-
2
-
-
34547474332
-
The Martini Force Field: Coarse Grained Model for Biomolecular Simulations
-
Marrink, S. J.; Risselada, H. J.; Yefimov, S.; Tieleman, D. P.; De Vries, A. H. The Martini Force Field: Coarse Grained Model for Biomolecular Simulations J. Phys. Chem. B 2007, 111, 7812-7824
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 7812-7824
-
-
Marrink, S.J.1
Risselada, H.J.2
Yefimov, S.3
Tieleman, D.P.4
De Vries, A.H.5
-
3
-
-
2342473866
-
Coarse Grain Models and the Computer Simulation of Soft Materials
-
Nielsen, S. O.; Lopez, C. F.; Goundla, S.; Klein, M. L. Coarse Grain Models and the Computer Simulation of Soft Materials J. Phys.: Condens. Matter 2004, 16, R418
-
(2004)
J. Phys.: Condens. Matter
, vol.16
, pp. 418
-
-
Nielsen, S.O.1
Lopez, C.F.2
Goundla, S.3
Klein, M.L.4
-
4
-
-
17044393884
-
Coarse-Grained Models for Proteins
-
Tozzini, V. Coarse-Grained Models for Proteins Curr. Opin. Struct. Biol. 2005, 15, 144-150
-
(2005)
Curr. Opin. Struct. Biol.
, vol.15
, pp. 144-150
-
-
Tozzini, V.1
-
5
-
-
84864777986
-
The Coarse-Grained Opep Force Field for Non-Amyloid and Amyloid Proteins
-
Chebaro, Y.; Pasquali, S.; Derreumaux, P. The Coarse-Grained Opep Force Field for Non-Amyloid and Amyloid Proteins J. Phys. Chem. B 2012, 116, 8741-8752
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 8741-8752
-
-
Chebaro, Y.1
Pasquali, S.2
Derreumaux, P.3
-
7
-
-
83455255623
-
The Elba Force Field for Coarse-Grain Modeling of Lipid Membranes
-
Orsi, M.; Essex, J. W. The Elba Force Field for Coarse-Grain Modeling of Lipid Membranes PLOS One 2011, 6, E28637
-
(2011)
PLOS One
, vol.6
, pp. 28637
-
-
Orsi, M.1
Essex, J.W.2
-
8
-
-
39449131104
-
Coarse-Grained Simulation: A High-Throughput Computational Approach to Membrane Proteins
-
Sansom, M. S.; Scott, K. A.; Bond, P. J. Coarse-Grained Simulation: A High-Throughput Computational Approach to Membrane Proteins Biochem. Soc. Trans. 2008, 36, 27-32
-
(2008)
Biochem. Soc. Trans.
, vol.36
, pp. 27-32
-
-
Sansom, M.S.1
Scott, K.A.2
Bond, P.J.3
-
9
-
-
62349124337
-
Multiscale Modeling of Emergent Materials: Biological and Soft Matter
-
Murtola, T.; Bunker, A.; Vattulainen, I.; Deserno, M.; Karttunen, M. Multiscale Modeling of Emergent Materials: Biological and Soft Matter Phys. Chem. Chem. Phys. 2009, 11, 1869-1892
-
(2009)
Phys. Chem. Chem. Phys.
, vol.11
, pp. 1869-1892
-
-
Murtola, T.1
Bunker, A.2
Vattulainen, I.3
Deserno, M.4
Karttunen, M.5
-
10
-
-
67649101377
-
Generic Coarse-Grained Model for Protein Folding and Aggregation
-
Bereau, T.; Deserno, M. Generic Coarse-Grained Model for Protein Folding and Aggregation J. Chem. Phys. 2009, 130, 235106
-
(2009)
J. Chem. Phys.
, vol.130
, pp. 235106
-
-
Bereau, T.1
Deserno, M.2
-
11
-
-
84871427342
-
Recent Successes in Coarse-Grained Modeling of DNA
-
Potoyan, D. A.; Savelyev, A.; Papoian, G. A. Recent Successes in Coarse-Grained Modeling of DNA WIREs Comput. Mol. Sci. 2013, 3, 69-83
-
(2013)
WIREs Comput. Mol. Sci.
