-
1
-
-
0042797442
-
-
Cambridge Univ Press, Cambridge, UK
-
Wales D.J. (2003) Energy Landscapes (Cambridge Univ Press, Cambridge, UK).
-
(2003)
Energy Landscapes
-
-
Wales, D.J.1
-
2
-
-
0000577041
-
Large-amplitude nonlinear motions in proteins
-
Garcia A.E. (1992) Large-amplitude nonlinear motions in proteins. Phys Rev Lett 68:2696-2699.
-
(1992)
Phys Rev Lett
, vol.68
, pp. 2696-2699
-
-
Garcia, A.E.1
-
5
-
-
67649503046
-
Deconstructing the native state: Energy landscapes, function and dynamics of globular proteins
-
Zhuravlev P.I., Materese C.K., Papoian G.A. (2009) Deconstructing the native state: Energy landscapes, function and dynamics of globular proteins. J Phys Chem B 113:8800-8812.
-
(2009)
J Phys Chem B
, vol.113
, pp. 8800-8812
-
-
Zhuravlev, P.I.1
Materese, C.K.2
Papoian, G.A.3
-
6
-
-
33745611125
-
Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction
-
DOI 10.1073/pnas.0603553103
-
Das P., Moll M., Stamati H., Kavraki L.E., Clementi C. (2006) Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction. Proc Natl Acad Sci USA 103:9885-9890. (Pubitemid 43993592)
-
(2006)
Proceedings of the National Academy of Sciences of the United States of America
, vol.103
, Issue.26
, pp. 9885-9890
-
-
Das, P.1
Moll, M.2
Stamati, H.3
Kavraki, L.E.4
Clementi, C.5
-
8
-
-
79953320021
-
Determination of reaction coordinates via locally scaled diffusion map
-
Rohrdanz M.A., Zheng W., Maggioni M., Clementi C. (2011) Determination of reaction coordinates via locally scaled diffusion map. J Chem Phys 134:124116.
-
(2011)
J Chem Phys
, vol.134
, pp. 124116
-
-
Rohrdanz, M..A.1
Zheng, W.2
Maggioni, M.3
Clementi, C.4
-
9
-
-
77957937199
-
Atomic-level characterization of the structural dynamics of proteins
-
Shaw D.E., et al. (2010) Atomic-level characterization of the structural dynamics of proteins. Science 330:341-346.
-
(2010)
Science
, vol.330
, pp. 341-346
-
-
Shaw, D.E.1
-
10
-
-
79954610833
-
Polymer reversal rate calculated via locally scaled diffusion map
-
Zheng W., Rohrdanz M.A., Maggioni M., Clementi C. (2011) Polymer reversal rate calculated via locally scaled diffusion map. J Chem Phys 134:144109.
-
(2011)
J Chem Phys
, vol.134
, pp. 144109
-
-
Zheng, W.1
Rohrdanz, M..A.2
Maggioni, M.3
Clementi, C.4
-
11
-
-
56249105081
-
Advillin folding takes place on a hypersurface of small dimensionality
-
Piana S., Laio A. (2008) Advillin folding takes place on a hypersurface of small dimensionality. Phys Rev Lett 101:208101.
-
(2008)
Phys Rev Lett
, vol.101
, pp. 208101
-
-
Piana, S.1
Laio, A.2
-
13
-
-
0034704222
-
Nonlinear dimensionality reduction by locally linear embedding
-
DOI 10.1126/science.290.5500.2323
-
Roweis S.T., Saul L.K. (2000) Nonlinear dimensionality reduction by locally linear embedding. Science 290:2323-2326. (Pubitemid 32041578)
-
(2000)
Science
, vol.290
, Issue.5500
, pp. 2323-2326
-
-
Roweis, S.T.1
Saul, L.K.2
-
14
-
-
34248590146
-
Fast and reliable analysis of molecular motion using proximity relations and dimensionality reduction
-
DOI 10.1002/prot.21337
-
Plaku E., Stamati H., Clementi C., Kavraki L.E. (2007) Fast and reliable analysis of molecular motion using proximity relations and dimensionality reduction. Proteins 67:897-907. (Pubitemid 46753937)
-
(2007)
Proteins: Structure, Function and Genetics
, vol.67
, Issue.4
, pp. 897-907
-
-
Plaku, E.1
Stamati, H.2
Clementi, C.3
Kavraki, L.E.4
-
15
-
-
77449099723
-
Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides
-
Stamati H., Clementi C., Kavraki L.E. (2010) Application of nonlinear dimensionality reduction to characterize the conformational landscape of small peptides. Proteins 78:223-235.
