-
1
-
-
77957231785
-
Induced fit, conformational selection and independent dynamic segments: An extended view of binding events
-
Csermely, P.; Palotai, R.; Nussinov, R. Induced fit, conformational selection and independent dynamic segments: An extended view of binding events. Trends Biochem. Sci. 2010, 35, 539-546.
-
(2010)
Trends Biochem. Sci
, vol.35
, pp. 539-546
-
-
Csermely, P.1
Palotai, R.2
Nussinov, R.3
-
2
-
-
84872859789
-
Molecular Recognition Ligand Association
-
Baron, R.; McCammon, J.A. Molecular Recognition and Ligand Association. Ann. Rev. Phys. Chem. 2013, 64, 151-175.
-
(2013)
Ann. Rev. Phys. Chem
, vol.64
, pp. 151-175
-
-
Baron, R.1
McCammon, J.A.2
-
3
-
-
1642357706
-
The many roles of computation in drug discovery
-
Jorgensen, W. The many roles of computation in drug discovery. Science 2004, 303, 1813-1818.
-
(2004)
Science
, vol.303
, pp. 1813-1818
-
-
Jorgensen, W.1
-
5
-
-
84872859789
-
Molecular Recognition and Ligand Association
-
Baron, R.; McCammon, J.A. Molecular Recognition and Ligand Association. Ann. Rev. Phys. Chem. 2013, 64, 151-175.
-
(2013)
Ann. Rev. Phys. Chem
, vol.64
, pp. 151-175
-
-
Baron, R.1
McCammon, J.A.2
-
6
-
-
84958160632
-
Atomistic-Level Portrayal of Drug-DNA Interplay: A History of Courtships and Meetings Revealed by Molecular Simulations
-
Vargiu, A.V.; Magistrato, A. Atomistic-Level Portrayal of Drug-DNA Interplay: A History of Courtships and Meetings Revealed by Molecular Simulations. ChemMedChem 2014, 9, 1966-1981.
-
(2014)
ChemMedChem
, vol.9
, pp. 1966-1981
-
-
Vargiu, A.V.1
Magistrato, A.2
-
7
-
-
70350340728
-
The role of dynamic conformational ensembles in biomolecular recognition
-
Boehr, D.D.; Nussinov, R.; Wright, P.E. The role of dynamic conformational ensembles in biomolecular recognition. Nat. Chem. Biol. 2009, 5, 789-796.
-
(2009)
Nat. Chem. Biol
, vol.5
, pp. 789-796
-
-
Boehr, D.D.1
Nussinov, R.2
Wright, P.E.3
-
8
-
-
33746271105
-
Biomolecular modeling: Goals, problems, perspectives
-
Van Gunsteren, W.F.; Bakowies, D.; Baron, R.; Chandrasekhar, I.; Christen, M.; Daura, X.; Gee, P.; Geerke, D.P.; Glaettli, A.; Huenenberger, P.H.; et al. Biomolecular modeling: Goals, problems, perspectives. Angew. Chem. Int. Ed. 2006, 45, 4064-4092.
-
(2006)
Angew. Chem. Int. Ed
, vol.45
, pp. 4064-4092
-
-
Van Gunsteren, W.F.1
Bakowies, D.2
Baron, R.3
Chandrasekhar, I.4
Christen, M.5
Daura, X.6
Gee, P.7
Geerke, D.P.8
Glaettli, A.9
Huenenberger, P.H.10
-
9
-
-
53249098376
-
Multiscale methods for macromolecular simulations
-
Sherwood, P.; Brooks, B.R.; Sansom, M.S.P. Multiscale methods for macromolecular simulations. Curr. Opin. Struc. Biol. 2008, 18, 630-640.
-
(2008)
Curr. Opin. Struc. Biol
, vol.18
, pp. 630-640
-
-
Sherwood, P.1
Brooks, B.R.2
Sansom, M.S.P.3
-
10
-
-
84884931806
-
Twenty-Five Years of Nucleic Acid Simulations
-
Cheatham, T.E., III; Case, D.A. Twenty-Five Years of Nucleic Acid Simulations. Biopolymers 2013, 99, 969-977.
