-
1
-
-
84992693092
-
-
IEEE Computer Society Los Alamitos, CA, USA
-
A. Beberg, V.S. Pande, Folding@home: lessons from eight years of distributed computing, in IEEE Computer Society Los Alamitos, CA, USA (2009), pp. 1-8
-
(2009)
Folding@home: Lessons from Eight Years of Distributed Computing
, pp. 1-8
-
-
Beberg, A.1
Pande, V.S.2
-
2
-
-
33750587438
-
Molecular dynamics with coupling to an external bath
-
H.J.C. Berendsen, J.P.M. Postma, A. DiNola, J.R. Haak, Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81, 3684-3690 (1984)
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
DiNola, A.3
Haak, J.R.4
-
3
-
-
63449118443
-
Using generalized ensemble simulations and Markov state models to identify conformational states
-
G.R. Bowman, X. Huang, V.S. Pande Using generalized ensemble simulations and Markov state models to identify conformational states. Methods 49(2), 197-201 (2009)
-
(2009)
Methods
, vol.49
, Issue.2
, pp. 197-201
-
-
Bowman, G.R.1
Huang, X.2
Pande, V.S.3
-
4
-
-
33846086933
-
Canonical sampling through velocity rescaling
-
G. Bussi, D. Donadio, M. Parrinello. Canonical sampling through velocity rescaling. J. Chem. Phys. 126, 014101 (2007)
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 014101
-
-
Bussi, G.1
Donadio, D.2
Parrinello, M.3
-
5
-
-
23444454552
-
The Amber biomolecular simulation programs
-
D.A. Case, T.E. Cheatham III, T. Darden, H. Gohlke, R. Luo, K.M. Merz Jr., A. Onufriev, C. Simmerling, B. Wang, R.J. Woods, The Amber biomolecular simulation programs. J. Comput. Chem. 26, 1668-1688 (2005)
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1668-1688
-
-
Case, D.A.1
Cheatham III, T.E.2
Darden, T.3
Gohlke, H.4
Luo, R.5
Merz Jr., K.M.6
Onufriev, A.7
Simmerling, C.8
Wang, B.9
Woods, R.J.10
-
6
-
-
34547683322
-
Markov methods for hierarchical coarse-graining of large protein dynamics
-
C. Chennubhotla, I. Bahar, Markov methods for hierarchical coarse-graining of large protein dynamics. J. Comput. Biol. 14(6),765-776, 2007
-
(2007)
J. Comput. Biol.
, vol.14
, Issue.6
, pp. 765-776
-
-
Chennubhotla, C.1
Bahar, I.2
-
7
-
-
34247382025
-
Long-time protein folding dynamics from short-time molecular dynamics simulations
-
J.D. Chodera, W.C. Swope, J.W. Pitera, K.A. Dill, Long-time protein folding dynamics from short-time molecular dynamics simulations. Multiscale Model. Simul. 5(4), 1214-1226 (2006)
-
(2006)
Multiscale Model. Simul.
, vol.5
, Issue.4
, pp. 1214-1226
-
-
Chodera, J.D.1
Swope, W.C.2
Pitera, J.W.3
Dill, K.A.4
-
8
-
-
13544256263
-
Robust perron cluster analysis in conformation dynamics
-
ed. by M. Dellnitz, S. Kirkland, M. Neumann, C. Schütte, Elsevier, Amsterdam
-
P. Deuflhard, M. Weber, Robust perron cluster analysis in conformation dynamics, in Linear Algebra and its Applications - Special Issue on Matrices and Mathematical Biology, ed. by M. Dellnitz, S. Kirkland, M. Neumann, C. Schütte, Vol. 398C (Elsevier, Amsterdam, 2005), pp. 161-184
-
(2005)
Linear Algebra and Its Applications - Special Issue on Matrices and Mathematical Biology
, vol.398 C
, pp. 161-184
-
-
Deuflhard, P.1
Weber, M.2
-
9
-
-
60849091381
-
The introduction of hydrogen bond and hydrophobicity effects into the rotational isomeric states model for conformational analysis of unfolded peptides
-
O. Engin, M. Sayar, B. Erman, The introduction of hydrogen bond and hydrophobicity effects into the rotational isomeric states model for conformational analysis of unfolded peptides. Phys. Biol. 6, 016001 (2009)
-
(2009)
Phys. Biol.