, vol.3
, pp. 69-83
-
-
Potoyan, D.A.1
Savelyev, A.2
Papoian, G.A.3
-
12
-
-
77952355398
-
A Coarse Grained Model for Atomic-Detailed DNA Simulations with Explicit Electrostatics
-
Dans, P. D.; Zeida, A.; Machado, M. R.; Pantano, S. A Coarse Grained Model for Atomic-Detailed DNA Simulations with Explicit Electrostatics J. Chem. Theory. Comput. 2010, 6, 1711-1725
-
(2010)
J. Chem. Theory. Comput.
, vol.6
, pp. 1711-1725
-
-
Dans, P.D.1
Zeida, A.2
Machado, M.R.3
Pantano, S.4
-
13
-
-
33847626738
-
A Coarse Grain Model for DNA
-
Knotts, T. A.; Rathore, N.; Schwartz, D. C.; De Pablo, J. J. A Coarse Grain Model for DNA J. Chem. Phys. 2007, 126, 084901
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 084901
-
-
Knotts, T.A.1
Rathore, N.2
Schwartz, D.C.3
De Pablo, J.J.4
-
14
-
-
84872126088
-
Modeling Protein-protein Recognition in Solution Using the Coarse-Grained Force Field Scorpion
-
Basdevant, N.; Borgis, D.; Ha-Duong, T. Modeling Protein-protein Recognition in Solution Using the Coarse-Grained Force Field Scorpion J. Chem. Theor. Comput. 2013, 9, 803-813
-
(2013)
J. Chem. Theor. Comput.
, vol.9
, pp. 803-813
-
-
Basdevant, N.1
Borgis, D.2
Ha-Duong, T.3
-
15
-
-
73949097591
-
Versatile Object-Oriented Toolkit for Coarse-Graining Applications
-
Ruhle, V.; Junghans, A.; Lukyanov, A.; Kremer, K.; Andrienko, D. Versatile Object-Oriented Toolkit for Coarse-Graining Applications J. Chem. Theor. Comput. 2009, 5, 3211-3223
-
(2009)
J. Chem. Theor. Comput.
, vol.5
, pp. 3211-3223
-
-
Ruhle, V.1
Junghans, A.2
Lukyanov, A.3
Kremer, K.4
Andrienko, D.5
-
16
-
-
84865383775
-
On Developing Coarse-Grained Models for Biomolecular Simulation: A Review
-
Riniker, S.; Allison, J. R.; Van Gunsteren, W. F. On Developing Coarse-Grained Models for Biomolecular Simulation: A Review Phys. Chem. Chem. Phys. 2012, 14, 12423-12430
-
(2012)
Phys. Chem. Chem. Phys.
, vol.14
, pp. 12423-12430
-
-
Riniker, S.1
Allison, J.R.2
Van Gunsteren, W.F.3
-
17
-
-
84898542617
-
The Power of Coarse Graining in Biomolecular Simulations
-
10.1002/Wcms.1169
-
Ingolfsson, H. I.; Lopez, C. A.; Uusitalo, J. J.; De Jong, D. H.; Gopal, S. M.; Periole, X.; Marrink, S. J. The Power of Coarse Graining in Biomolecular Simulations WIREs Comput. Mol. Sci. 2013, 10.1002/Wcms.1169
-
(2013)
WIREs Comput. Mol. Sci.
-
-
Ingolfsson, H.I.1
Lopez, C.A.2
Uusitalo, J.J.3
De Jong, D.H.4
Gopal, S.M.5
Periole, X.6
Marrink, S.J.7
-
18
-
-
84880152678
-
Coarse-Grained Simulations of RNA and DNA Duplexes
-
Cragnolini, T.; Derreumaux, P.; Pasquali, S. Coarse-Grained Simulations of RNA and DNA Duplexes J. Phys. Chem. B 2013, 117, 8047-8060
-
(2013)
J. Phys. Chem. B
, vol.117
, pp. 8047-8060
-
-
Cragnolini, T.1
Derreumaux, P.2
Pasquali, S.3
-
19
-
-
84886869244
-
Assessing the Accuracy of the Sirah Force Field to Model DNA at Coarse Grain Level
-
In; Setubal, J. C. Almeida, N. F. Springer International Publishing: New York
-
Dans, P. D.; Darré, L.; Machado, M. R.; Zeida, A.; Brandner, A. F.; Pantano, S. Assessing the Accuracy of the Sirah Force Field to Model DNA at Coarse Grain Level. In Advances in Bioinformatics and Computational Biology; Setubal, J. C.; Almeida, N. F., Eds.; Springer International Publishing: New York, 2013; pp 71-81.