-
(2013)
Biopolymers
, vol.99
, pp. 969-977
-
-
Cheatham, T.E.1
Case, D.A.2
-
11
-
-
70349779536
-
Discovery through the Computational Microscope
-
Lee, E.H.; Hsin, J.; Sotomayor, M.; Comellas, G.; Schulten, K. Discovery through the Computational Microscope. Structure 2009, 17, 1295-1306.
-
(2009)
Structure
, vol.17
, pp. 1295-1306
-
-
Lee, E.H.1
Hsin, J.2
Sotomayor, M.3
Comellas, G.4
Schulten, K.5
-
12
-
-
84905400486
-
Charged residues distribution modulates selectivity of the open state of human isoforms of the voltage dependent anion-selective channel
-
Amodeo, G.F.; Scorciapino, M.A.; Messina, A.; De Pinto, V.; Ceccarelli, M. Charged residues distribution modulates selectivity of the open state of human isoforms of the voltage dependent anion-selective channel. PLoS ONE 2014, 9, e103879.
-
(2014)
PLoS ONE
, vol.9
, pp. e103879
-
-
Amodeo, G.F.1
Scorciapino, M.A.2
Messina, A.3
De Pinto, V.4
Ceccarelli, M.5
-
13
-
-
38949151546
-
Molecular simulations of protein dynamics: New windows on mechanisms in biology
-
Dodson, G.G.; Lane, D.P.; Verma, C.S. Molecular simulations of protein dynamics: New windows on mechanisms in biology. EMBO Rep. 2008, 9, 144-150.
-
(2008)
EMBO Rep
, vol.9
, pp. 144-150
-
-
Dodson, G.G.1
Lane, D.P.2
Verma, C.S.3
-
14
-
-
84861367246
-
Biomolecular Simulation: A Computational Microscope for Molecular Biology
-
Dror, R.O.; Dirks, R.M.; Grossman, J.P.; Xu, H.; Shaw, D.E. Biomolecular Simulation: A Computational Microscope for Molecular Biology. Ann. Rev. Biophys. 2012, 41, 429-452.
-
(2012)
Ann. Rev. Biophys
, vol.41
, pp. 429-452
-
-
Dror, R.O.1
Dirks, R.M.2
Grossman, J.P.3
Xu, H.4
Shaw, D.E.5
-
15
-
-
85008253380
-
Significance of Molecular Dynamics Simulations for Life Sciences
-
Karplus, M.; Lavery, R. Significance of Molecular Dynamics Simulations for Life Sciences. Isr. J. Chem. 2014, 54, 1042-1051.
-
(2014)
Isr. J. Chem
, vol.54
, pp. 1042-1051
-
-
Karplus, M.1
Lavery, R.2
-
16
-
-
84934927811
-
The impact of molecular dynamics on drug design: Applications for the characterization of ligand-macromolecule complexes
-
Mortier, J.; Rakers, C.; Bermudez, M.; Murgueitio, M.S.; Riniker, S.; Wolber, G. The impact of molecular dynamics on drug design: Applications for the characterization of ligand-macromolecule complexes. Drug Discov. Today 2015, 20, 686-702.
-
(2015)
Drug Discov. Today
, vol.20
, pp. 686-702
-
-
Mortier, J.1
Rakers, C.2
Bermudez, M.3
Murgueitio, M.S.4
Riniker, S.5
Wolber, G.6
-
18
-
-
0012818236
-
Testing and comparison of empirical force fields: Techniques and problems
-
Gunsteren, W.F.V., Weiner, P., Wilkinson, A.J., Eds.; ESCOM: Leiden, The Netherlands
-
Gelin, B.R. Testing and comparison of empirical force fields: Techniques and problems. In Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications; Gunsteren, W.F.V., Weiner, P., Wilkinson, A.J., Eds.; ESCOM: Leiden, The Netherlands, 1993; Volume 2, pp. 127-146.
-
(1993)
Computer Simulation of Biomolecular Systems: Theoretical and Experimental Applications
, vol.2
, pp. 127-146
-
-
Gelin, B.R.1
-
19
-
-
0029011701
-
A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules
-
Cornell, W.D.; Cieplak, P.; Bayly, C.I.; Gould, I.R.G.; Merz, K.M.J.; Ferguson, D.M.; Spellmeyer, D.C.; Fox, T.; Caldwell, J.W.; Kollman, P.A. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules. J. Am. Chem. Soc. 1995, 117, 5179-5197.