, vol.6
, pp. 016001
-
-
Engin, O.1
Sayar, M.2
Erman, B.3
-
10
-
-
33645961739
-
A smooth particle mesh Ewald method
-
U. Essmann, L. Perera, M.L. Berkowitz, T. Darden, H. Lee, L.G. Pedersen. A smooth particle mesh Ewald method. J. Chem. Phys. 103, 8577-8592 (1995)
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 8577-8592
-
-
Essmann, U.1
Perera, L.2
Berkowitz, M.L.3
Darden, T.4
Lee, H.5
Pedersen, L.G.6
-
11
-
-
33748448490
-
A natural coarse graining for simulating large biomolecular motion
-
H. Gohlke, M.F. Thorpe, A natural coarse graining for simulating large biomolecular motion. Biophys. J. 91(6), 2115-2120 (2006)
-
(2006)
Biophys. J.
, vol.91
, Issue.6
, pp. 2115-2120
-
-
Gohlke, H.1
Thorpe, M.F.2
-
12
-
-
45449095403
-
-
Springer, Berlin, Heidelberg
-
M. Griebel, S. Knapek, G. Zumbusch, Numerical Simulation in Molecular Dynamics (Springer, Berlin, Heidelberg, 2007)
-
(2007)
Numerical Simulation in Molecular Dynamics
-
-
Griebel, M.1
Knapek, S.2
Zumbusch, G.3
-
13
-
-
0000388705
-
LINCS: A linear constraint solver for molecular simulations
-
B. Hess, H. Bekker, H.J.C. Berendsen, J.G.E.M. Fraaije, LINCS: a linear constraint solver for molecular simulations. J. Comput. Chem. 18, 1463-1472 (1997)
-
(1997)
J. Comput. Chem.
, vol.18
, pp. 1463-1472
-
-
Hess, B.1
Bekker, H.2
Berendsen, H.J.C.3
Fraaije, J.G.E.M.4
-
14
-
-
46249092554
-
GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
-
B. Hess, C. Kutzner, D. van der Spoel, E. Indahl, GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theory Comput. 4(3), 435-447 (2008)
-
(2008)
J. Chem. Theory Comput.
, vol.4
, Issue.3
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
Van Der Spoel, D.3
Indahl, E.4
-
15
-
-
27744488441
-
Characterization of the TIP4P-Ew water model: Vapor pressure and boiling point
-
H.W. Horn, W.C. Swope, J.W. Pitera, Characterization of the TIP4P-Ew water model: vapor pressure and boiling point. J. Chem. Phys. 123, 194504 (2005)
-
(2005)
J. Chem. Phys.
, vol.123
, pp. 194504
-
-
Horn, H.W.1
Swope, W.C.2
Pitera, J.W.3
-
16
-
-
33748518255
-
Comparison of multiple Amber force fields and development of improved protein backbone parameters
-
V. Hornak, R. Abel, A. Okur, B. Strockbine, A. Roitberg, C. Simmerling, Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins 65, 712-725 (2006)
-
(2006)
Proteins
, vol.65
, pp. 712-725
-
-
Hornak, V.1
Abel, R.2
Okur, A.3
Strockbine, B.4
Roitberg, A.5
Simmerling, C.6
-
18
-
-
0001041959
-
Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I
-
A. Jakalian, B.L. Bush, D.B. Jack, C.I. Bayly, Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method. J. Comput. Chem. 21, 132-146 (2000)
-
(2000)
Method. J. Comput. Chem.
, vol.21
, pp. 132-146
-
-
Jakalian, A.1
Bush, B.L.2
Jack, D.B.3
Bayly, C.I.4
-
19
-
-
0036890178
-
Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation
-
A. Jakalian, D.B. Jack, C.I. Bayly, Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation. J. Comput. Chem. 23, 1623-1641 (2002)
-
(2002)