-
(2013)
Advances in Bioinformatics and Computational Biology
, pp. 71-81
-
-
Dans, P.D.1
Darré, L.2
Machado, M.R.3
Zeida, A.4
Brandner, A.F.5
Pantano, S.6
-
20
-
-
84863689619
-
Coarse-Grained Molecular Models of Water: A Review
-
Hadley, K. R.; Mccabe, C. Coarse-Grained Molecular Models of Water: A Review Mol. Simul. 2012, 38, 671-681
-
(2012)
Mol. Simul.
, vol.38
, pp. 671-681
-
-
Hadley, K.R.1
McCabe, C.2
-
22
-
-
78651282789
-
Another Coarse Grain Model for Aqueous Solvation: Wat Four?
-
Darré, L.; Machado, M. R.; Dans, P. D.; Herrera, F. E.; Pantano, S. Another Coarse Grain Model for Aqueous Solvation: Wat Four? J. Chem. Theory. Comput. 2010, 6, 3793-3807
-
(2010)
J. Chem. Theory. Comput.
, vol.6
, pp. 3793-3807
-
-
Darré, L.1
Machado, M.R.2
Dans, P.D.3
Herrera, F.E.4
Pantano, S.5
-
23
-
-
80053475897
-
A Hybrid All-Atom/Coarse Grain Model for Multiscale Simulations of DNA
-
Machado, M. R.; Dans, P. D.; Pantano, S. A Hybrid All-Atom/Coarse Grain Model for Multiscale Simulations of DNA Phys. Chem. Chem. Phys. 2011, 13, 18134-18144
-
(2011)
Phys. Chem. Chem. Phys.
, vol.13
, pp. 18134-18144
-
-
Machado, M.R.1
Dans, P.D.2
Pantano, S.3
-
24
-
-
33748266722
-
Mixed Atomistic and Coarse-Grained Molecular Dynamics: Simulation of a Membrane-Bound Ion Channel
-
Shi, Q.; Izvekov, S.; Voth, G. A. Mixed Atomistic and Coarse-Grained Molecular Dynamics: Simulation of a Membrane-Bound Ion Channel J. Phys. Chem. B 2006, 110, 15045-15048
-
(2006)
J. Phys. Chem. B
, vol.110
, pp. 15045-15048
-
-
Shi, Q.1
Izvekov, S.2
Voth, G.A.3
-
25
-
-
0038400062
-
Dual-Resolution Coarse-Grained Simulation of the Bisphenol-A- Polycarbonate/Nickel Interface
-
Abrams, C. F.; Delle, S. L.; Kremer, K. Dual-Resolution Coarse-Grained Simulation of the Bisphenol-A-Polycarbonate/Nickel Interface Phys. Rev. E 2003, 67, 021807
-
(2003)
Phys. Rev. e
, vol.67
, pp. 021807
-
-
Abrams, C.F.1
Delle, S.L.2
Kremer, K.3
-
26
-
-
29144483372
-
Adaptive Resolution Molecular-Dynamics Simulation: Changing the Degrees of Freedom on the Fly
-
Praprotnik, M.; Delle, S. L.; Kremer, K. Adaptive Resolution Molecular-Dynamics Simulation: Changing the Degrees of Freedom on the Fly J. Chem. Phys. 2005, 123, 224106-224120
-
(2005)
J. Chem. Phys.
, vol.123
, pp. 224106-224120
-
-
Praprotnik, M.1
Delle, S.L.2
Kremer, K.3
-
27
-
-
79955709659
-
Dual-Resolution Molecular Dynamics Simulation of Antimicrobials in Biomembranes
-
Orsi, M.; Noro, M. G.; Essex, J. W. Dual-Resolution Molecular Dynamics Simulation of Antimicrobials in Biomembranes J. R. Soc., Interface 2011, 8, 826-841
-
(2011)
J. R. Soc., Interface
, vol.8
, pp. 826-841
-
-
Orsi, M.1
Noro, M.G.2
Essex, J.W.3
-
28
-
-
84868350493
-
Mixing Atoms and Coarse-Grained Beads in Modelling Polymer Melts
-
Di Pasquale, N.; Marchisio, D.; Carbone, P. Mixing Atoms and Coarse-Grained Beads in Modelling Polymer Melts J. Chem. Phys. 2012, 137, 164111
-
(2012)