-
(1995)
J. Am. Chem. Soc
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
Gould, I.R.G.4
Merz, K.M.J.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
20
-
-
0034639970
-
A density functional normal mode calculation of a bacteriochlorophyll a derivative
-
Ceccarelli, M.; Lutz, M.; Marchi, M. A density functional normal mode calculation of a bacteriochlorophyll a derivative. J. Am. Chem. Soc. 2000, 122, 3532-3533.
-
(2000)
J. Am. Chem. Soc
, vol.122
, pp. 3532-3533
-
-
Ceccarelli, M.1
Lutz, M.2
Marchi, M.3
-
21
-
-
0038339489
-
Simulation and Modeling of the Rhodobacter sphaeroides Bacterial Reaction Center II: Primary Charge Separation
-
Ceccarelli, M.; Marchi, M. Simulation and Modeling of the Rhodobacter sphaeroides Bacterial Reaction Center II: Primary Charge Separation. J. Phys. Chem. B 2003, 107, 5630-5641.
-
(2003)
J. Phys. Chem. B
, vol.107
, pp. 5630-5641
-
-
Ceccarelli, M.1
Marchi, M.2
-
22
-
-
84892963298
-
Assessing the accuracy of physical models used in protein-folding simulations: Quantitative evidence from long molecular dynamics simulations
-
Piana, S.; Klepeis, J.L.; Shaw, D.E. Assessing the accuracy of physical models used in protein-folding simulations: Quantitative evidence from long molecular dynamics simulations. Curr. Opin. Struct. Biol. 2014, 24, 98-105.
-
(2014)
Curr. Opin. Struct. Biol
, vol.24
, pp. 98-105
-
-
Piana, S.1
Klepeis, J.L.2
Shaw, D.E.3
-
23
-
-
84901047861
-
Molecular Dynamics Simulations of Nucleic Acids from Tetranucleotides to the Ribosome
-
Šponer, J.; Banáš, P.; Jurečka, P.; Zgarbová, M.; Kührová, P.; Havrila, M.; Krepl, M.; Stadlbauer, P.; Otyepka, M. Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome. J. Phys. Chem. Lett. 2014, 5, 1771-1782.
-
(2014)
J. Phys. Chem. Lett
, vol.5
, pp. 1771-1782
-
-
Šponer, J.1
Banáš, P.2
Jurečka, P.3
Zgarbová, M.4
Kührová, P.5
Havrila, M.6
Krepl, M.7
Stadlbauer, P.8
Otyepka, M.9
-
24
-
-
84867820827
-
LAMBADA and InflateGRO2: Efficient Membrane Alignment and Insertion of Membrane Proteins for Molecular Dynamics Simulations
-
Schmidt, T.H.; Kandt, C. LAMBADA and InflateGRO2: Efficient Membrane Alignment and Insertion of Membrane Proteins for Molecular Dynamics Simulations. J. Chem. Inf. Mod. 2012, 52, 2657-2669.
-
(2012)
J. Chem. Inf. Mod
, vol.52
, pp. 2657-2669
-
-
Schmidt, T.H.1
Kandt, C.2
-
25
-
-
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
-
26
-
-
84916232194
-
AMBER-DYES: Characterization of Charge Fluctuations and Force Field Parameterization of Fluorescent Dyes for Molecular Dynamics Simulations
-
Graen, T.; Hoefling, M.; Grubmueller, H. AMBER-DYES: Characterization of Charge Fluctuations and Force Field Parameterization of Fluorescent Dyes for Molecular Dynamics Simulations. J. Chem. Theory Comput. 2014, 10, 5505-5512.
-
(2014)
J. Chem. Theory Comput
, vol.10
, pp. 5505-5512
-
-
Graen, T.1
Hoefling, M.2
Grubmueller, H.3
-
27
-
-
38549152775
-
R.E.DD.B.: A database for RESP and ESP atomic charges, and force field libraries
-
Dupradeau, F.Y.; Cézard, C.; Lelong, R.; Stanislawiak, E.; Pêcher, J.; Delepine, J.C.; Cieplak, P. R.E.DD.B.: A database for RESP and ESP atomic charges, and force field libraries. Nucleic Acids Res. 2008, 36, D360-D367.
