Phys., 130, 144115, 10.1063/1.3103496

2006, Appl. Comput. Harmon. Anal., 21, 5, 10.1016/j.acha.2006.04.006

2006, Appl. Comput. Harmon. Anal., 21, 53, 10.1016/j.acha.2006.04.004

2005, Proc. Natl. Acad. Sci. U.S.A., 102, 7426, 10.1073/pnas.0500334102

2005, Proc. Natl. Acad. Sci. U.S.A., 102, 7432, 10.1073/pnas.0500896102

2008, Multiscale Model. Simul., 7, 842, 10.1137/070696325

2008, J. Mach. Learn. Res., 9, 1711, 10.1213/ane.0b013e3181618702

2007, J. Mach. Learn. Res., 8, 2169

2008, Proc. Nat. Acad. Sci. U.S.A., 105, 1803, 10.1073/pnas.0710175104

2009, Multiscale Estimation of Intrinsic Dimensionality of Data Sets

See supplementary material at http://dx.doi.org/10.1063/1.3569857 for more details.

1940, Physica, 7, 284, 10.1016/S0031-8914(40)90098-2

2008, J. Chem. Phys., 128, 114903, 10.1063/1.2890006

2005, New J. Phys., 7, 34, 10.1088/1367-2630/7/1/034

2006

2000, J. Mol. Biol., 298, 937, 10.1006/jmbi.2000.3693

2004, Protein Sci., 13, 1750, 10.1110/ps.03580104

2000, Nat. Struct. Biol., 7, 336, 10.1038/74111

1998, Nat. Struct. Biol., 5, 714, 10.1038/1412

2006, Proc. Natl. Acad. Sci. U.S.A., 103, 586, 10.1073/pnas.0509768103

2007, Proteins, 67, 897, 10.1002/prot.21337

2005, Proc. Natl. Acad. Sci. U.S.A., 102, 10141, 10.1073/pnas.0409471102

2005, J. Comput. Chem., 26, 1701, 10.1002/jcc.20291

2002, Proc. Natl. Acad. Sci. U.S.A., 99, 5349, 10.1073/pnas.072387799

Thông tin
Thông tin xuất bản

Journal of Chemical Physics

Tập 134 Số 12

Thông tin tác giả