J. Chem. Phys.
, vol.137
, pp. 164111
-
-
Di Pasquale, N.1
Marchisio, D.2
Carbone, P.3
-
29
-
-
38949113657
-
Prediction of Partition Coefficients by Multiscale Hybrid Atomic-Level/Coarse-Grain Simulations
-
Michel, J.; Orsi, M.; Essex, J. W. Prediction of Partition Coefficients by Multiscale Hybrid Atomic-Level/Coarse-Grain Simulations J. Phys. Chem. B 2008, 112, 657-660
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 657-660
-
-
Michel, J.1
Orsi, M.2
Essex, J.W.3
-
30
-
-
79959749835
-
Hybrid Simulations: Combining Atomistic and Coarse-Grained Force Fields Using Virtual Sites
-
Rzepiela, A. J.; Louhivuori, M.; Peter, C.; Marrink, S. J. Hybrid Simulations: Combining Atomistic and Coarse-Grained Force Fields Using Virtual Sites Phys. Chem. Chem. Phys. 2011, 13, 10437-10448
-
(2011)
Phys. Chem. Chem. Phys.
, vol.13
, pp. 10437-10448
-
-
Rzepiela, A.J.1
Louhivuori, M.2
Peter, C.3
Marrink, S.J.4
-
31
-
-
58049208953
-
Conservative Algorithm for an Adaptive Change of Resolution in Mixed Atomistic/Coarse-Grained Multiscale Simulations
-
Heyden, A.; Thrular, J. Conservative Algorithm for an Adaptive Change of Resolution in Mixed Atomistic/Coarse-Grained Multiscale Simulations J. Chem. Theory. Comput. 2008, 4, 217-221
-
(2008)
J. Chem. Theory. Comput.
, vol.4
, pp. 217-221
-
-
Heyden, A.1
Thrular, J.2
-
32
-
-
84876058834
-
A Multiscale Coarse-Grained Polarizable Solvent Model for Handling Long Tail Bulk Electrostatics
-
Masella, M.; Borgis, D.; Cuniasse, P. A Multiscale Coarse-Grained Polarizable Solvent Model for Handling Long Tail Bulk Electrostatics J. Comput. Chem. 2013, 34, 1112-1124
-
(2013)
J. Comput. Chem.
, vol.34
, pp. 1112-1124
-
-
Masella, M.1
Borgis, D.2
Cuniasse, P.3
-
33
-
-
28844494903
-
Coarse-Grained Model of Proteins Incorporating Atomistic Detail of the Active Site
-
Neri, M.; Anselmi, C.; Cascella, M.; Maritan, A.; Carloni, P. Coarse-Grained Model of Proteins Incorporating Atomistic Detail of the Active Site Phys. Rev. Lett. 2005, 95, 218102
-
(2005)
Phys. Rev. Lett.
, vol.95
, pp. 218102
-
-
Neri, M.1
Anselmi, C.2
Cascella, M.3
Maritan, A.4
Carloni, P.5
-
34
-
-
84871675526
-
Mixing Coarse-Grained and Fine-Grained Water in Molecular Dynamics Simulations of a Single System
-
Riniker, S.; Van Gunsteren, W. F. Mixing Coarse-Grained and Fine-Grained Water in Molecular Dynamics Simulations of a Single System J. Chem. Phys. 2012, 137, 044120
-
(2012)
J. Chem. Phys.
, vol.137
, pp. 044120
-
-
Riniker, S.1
Van Gunsteren, W.F.2
-
35
-
-
84882317084
-
Simple Method for Simulating the Mixture of Atomistic and Coarse-Grained Molecular Systems
-
Pandian, S.; Choi, S. M.; Rhee, Y. M. Simple Method for Simulating the Mixture of Atomistic and Coarse-Grained Molecular Systems J. Chem. Theory Comput. 2013, 9, 3728-3739
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 3728-3739
-
-
Pandian, S.1
Choi, S.M.2
Rhee, Y.M.3
-
36
-
-
0004067382
-
-
Reidel: Dordrecht, The Netherlands.
-
Berendsen, H. J. C.; Postma, J. P. M.; Van Gunsteren, W. F.; Hermans, J. Intermolecular Forces; Reidel: Dordrecht, The Netherlands, 1981.