-
(2010)
Proteins
, vol.78
, pp. 223-235
-
-
Stamati, H.1
Clementi, C.2
Kavraki, L.E.3
-
16
-
-
70349493010
-
Detecting intrinsic slow variables in stochastic dynamical systems by anisotropic diffusion maps
-
Singer A., Erban R., Kevrekidis I.G., Coifman R.R. (2009) Detecting intrinsic slow variables in stochastic dynamical systems by anisotropic diffusion maps. Proc Natl Acad Sci USA 106:16090-16095.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 16090-16095
-
-
Singer, A.1
Erban, R.2
Kevrekidis, I.G.3
Coifman, R.R.4
-
17
-
-
67349240203
-
Local linear transformation embedding
-
Hou C., Wang J., Wu Y., Yi D. (2009) Local linear transformation embedding. Neurocomputing 72:2368-2378.
-
(2009)
Neurocomputing
, vol.72
, pp. 2368-2378
-
-
Hou, C.1
Wang, J.2
Wu, Y.3
Yi, D.4
-
19
-
-
0034704229
-
A global geometric framework for nonlinear dimensionality reduction
-
Tenenbaum JB, Silva Vd, Langford JC (2000) A global geometric framework for nonlinear dimensionality reduction. Science 290:2319-2323.
-
(2000)
Science
, vol.290
, pp. 2319-2323
-
-
Tenenbaum, J.B.1
Silva, Vd.2
Langford, J.C.3
-
20
-
-
77953290584
-
A Gromov- Hausdorff framework with diffusion geometry for topologically-robust non-rigid shape matching
-
Bronstein A.M., Bronstein M.M., Kimmel R., Mahmoudi M., Sapiro G. (2010) A Gromov- Hausdorff framework with diffusion geometry for topologically-robust non-rigid shape matching. Int J Comput Vis 89:266-286.
-
(2010)
Int J Comput Vis
, vol.89
, pp. 266-286
-
-
Bronstein, A.M.1
Bronstein, M.M.2
Kimmel, R.3
Mahmoudi, M.4
Sapiro, G.5
-
23
-
-
19644366699
-
Geometric diffusions as a tool for harmonic analysis and structure definition of data: Multiscale methods
-
DOI 10.1073/pnas.0500896102
-
Coifman R.R., et al. (2005) Geometric diffusions as a tool for harmonic analysis and structure definition of data: Multiscale methods. Proc Natl Acad Sci USA 102:7432-7437. (Pubitemid 40740989)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.21
, pp. 7432-7437
-
-
Coifman, R.R.1
Lafon, S.2
Lee, A.B.3
Maggioni, M.4
Nadler, B.5
Warner, F.6
Zucker, S.W.7
-
25
-
-
0042378381
-
Laplacian eigenmaps for dimensionality reduction and data representation
-
DOI 10.1162/089976603321780317
-
Belkin M., Niyogi P. (2003) Laplacian eigenmaps for dimensionality reduction and data representation. Neural Comput 15:1373-1396. (Pubitemid 37049796)
-
(2003)
Neural Computation
, vol.15
, Issue.6
, pp. 1373-1396
-
-
Belkin, M.1
Niyogi, P.2
-
30
-
-
45149142173
-
Volumes of diced hyperspheres: Resuming the tam-zardecki formula
-
Langerholc J. (1989) Volumes of diced hyperspheres: Resuming the tam-zardecki formula. Appl Math Comput 30:1-18.
-
(1989)
Appl Math Comput
, vol.30
, pp. 1-18
-
-
Langerholc, J.1
-
31
-
-
0003798627
-
-
MIT Press, Cambridge, MA
-
Schölkopf B., Smola A., Muller K.R. (1999) Advances in Kernel Methods: Support Vector Learning (MIT Press, Cambridge, MA), pp 327-352.