-
(2008)
Nucleic Acids Res
, vol.36
, pp. D360-D367
-
-
Dupradeau, F.Y.1
Cézard, C.2
Lelong, R.3
Stanislawiak, E.4
Pêcher, J.5
Delepine, J.C.6
Cieplak, P.7
-
28
-
-
77954566051
-
The R.E.D. Tools: Advances in RESP and ESP charge derivation and force field library building
-
Dupradeau, F.Y.; Pigache, A.; Zaffran, T.; Savineau, C.; Lelong, R.; Grivel, N.; Lelong, D.; Rosanski, W.; Cieplak, P. The R.E.D. tools: Advances in RESP and ESP charge derivation and force field library building. Phys. Chem. Chem. Phys. 2010, 12, 7821-7839.
-
(2010)
Phys. Chem. Chem. Phys
, vol.12
, pp. 7821-7839
-
-
Dupradeau, F.Y.1
Pigache, A.2
Zaffran, T.3
Savineau, C.4
Lelong, R.5
Grivel, N.6
Lelong, D.7
Rosanski, W.8
Cieplak, P.9
-
29
-
-
84860154396
-
-
(accessed on 20 July 2014).
-
AMBER Parameter Database. Available online: http://www.pharmacy.manchester.ac.uk/bryce/ amber/ (accessed on 20 July 2014).
-
AMBER Parameter Database
-
-
-
30
-
-
84941235455
-
-
(accessed on 30 November 2014).
-
Marvin 14.8.25.0. ChemAxon 2014. Available online: http://www.chemaxon.com (accessed on 30 November 2014).
-
Marvin 14.8.25.0. ChemAxon 2014
-
-
-
31
-
-
84904760980
-
-
University of California: San Francisco, CA, USA
-
Case, D.; Babin, V.; Berryman, J.; Betz, R.; Cai, Q.; Cerutti, D.; Cheatham, T., III; Darden, T.; Duke, R.; Gohlke, H.; et al. Amber 14. University of California: San Francisco, CA, USA, 2014.
-
(2014)
Amber 14
-
-
Case, D.1
Babin, V.2
Berryman, J.3
Betz, R.4
Cai, Q.5
Cerutti, D.6
Cheatham, T.7
Darden, T.8
Duke, R.9
Gohlke, H.10
-
32
-
-
75749083809
-
-
Gaussian Inc.: Wallingford CT USA
-
Frisch, M.J.; Trucks, G.W.; Schlegel, H.B.; Scuseria, G.E.; Robb, M.A.; Cheeseman, J.R.; Scalmani, G.; Barone, V.; Mennucci, B.; Petersson, G.A.; et al. Gaussian09 Revision A.02; Gaussian Inc.: Wallingford, CT, USA, 2009.
-
(2009)
Gaussian09 Revision A.02
-
-
Frisch, M.J.1
Trucks, G.W.2
Schlegel, H.B.3
Scuseria, G.E.4
Robb, M.A.5
Cheeseman, J.R.6
Scalmani, G.7
Barone, V.8
Mennucci, B.9
Petersson, G.A.10
-
33
-
-
84899087499
-
TRANSLOCATION Project: How to Get Good Drugs into Bad Bugs
-
Stavenger, R.A.;Winterhalter, M. TRANSLOCATION Project: How to Get Good Drugs into Bad Bugs. Sci. Transl. Med. 2014, 6, 228ed7.
-
(2014)
Sci. Transl. Med
, vol.6
, pp. 228ed7
-
-
Stavenger, R.A.1
Winterhalter, M.2
-
34
-
-
23444456920
-
Prevention of drug access to bacterial targets: Permeability barriers and active efflux
-
Nikaido, H. Prevention of drug access to bacterial targets: Permeability barriers and active efflux. Science 1994, 264, 382-388.
-
(1994)
Science
, vol.264
, pp. 382-388
-
-
Nikaido, H.1
-
35
-
-
52449131735
-
Physical insights into permeation of and resistance to antibiotics in bacteria
-
Ceccarelli, M.; Ruggerone, P. Physical insights into permeation of and resistance to antibiotics in bacteria. Curr. Drug Targ. 2008, 9, 779-788.
-
(2008)
Curr. Drug Targ
, vol.9
, pp. 779-788
-
-
Ceccarelli, M.1
Ruggerone, P.2
-
36
-
-
2942532422
-
Development and testing of a general amber force field
-
Wang, J.; Wolf, R.M.; Caldwell, J.W.; Kollman, P.A.; Case, D.A. Development and testing of a general amber force field. J. Comput. Chem. 2004, 25, 1157-1174.