-
(1981)
Intermolecular Forces
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
Hermans, J.4
-
37
-
-
84867352735
-
Mixing Atomistic and Coarse Grain Solvation Models for Md Simulations: Let Wt4 Handle the Bulk
-
Darré, L.; Tek, A.; Baaden, M.; Pantano, S. Mixing Atomistic and Coarse Grain Solvation Models for Md Simulations: Let Wt4 Handle the Bulk J. Chem. Theory Comput. 2012, 8, 3880-3894
-
(2012)
J. Chem. Theory Comput.
, vol.8
, pp. 3880-3894
-
-
Darré, L.1
Tek, A.2
Baaden, M.3
Pantano, S.4
-
38
-
-
34547485422
-
How Protein Surfaces Induce Anomalous Dynamics of Hydration Water
-
Pizzitutti, F.; Marchi, M.; Sterpone, F.; Rossky, P. J. How Protein Surfaces Induce Anomalous Dynamics of Hydration Water J. Phys. Chem. B 2007, 111, 7584-7590
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 7584-7590
-
-
Pizzitutti, F.1
Marchi, M.2
Sterpone, F.3
Rossky, P.J.4
-
39
-
-
70349481617
-
Anomalous Dynamics of Hydration Water in Carbohydrate Solutions
-
Pomata, M. H.; Sonoda, M. T.; Skaf, M. S.; Elola, M. D. Anomalous Dynamics of Hydration Water in Carbohydrate Solutions J. Phys. Chem. B 2009, 113, 12999-13006
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 12999-13006
-
-
Pomata, M.H.1
Sonoda, M.T.2
Skaf, M.S.3
Elola, M.D.4
-
40
-
-
32444440762
-
A Molecular Jump Mechanism of Water Reorientation
-
Laage, D.; Hynes, J. T. A Molecular Jump Mechanism of Water Reorientation Science 2006, 311, 832-835
-
(2006)
Science
, vol.311
, pp. 832-835
-
-
Laage, D.1
Hynes, J.T.2
-
41
-
-
4444351490
-
Empirical Force Fields for Biological Macromolecules: Overview and Issues
-
Mackerell, A. D., Jr. Empirical Force Fields for Biological Macromolecules: Overview and Issues J. Comput. Chem. 2004, 25, 1584-1604
-
(2004)
J. Comput. Chem.
, vol.25
, pp. 1584-1604
-
-
Mackerell Jr., A.D.1
-
42
-
-
0004016501
-
Comparison of Simple Potential Functions for Simulating Liquid Water
-
Jorgensen, W. L.; Chandrasekaran, R.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of Simple Potential Functions for Simulating Liquid Water J. Chem. Phys. 1983, 79, 926-935
-
(1983)
J. Chem. Phys.
, vol.79
, pp. 926-935
-
-
Jorgensen, W.L.1
Chandrasekaran, R.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
43
-
-
1242346370
-
The Missing Term in Effective Pair Potentials
-
Berendsen, H. J. C.; Grigera, J. R.; Straatsma, T. P. The Missing Term in Effective Pair Potentials J. Phys. Chem. 1987, 91, 6269-6271
-
(1987)
J. Phys. Chem.
, vol.91
, pp. 6269-6271
-
-
Berendsen, H.J.C.1
Grigera, J.R.2
Straatsma, T.P.3
-
44
-
-
0036836445
-
A Reappraisal of What We Have Learnt during Three Decades of Computer Simulations on Water
-
Guillot, B. A Reappraisal of What We Have Learnt during Three Decades of Computer Simulations on Water J. Mol. Liq. 2002, 101, 219-260
-
(2002)
J. Mol. Liq.
, vol.101
, pp. 219-260
-
-
Guillot, B.1
-
45
-
-
0035109198
-
Designed Protein G Core Variants Fold to Native-Like Structures: Sequence Selection by Orbit Tolerates Variation in Backbone Specification
-
Ross, S. A.; Sarisky, C. A.; Su, A.; Mayo, S. L. Designed Protein G Core Variants Fold to Native-Like Structures: Sequence Selection by Orbit Tolerates Variation in Backbone Specification Protein Sci. 2001, 10, 450-454
-
(2001)
Protein Sci.