J. Comput. Chem.
, vol.23
, pp. 1623-1641
-
-
Jakalian, A.1
Jack, D.B.2
Bayly, C.I.3
-
21
-
-
0037162186
-
Conformational dynamics of trialanine in water: A molecular dynamics study
-
Y. Mu, G. Stock, Conformational dynamics of trialanine in water: a molecular dynamics study. J. Phys. Chem. B 106, 5294-5301 (2002)
-
(2002)
J. Phys. Chem. B
, vol.106
, pp. 5294-5301
-
-
Mu, Y.1
Stock, G.2
-
22
-
-
0038241788
-
Conformational dynamics of trialanine in Water.2 Comparison of AMBER, CHARMM, GROMOS, and OPLS Force Fields to NMR and infrared experiments
-
Y. Mu, D. Kosov, G. Stock, Conformational dynamics of trialanine in Water.2 Comparison of AMBER, CHARMM, GROMOS, and OPLS Force Fields to NMR and infrared experiments J. Phys. Chem. B 107, 5064-5073, (2003)
-
(2003)
J. Phys. Chem. B
, vol.107
, pp. 5064-5073
-
-
Mu, Y.1
Kosov, D.2
Stock, G.3
-
23
-
-
49849097184
-
Building Markov state models along pathways to determine free energies and rates of transitions
-
A. Pan, B. Roux, Building Markov state models along pathways to determine free energies and rates of transitions. J Chem. Phys. 129(6), 064107 (2008)
-
(2008)
J Chem. Phys.
, vol.129
, Issue.6
, pp. 064107
-
-
Pan, A.1
Roux, B.2
-
24
-
-
79957488000
-
Markov models of molecular kinetics: Generation and validation
-
J.-H. Prinz, H. Wu, M. Sarich, B. Keller, M. Fischbach, M. Held, J.D. Chodera, C. Schütte, F. Noe, Markov models of molecular kinetics: generation and validation. J. Chem. Phys. 134, 174105 (2011)
-
(2011)
J. Chem. Phys.
, vol.134
, pp. 174105
-
-
Prinz, J.-H.1
Wu, H.2
Sarich, M.3
Keller, B.4
Fischbach, M.5
Held, M.6
Chodera, J.D.7
Schütte, C.8
Noe, F.9
-
26
-
-
33750945327
-
A backbone-based theory of protein folding
-
G. Rose, P. Fleming, J. Banavar, A.Maritan, A backbone-based theory of protein folding. Proc. Natl. Acad. Sci. U. S. A. 103(45), 16623-16633 (2006)
-
(2006)
Proc. Natl. Acad. Sci. U. S. A.
, vol.103
, Issue.45
, pp. 16623-16633
-
-
Rose, G.1
Fleming, P.2
Banavar, J.3
Maritan, A.4
-
27
-
-
77956841151
-
On the approximation quality of Markov state models
-
M. Sarich, F. Noe, C. Schütte, On the approximation quality of Markov state models. Multiscale Model. Simul. 8, 1154-1177 (2010)
-
(2010)
Multiscale Model. Simul.
, vol.8
, pp. 1154-1177
-
-
Sarich, M.1
Noe, F.2
Schütte, C.3
-
28
-
-
0003767327
-
-
Habilitation Thesis, Fachbereich Mathematik und Informatik, Freie Universität Berlin
-
C. Schütte, Conformational dynamics: modelling, theory, algorithm, and application to biomolecules. Habilitation Thesis, Fachbereich Mathematik und Informatik, Freie Universität Berlin, 1999
-
(1999)
Conformational Dynamics: Modelling, Theory, Algorithm, and Application to Biomolecules
-
-
Schütte, C.1
-
29
-
-
0000573002
-
A direct approach to conformational dynamics based on hybrid Monte Carlo
-
Special Issue Comp. Biophysics, Academic
-
C. Schütte, A. Fischer, W. Huisinga, P. Deuflhard, A direct approach to conformational dynamics based on hybrid Monte Carlo. J. Comput. Phys. 151,146-169, 1999. Special Issue Comp. Biophysics, Academic
-
(1999)