-
(2004)
J. Comput. Chem
, vol.25
, pp. 1157-1174
-
-
Wang, J.1
Wolf, R.M.2
Caldwell, J.W.3
Kollman, P.A.4
Case, D.A.5
-
37
-
-
54949108677
-
PubChem: Integrated Platform of Small Molecules and Biological Activities
-
Bolton, E.E.; Wangand, Y.; Thiessenand, P.A.; Bryant, S.H. PubChem: Integrated Platform of Small Molecules and Biological Activities. Annu. Rep. Comput. Chem. 2008, 4, 217-241.
-
(2008)
Annu. Rep. Comput. Chem
, vol.4
, pp. 217-241
-
-
Bolton, E.E.1
Wangand, Y.2
Thiessenand, P.A.3
Bryant, S.H.4
-
38
-
-
0033235339
-
Nobel Lecture: Electronic structure of matter-wave functions and density functionals
-
Kohn, W. Nobel Lecture: Electronic structure of matter-wave functions and density functionals. Rev. Mod. Phys. 1999, 71, 1253-1266.
-
(1999)
Rev. Mod. Phys
, vol.71
, pp. 1253-1266
-
-
Kohn, W.1
-
39
-
-
0000189651
-
Density-functional thermochemistry III. the role of exact exchange
-
Becke, A.D. Density-functional thermochemistry. III. The role of exact exchange. J. Chem. Phys. 1993, 98, 5648-5652.
-
(1993)
J. Chem. Phys
, vol.98
, pp. 5648-5652
-
-
Becke, A.D.1
-
40
-
-
33645716728
-
Comparison of Density Functional and MP2 Calculations on the Water Monomer and Dimer
-
Kim, K.; Jordan, K.D. Comparison of Density Functional and MP2 Calculations on the Water Monomer and Dimer. J. Phys. Chem. 1994, 98, 10089-10094.
-
(1994)
J. Phys. Chem
, vol.98
, pp. 10089-10094
-
-
Kim, K.1
Jordan, K.D.2
-
41
-
-
0033549476
-
Quantum Chemical Models (Nobel Lecture).
-
Pople, J.A. Quantum Chemical Models (Nobel Lecture). Angew. Chem. Int. Ed. 1999, 38, 1894-1902.
-
(1999)
Angew. Chem. Int. Ed
, vol.38
, pp. 1894-1902
-
-
Pople J. ., A.1
-
42
-
-
33846871670
-
On-line database of the spectral properties of polycyclic aromatic hydrocarbons
-
Malloci, G.; Joblin, C.; Mulas, G. On-line database of the spectral properties of polycyclic aromatic hydrocarbons. Chem. Phys. 2007, 332, 353-359.
-
(2007)
Chem. Phys
, vol.332
, pp. 353-359
-
-
Malloci, G.1
Joblin, C.2
Mulas, G.3
-
43
-
-
79958771826
-
Electronic and optical properties of families of polycyclic aromatic hydrocarbons: A systematic (time-dependent) density functional theory study
-
Malloci, G.; Cappellini, G.; Mulas, G.; Mattoni, A. Electronic and optical properties of families of polycyclic aromatic hydrocarbons: A systematic (time-dependent) density functional theory study. Chem. Phys. 2011, 384, 19-27.
-
(2011)
Chem. Phys
, vol.384
, pp. 19-27
-
-
Malloci, G.1
Cappellini, G.2
Mulas, G.3
Mattoni, A.4
-
44
-
-
84961980477
-
Quantum Mechanical Continuum Solvation Models
-
Tomasi, J.; Mennucci, B.; Cammi, R. Quantum Mechanical Continuum Solvation Models. Chem. Rev. 2005, 105, 2999-3094.
-
(2005)
Chem. Rev
, vol.105
, pp. 2999-3094
-
-
Tomasi, J.1
Mennucci, B.2
Cammi, R.3
-
45
-
-
40549115627
-
Cclib: A library for package-independent computational chemistry algorithms
-
O'Boyle, N.M.; Tenderholt, A.L.; Langner, K.M. cclib: A library for package-independent computational chemistry algorithms. J. Comput. Chem. 2008, 29, 839-845.