-
(1999)
Advances in Kernel Methods: Support Vector Learning
, pp. 327-352
-
-
Schölkopf, B.1
Smola, A.2
Muller, K.R.3
-
32
-
-
77951298811
-
Nonlinear dimensionality reduction by topologically constrained isometric embedding
-
Rosman G., Bronstein M.M., Bronstein A.M., Kimmel R. (2010) Nonlinear dimensionality reduction by topologically constrained isometric embedding. Int J Comput Vis 89:56-58.
-
(2010)
Int J Comput Vis
, vol.89
, pp. 56-58
-
-
Rosman, G.1
Bronstein, M.M.2
Bronstein, A.M.3
Kimmel, R.4
-
33
-
-
84887006810
-
A nonlinear mapping for data structure analysis
-
Sammon J.W. (1969) A nonlinear mapping for data structure analysis. IEEE Trans Comput 18:401-409.
-
(1969)
IEEE Trans Comput
, vol.18
, pp. 401-409
-
-
Sammon, J.W.1
-
35
-
-
0022064511
-
A best possible heuristic for the k-center problem
-
Hochbaum D.S., Shmoys D.B. (1985) A best possible heuristic for the k-center problem. Math Oper Res 10:180-184.
-
(1985)
Math Oper Res
, vol.10
, pp. 180-184
-
-
Hochbaum, D.S.1
Shmoys, D.B.2
-
36
-
-
33745593949
-
-
Technical Report, Stanford University. Available at Accessed September 10, 2010
-
De Silva V., Tenenbaum B. (2004) Sparse multidimensional scaling using landmark points. Technical Report, Stanford University. Available at http://graphics.stanford.edu/courses/cs468-05-winter/Papers/Landmarks/ Silva-landmarks5.pdf. Accessed September 10, 2010.
-
(2004)
Sparse Multidimensional Scaling Using Landmark Points
-
-
De Silva, V.1
Tenenbaum, B.2
-
37
-
-
0029619259
-
Knowledge-based protein secondary structure assignment
-
DOI 10.1002/prot.340230412
-
Frishman D., Argos P. (1995) Knowledge-based protein secondary structure assignment. Proteins 23:566-579. (Pubitemid 26009520)
-
(1995)
Proteins: Structure, Function and Genetics
, vol.23
, Issue.4
, pp. 566-579
-
-
Frishman, D.1
Argos, P.2
-
38
-
-
46249092554
-
Gromacs 4: Algorithms for highly efficient, load-balanced and scalable molecular simulation
-
Hess B., Kutzner C., Van der Spoel D., Lindahl E. (2008) Gromacs 4: Algorithms for highly efficient, load-balanced and scalable molecular simulation. J Chem Theory Comput 4:435-447.
-
(2008)
J Chem Theory Comput
, vol.4
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
Van Der Spoel, D.3
Lindahl, E.4
-
39
-
-
2542564912
-
Advances and continuing challeges in achieving realistic and predictive simulations of the properties of organic and biological molecules
-
Kollman P.A. (1996) Advances and continuing challeges in achieving realistic and predictive simulations of the properties of organic and biological molecules. Acc Chem Res 29:461-469.
-
(1996)
Acc Chem Res
, vol.29
, pp. 461-469
-
-
Kollman, P.A.1
-
40
-
-
33846086933
-
Cannonical sampling through velocity rescaling
-
Bussi G., Donadio D., Parrinello M.J. (2007) Cannonical sampling through velocity rescaling. J Chem Phys 126:014101.
-
(2007)
J Chem Phys
, vol.126
, pp. 014101
-
-
Bussi, G.1
Donadio, D.2
Parrinello, M.J.3
-
41
-
-
69349100797
-
Plumed: A portable plugin for free-energy calculations with molecular dynamics
-
Bonomi M., et al. (2009) Plumed: A portable plugin for free-energy calculations with molecular dynamics. Comput Phys Commun 180:1961-1972.
-
(2009)
Comput Phys Commun
, vol.180
, pp. 1961-1972
-
-
Bonomi, M.1
|