J. Comput. Phys.
, vol.151
, pp. 146-169
-
-
Schütte, C.1
Fischer, A.2
Huisinga, W.3
Deuflhard, P.4
-
30
-
-
0014432211
-
A two-dimensional interpolation function for irregularly spaced data
-
ACM, New York
-
D. Shepard, A two-dimensional interpolation function for irregularly spaced data, in Proceeding of the 1968 23rd ACM national conference (ACM, New York, 1968), pp. 517-524
-
(1968)
Proceeding of the 1968 23rd ACM National Conference
, pp. 517-524
-
-
Shepard, D.1
-
31
-
-
17444389688
-
Coarse master equation from Bayesian analysis of replica molecular dynamics simulations
-
S. Sriraman, I. Kevrekidis, G. Hummer, Coarse master equation from Bayesian analysis of replica molecular dynamics simulations. J. Phys. Chem. B 109(14), 6479-6484 (2005)
-
(2005)
J. Phys. Chem. B
, vol.109
, Issue.14
, pp. 6479-6484
-
-
Sriraman, S.1
Kevrekidis, I.2
Hummer, G.3
-
32
-
-
84882878737
-
Amira: A highly interactive system for visual data analysis
-
ed. by C.D. Hansen, C.R. Johnson, Chapter 38 Elsevier, Amsterdam
-
D. Stalling, M. Westerhoff, H.-C. Hege. Amira: a highly interactive system for visual data analysis, in The Visualization Handbook, ed. by C.D. Hansen, C.R. Johnson, Chapter 38 (Elsevier, Amsterdam, 2005) pp. 749-767
-
(2005)
The Visualization Handbook
, pp. 749-767
-
-
Stalling, D.1
Westerhoff, M.2
Hege, H.-C.3
-
33
-
-
2942567954
-
Describing protein folding kinetics by molecular dynamics simulation.1. Theory
-
W.C. Swope, J.W. Pitera, Describing protein folding kinetics by molecular dynamics simulation.1. Theory. J. Phys. Chem. B 108, 6571-6581 (2004)
-
(2004)
J. Phys. Chem. B
, vol.108
, pp. 6571-6581
-
-
Swope, W.C.1
Pitera, J.W.2
-
34
-
-
84946450438
-
Algorithms for macromolecular dynamics and constraint dynamics
-
W.F. van Gunsteren, H.J.C. Berendsen, Algorithms for macromolecular dynamics and constraint dynamics. Mol. Phys. 34, 1311-1327 (1977)
-
(1977)
Mol. Phys.
, vol.34
, pp. 1311-1327
-
-
Van Gunsteren, W.F.1
Berendsen, H.J.C.2
-
35
-
-
2942532422
-
Development and testing of a general Amber force field
-
J. Wang, W. Wang, J. Caldwell, P.A. Kollman, D.A. Case, Development and testing of a general Amber force field. Comput. Chem. 25, 1157-1174 (2004)
-
(2004)
Comput. Chem.
, vol.25
, pp. 1157-1174
-
-
Wang, J.1
Wang, W.2
Caldwell, J.3
Kollman, P.A.4
Case, D.A.5
-
36
-
-
33748538349
-
Automatic atom type and bond type perception in molecular mechanical calculations
-
J. Wang, W. Wang, P.A. Kollman, D.A. Case, Automatic atom type and bond type perception in molecular mechanical calculations. J. Mol. Graph. Model. 25, 247-260 (2006)
-
(2006)
J. Mol. Graph. Model.
, vol.25
, pp. 247-260
-
-
Wang, J.1
Wang, W.2
Kollman, P.A.3
Case, D.A.4
-
37
-
-
45849139859
-
-
Doctoral thesis, Department of Mathematics and Computer Science, Freie Universität, Berlin, Published by Verlag Dr. Hut, München
-
M. Weber, Meshless Methods in Conformation Dynamics. Doctoral thesis, Department of Mathematics and Computer Science, Freie Universität, Berlin, 2006. Published by Verlag Dr. Hut, München
-
(2006)
Meshless Methods in Conformation Dynamics
-
-
Weber, M.1
-
39
-
-
84864838724
-
An indicator for the number of clusters using a linear map to simplex structure
-
ed. by M. Spiliopoulou et al. Studies in Classification, Data Analysis, and Knowledge Organization Springer, Berlin, Heidelberg
-
M. Weber, W. Rungsarityotin, A. Schliep, An indicator for the number of clusters using a linear map to simplex structure, in From Data and Information Analysis to Knowledge Engineering, Proceedings of the 29th Annual Conference of the Gesellschaft für Klassifikation e.V., Universität Magdeburg, März 2005, ed. by M. Spiliopoulou et al. Studies in Classification, Data Analysis, and Knowledge Organization (Springer, Berlin, Heidelberg, 2006), pp. 103-110
-
(2006)
From Data and Information Analysis to Knowledge Engineering, Proceedings of the 29th Annual Conference of the Gesellschaft für Klassifikation E.V., Universität Magdeburg, März 2005
, pp. 103-110
-
-
Weber, M.1
Rungsarityotin, W.2
Schliep, A.3
|