, vol.10
, pp. 450-454
-
-
Ross, S.A.1
Sarisky, C.A.2
Su, A.3
Mayo, S.L.4
-
46
-
-
46249092554
-
Gromacs 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
-
Hess, B.; Kutzner, C.; Van De Spoel, D.; Lindahl, E. Gromacs 4: Algorithms for Highly Efficient, Load-Balanced, And Scalable Molecular Simulation J. Chem. Theory Comput. 2008, 4, 435-447
-
(2008)
J. Chem. Theory Comput.
, vol.4
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
Van De Spoel, D.3
Lindahl, E.4
-
47
-
-
33645961739
-
A Smooth Particle Mesh Ewald Method
-
Essman, U.; Perera, L.; Berkowitz, M.; Darden, T.; Lee, H.; Pedersen, L. A Smooth Particle Mesh Ewald Method J. Chem. Phys. 1995, 103, 8577-8593
-
(1995)
J. Chem. Phys.
, vol.103
, pp. 8577-8593
-
-
Essman, U.1
Perera, L.2
Berkowitz, M.3
Darden, T.4
Lee, H.5
Pedersen, L.6
-
48
-
-
33846823909
-
Particle Mesh Ewald - An N log(N) Method for Ewald Sums in Large Systems
-
Darden, T.; York, D.; Pedersen, L. Particle Mesh Ewald-An N.log(N) Method for Ewald Sums in Large Systems J. Chem. Phys. 1993, 98, 10089-10092
-
(1993)
J. Chem. Phys.
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
49
-
-
0000388705
-
Lincs: A Linear Constraint Solver for Molecular Simulations
-
Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. Lincs: A Linear Constraint Solver for Molecular Simulations J. Comput. Chem. 1997, 18, 1463-1472
-
(1997)
J. Comput. Chem.
, vol.18
, pp. 1463-1472
-
-
Hess, B.1
Bekker, H.2
Berendsen, H.J.C.3
Fraaije, J.4
-
50
-
-
84986440341
-
Settle: An Analytical Version of the Shake and Rattle Algorithm for Rigid Water Models
-
Miyamoto, S.; Kollman, P. A. Settle: an Analytical Version of the Shake and Rattle Algorithm for Rigid Water Models J. Comput. Chem. 1992, 13, 952-962
-
(1992)
J. Comput. Chem.
, vol.13
, pp. 952-962
-
-
Miyamoto, S.1
Kollman, P.A.2
-
51
-
-
33750587438
-
Molecular-Dynamics with Coupling to an External Bath
-
Berendsen, H. J. C.; Postma, J. P. M.; Van Gunsteren, W. F.; Dinola, A.; Haak, J. R. Molecular-Dynamics with Coupling to an External Bath J. Chem. Phys. 1984, 81, 3684-3690
-
(1984)
J. Chem. Phys.
, vol.81
, pp. 3684-3690
-
-
Berendsen, H.J.C.1
Postma, J.P.M.2
Van Gunsteren, W.F.3
Dinola, A.4
Haak, J.R.5
-
52
-
-
84873626426
-
Simple Quantitative Tests to Validate Sampling from Thermodynamic Ensembles
-
Shirts, M. Simple Quantitative Tests to Validate Sampling from Thermodynamic Ensembles J. Chem. Theory Comput. 2013, 9, 909-926
-
(2013)
J. Chem. Theory Comput.
, vol.9
, pp. 909-926
-
-
Shirts, M.1
-
53
-
-
33846086933
-
Canonical Sampling through Velocity Rescaling
-
Bussi, G.; Donadio, D.; Parrinello, M. Canonical Sampling through Velocity Rescaling J. Chem. Phys. 2007, 126, 014101
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 014101
-
-
Bussi, G.1
Donadio, D.2
Parrinello, M.3
-
54
-
-
0019707626
-
Polymorphic Transitions in Single Crystals: A New Molecular Dynamics Method
-
Parrinello, M.; Rahman, A. Polymorphic Transitions in Single Crystals: A New Molecular Dynamics Method J. Appl. Phys. 1981, 52, 7182-7191
-
(1981)
J. Appl. Phys.
, vol.52
, pp. 7182-7191
-
-
Parrinello, M.1
Rahman, A.2
-
55
-
-
77953513118
-
Improved Side-Chain Torsion Potentials for the Amber Ff99sb Protein Force Field
-
Lindorff-Larsen, K.; Piana, S.; Palmo, K.; Maragakis, P.; Klepeis, J. L.; Dror, R. O.; Shaw, D. E. Improved Side-Chain Torsion Potentials for the Amber Ff99sb Protein Force Field Proteins 2010, 78, 1950-1958
-
(2010)
Proteins
, vol.78
, pp. 1950-1958
-
-
Lindorff-Larsen, K.1
Piana, S.2
Palmo, K.3
Maragakis, P.4
Klepeis, J.L.5
Dror, R.O.6
Shaw, D.E.7
-
57
-
-
84861719017
-
Cheshift-2: Graphic Validation of Protein Structures
-
Martin, O. A.; Vila, J. A.; Scheraga, H. A. Cheshift-2: Graphic Validation of Protein Structures Bioinformatics 2012, 28, 1538-1539
-
(2012)
Bioinformatics
, vol.28
, pp. 1538-1539
-
-
Martin, O.A.1
Vila, J.A.2
Scheraga, H.A.3
-
58
-
-
70350126577
-
Quantum-Mechanics-Derived 13calpha Chemical Shift Server (Cheshift) for Protein Structure Validation
-
Vila, J. A.; Arnautova, Y. A.; Martin, O. A.; Scheraga, H. A. Quantum-Mechanics-Derived 13calpha Chemical Shift Server (Cheshift) for Protein Structure Validation Proc. Natl. Acad. Sci. U.S.A. 2009, 106, 16972-16977
-
(2009)
Proc. Natl. Acad. Sci. U.S.A.