-
(2008)
J. Comput. Chem
, vol.29
, pp. 839-845
-
-
O'Boyle, N.M.1
Tenderholt, A.L.2
Langner, K.M.3
-
46
-
-
78449275560
-
Gabedit - A graphical user interface for computational chemistry softwares
-
Allouche, A.R. Gabedit - A graphical user interface for computational chemistry softwares. J. Comput. Chem. 2011, 32, 174-182.
-
(2011)
J. Comput. Chem
, vol.32
, pp. 174-182
-
-
Allouche, A.R.1
-
47
-
-
84986468608
-
An approach to computing electrostatic charges for molecules
-
Singh, U.C.; Kollman, P.A. An approach to computing electrostatic charges for molecules. J. Comput. Chem. 1984, 5, 129-145.
-
(1984)
J. Comput. Chem
, vol.5
, pp. 129-145
-
-
Singh, U.C.1
Kollman, P.A.2
-
48
-
-
84986513567
-
Determining atom-centered monopoles from molecular electrostatic potentials. the need for high sampling density in formamide conformational analysis
-
Breneman, C.M.; Wiberg, K.B. Determining atom-centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis. J. Comput. Chem. 1990, 11, 361-373.
-
(1990)
J. Comput. Chem
, vol.11
, pp. 361-373
-
-
Breneman, C.M.1
Wiberg, K.B.2
-
49
-
-
3042524904
-
A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model
-
Bayly, C.I.; Cieplak, P.; Cornell, W.; Kollman, P.A. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model. J. Phys. Chem. 1993, 97, 10269-10280.
-
(1993)
J. Phys. Chem
, vol.97
, pp. 10269-10280
-
-
Bayly, C.I.1
Cieplak, P.2
Cornell, W.3
Kollman, P.A.4
-
50
-
-
33748538349
-
Automatic atom type and bond type perception in molecular mechanical calculations
-
Wang, J.; Wang, W.; Kollman, P.A.; Case, D.A. Automatic atom type and bond type perception in molecular mechanical calculations. J. Mol. Graph. Model. 2006, 25, 247-260.
-
(2006)
J. Mol. Graph. Model
, vol.25
, pp. 247-260
-
-
Wang, J.1
Wang, W.2
Kollman, P.A.3
Case, D.A.4
-
51
-
-
37249091134
-
Computation of Octanol-Water Partition Coefficients by Guiding an Additive Model with Knowledge
-
Cheng, T.; Zhao, Y.; Li, X.; Lin, F.; Xu, Y.; Zhang, X.; Li, Y.; Wang, R.; Lai, L. Computation of Octanol-Water Partition Coefficients by Guiding an Additive Model with Knowledge. J. Chem. Inf. Model. 2007, 47, 2140-2148.
-
(2007)
J. Chem. Inf. Model
, vol.47
, pp. 2140-2148
-
-
Cheng, T.1
Zhao, Y.2
Li, X.3
Lin, F.4
Xu, Y.5
Zhang, X.6
Li, Y.7
Wang, R.8
Lai, L.9
-
52
-
-
65449186590
-
PLATINUM: A web tool for analysis of hydrophobic/hydrophilic organization of biomolecular complexes
-
Pyrkov, T.V.; Chugunov, A.O.; Krylov, N.A.; Nolde, D.E.; Efremov, R.G. PLATINUM: A web tool for analysis of hydrophobic/hydrophilic organization of biomolecular complexes. Bioinformatics 2009, 25, 1201-1202.
-
(2009)
Bioinformatics
, vol.25
, pp. 1201-1202
-
-
Pyrkov, T.V.1
Chugunov, A.O.2
Krylov, N.A.3
Nolde, D.E.4
Efremov, R.G.5
-
53
-
-
0004016501
-
Comparison of simple potential functions for simulating liquid water
-
Jorgensen, W.L.; Chandrasekhar, J.; 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
Chandrasekhar, J.2
Madura, J.D.3
Impey, R.W.4
Klein, M.L.5
-
54
-
-
49449085241
-
Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations
-
Joung, I.S.; Cheatham, T.E. Determination of Alkali and Halide Monovalent Ion Parameters for Use in Explicitly Solvated Biomolecular Simulations. J. Phys. Chem. B 2008, 112, 9020-9041.