, vol.106
, pp. 16972-16977
-
-
Vila, J.A.1
Arnautova, Y.A.2
Martin, O.A.3
Scheraga, H.A.4
-
59
-
-
0344103144
-
Density, Thermal Expansivity, and Compressibility of Liquid Water from 0 to 150 C: Correlations and Tables for Atmospheric Pressure and Saturation Reviewed and Expressed on 1968 Temperature Scale
-
Kell, G. S. Density, Thermal Expansivity, and Compressibility of Liquid Water From 0 to 150 C: Correlations and Tables for Atmospheric Pressure and Saturation Reviewed and Expressed on 1968 Temperature Scale J. Chem. Eng. Data 1975, 20, 97-105
-
(1975)
J. Chem. Eng. Data
, vol.20
, pp. 97-105
-
-
Kell, G.S.1
-
60
-
-
0002547850
-
Computer Simulation and the Dielectric Constant at Finite Wavelength
-
Neumann, M. Computer Simulation and the Dielectric Constant at Finite Wavelength Mol. Phys. 1986, 57, 97-121
-
(1986)
Mol. Phys.
, vol.57
, pp. 97-121
-
-
Neumann, M.1
-
61
-
-
21844495517
-
NMR Relaxation Studies in Water-Alcohol Mixtures: The Water-Rich Region
-
Ludwig, R. NMR Relaxation Studies in Water-Alcohol Mixtures: The Water-Rich Region Chem. Phys. 1995, 329, 329-337
-
(1995)
Chem. Phys.
, vol.329
, pp. 329-337
-
-
Ludwig, R.1
-
62
-
-
84953658885
-
A Database for Static Dielectric Constant of Water and Steam
-
Fernandez, D. P.; Mulev, Y.; Goodwin, A. R. H.; Levelt Sengers, J. M. H. A Database for Static Dielectric Constant of Water and Steam J. Phys. Chem. Ref. Data 1995, 24, 33-71
-
(1995)
J. Phys. Chem. Ref. Data
, vol.24
, pp. 33-71
-
-
Fernandez, D.P.1
Mulev, Y.2
Goodwin, A.R.H.3
Levelt Sengers, J.M.H.4
-
64
-
-
24144479792
-
Solvation Free Energies of Amino Acid Side Chain Analogs for Common Molecular Mechanics Water Models
-
Shirts, M. R.; Pande, V. S. Solvation Free Energies of Amino Acid Side Chain Analogs for Common Molecular Mechanics Water Models J. Chem. Phys. 2005, 122, 134508
-
(2005)
J. Chem. Phys.
, vol.122
, pp. 134508
-
-
Shirts, M.R.1
Pande, V.S.2
-
65
-
-
0000508683
-
Tracer-Diffusion in Liquids. II. The Self-Diffusion as Sodium Ion in Aqueous Sodium Chloride Solutions
-
Wang, J. H.; Miller, S. Tracer-Diffusion in Liquids. II. The Self-Diffusion as Sodium Ion in Aqueous Sodium Chloride Solutions J. Am. Chem. Soc. 1952, 74, 1611-1612
-
(1952)
J. Am. Chem. Soc.
, vol.74
, pp. 1611-1612
-
-
Wang, J.H.1
Miller, S.2
-
66
-
-
5244220867
-
Tracer-Diffusion in Liquids. III. The Self-Diffusion as Sodium Ion in Aqueous Sodium Chloride Solutions
-
Wang, J. H. Tracer-Diffusion In Liquids. III. The Self-Diffusion as Sodium Ion in Aqueous Sodium Chloride Solutions J. Am. Chem. Soc. 1952, 74, 1612-1615
-
(1952)
J. Am. Chem. Soc.
, vol.74
, pp. 1612-1615
-
-
Wang, J.H.1
-
67
-
-
34147162778
-
The Effect of Droplet Size on Surface Tension
-
Tolman, R. C. The Effect of Droplet Size on Surface Tension J. Chem. Phys. 1949, 17, 333-337
-
(1949)
J. Chem. Phys.
, vol.17
, pp. 333-337
-
-
Tolman, R.C.1
-
68
-
-
84878245329
-
A Molecular Dynamics Study on Inner Pressure of Microbubbles in Liquid Argon and Water
-
Takahashi, H.; Morita, A. A Molecular Dynamics Study on Inner Pressure of Microbubbles in Liquid Argon and Water Chem. Phys. Lett. 2013, 573, 35-40
-
(2013)
Chem. Phys. Lett.
, vol.573
, pp. 35-40
-
-
Takahashi, H.1
Morita, A.2
-
69
-
-
27644598711
-
The Tolman Length: Is It Positive or Negative?
-
Lei, Y. A.; Bykov, T.; Yoo, S.; Zeng, X. C. The Tolman Length: Is It Positive or Negative? J. Am. Chem. Soc. 2005, 127, 15346-15347
-
(2005)
J. Am. Chem. Soc.
, vol.127
, pp. 15346-15347
-
-
Lei, Y.A.1
Bykov, T.2
Yoo, S.3
Zeng, X.C.4
-
70
-
-
84864755959
-
Structural Effects of an Atomic-Level Layer of Water Molecules around Proteins Solvated in Supra-Molecular Coarse-Grained Water
-
Riniker, S.; Eichenberger, A. P.; Van Gunsteren, W. F. Structural Effects of an Atomic-Level Layer of Water Molecules around Proteins Solvated in Supra-Molecular Coarse-Grained Water J. Phys. Chem. B 2012, 116, 8873-8879
-
(2012)
J. Phys. Chem. B
, vol.116
, pp. 8873-8879
-
-
Riniker, S.1
Eichenberger, A.P.2
Van Gunsteren, W.F.3
-
71
-
-
68149100477
-
13Cα Chemical Shifts for X-ray Protein Models?
-
13Cα Chemical Shifts for X-ray Protein Models? Acta Crystallogr., D. Biol. Crystallogr. 2009, 65, 697-703
-
(2009)
Acta Crystallogr., D. Biol. Crystallogr.
, vol.65
, pp. 697-703
-
-
Arnautova, Y.A.1
Vila, J.A.2
Martin, O.A.3
Scheraga, H.A.4
-
72
-
-
85013746467
-
-
2 nd ed. Academic Press: Amsterdam.
-
Cavanagh, J.; Fairbrother, W. J.; Palmer, A. G., III; Rance, M.; Skelton, N. J. Protein NMR Spectroscopy: Principles and Practice, 2 nd ed.; Academic Press: Amsterdam, 2007.
-
(2007)
Protein NMR Spectroscopy: Principles and Practice
-
-
Cavanagh, J.1
Fairbrother, W.J.2
Palmer III, A.G.3
Rance, M.4
Skelton, N.J.5
-
73
-
-
79952076954
-
A Simple, Efficient Polarizable Coarse-Grained Water Model for Molecular Dynamics Simulations
-
Riniker, S.; Van Gunsteren, W. F. A Simple, Efficient Polarizable Coarse-Grained Water Model for Molecular Dynamics Simulations J. Chem. Phys. 2011, 134, 084110
-
(2011)
J. Chem. Phys.
, vol.134
, pp. 084110
-
-
Riniker, S.1
Van Gunsteren, W.F.2
-
74
-
-
84860829715
-
Cavities Determine the Pressure Unfolding of Proteins
-
Roche, J.; Caro, J. A.; Norberto, D. R.; Barthe, P.; Roumestand, C.; Schlessman, J. L.; Garcia, A. E.; Garcia-Moreno, B. E.; Royer, C. A. Cavities Determine the Pressure Unfolding of Proteins Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 6945-6950
-
(2012)
Proc. Natl. Acad. Sci. U.S.A.
, vol.109
, pp. 6945-6950
-
-
Roche, J.1
Caro, J.A.2
Norberto, D.R.3
Barthe, P.4
Roumestand, C.5
Schlessman, J.L.6
Garcia, A.E.7
Garcia-Moreno, B.E.8
Royer, C.A.9
|