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 9020-9041
-
-
Joung, I.S.1
Cheatham, T.E.2
-
55
-
-
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
-
56
-
-
0026869597
-
Langevin dynamics of peptides: The frictional dependence of isomerization rates of N-acetylalanyl-N0-methylamide
-
Loncharich, R.J.; Brooks, B.R.; Pastor, R.W. Langevin dynamics of peptides: The frictional dependence of isomerization rates of N-acetylalanyl-N0-methylamide. Biopolymers 1992, 32, 523-535.
-
(1992)
Biopolymers
, vol.32
, pp. 523-535
-
-
Loncharich, R.J.1
Brooks, B.R.2
Pastor, R.W.3
-
57
-
-
84880022273
-
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
-
Roe, D.R.; Cheatham, T.E. PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data. J. Chem. Theory Comput. 2013, 9, 3084-3095.
-
(2013)
J. Chem. Theory Comput
, vol.9
, pp. 3084-3095
-
-
Roe, D.R.1
Cheatham, T.E.2
-
58
-
-
40449084229
-
Effects of ion concentration on the hydrogen bonded structure of water in the vicinity of ions in aqueous NaCl solutions
-
Nag, A.; Chakraborty, D.; Chandra, A. Effects of ion concentration on the hydrogen bonded structure of water in the vicinity of ions in aqueous NaCl solutions. J. Chem. Sci. 2008, 120, 71-77.
-
(2008)
J. Chem. Sci
, vol.120
, pp. 71-77
-
-
Nag, A.1
Chakraborty, D.2
Chandra, A.3
-
59
-
-
4243422452
-
Effect of Environment on Hydrogen Bond Dynamics in Liquid Water
-
Luzar, A.; Chandler, D. Effect of Environment on Hydrogen Bond Dynamics in Liquid Water. Phys. Rev. Lett. 1996, 76, 928-931.
-
(1996)
Phys. Rev. Lett
, vol.76
, pp. 928-931
-
-
Luzar, A.1
Chandler, D.2
-
60
-
-
0002300553
-
Hydrogen-bond kinetics in liquid Water
-
Luzar, A.; Chandler, D. Hydrogen-bond kinetics in liquid Water. Nature 1996, 379, 55-57.
-
(1996)
Nature
, vol.379
, pp. 55-57
-
-
Luzar, A.1
Chandler, D.2
-
61
-
-
0001427242
-
Hydrogen bonded clusters in the liquid phase: I. Analysis of the velocity correlation function of water triplets
-
Sutmann, G.; Vallauri, R. Hydrogen bonded clusters in the liquid phase: I. Analysis of the velocity correlation function of water triplets. J. Phys. Condens. Matter 1998, 10, 9231-9240.
-
(1998)
J. Phys. Condens. Matter
, vol.10
, pp. 9231-9240
-
-
Sutmann, G.1
Vallauri, R.2
-
62
-
-
4243838224
-
Effects of Ion Atmosphere on Hydrogen-Bond Dynamics in Aqueous Electrolyte Solutions
-
Chandra, A. Effects of Ion Atmosphere on Hydrogen-Bond Dynamics in Aqueous Electrolyte Solutions. Phys. Rev. Lett. 2000, 85, 768-771.
-
(2000)
Phys. Rev. Lett
, vol.85
, pp. 768-771
-
-
Chandra, A.1
-
63
-
-
36649006642
-
Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms
-
Shao, J.; Tanner, S.W.; Thompson, N.; Cheatham, T.E. Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms. J. Chem. Theory Comput. 2007, 3, 2312-2334.
-
(2007)
J. Chem. Theory Comput
, vol.3
, pp. 2312-2334
-
-
Shao, J.1
Tanner, S.W.2
Thompson, N.3
Cheatham, T.E.4
-
64
-
-
36248975150
-
-
Nijenborgh 4 9747 AG Groningen The Netherlands. (accessed on 29 June 2014).
-
van der Spoel, D.; van Buuren, A.R.; Apol, E.; Meulenhoff, P.J.; Tieleman, D.P.; Sijbers, A.L.T.M.; Hess, B.; Feenstra, K.A.; Lindahl, E.; van Drunen, R.; Berendsen, H.J.C. Gromacs User Manual version 3.0. Nijenborgh 4, 9747 AG Groningen, The Netherlands. 2001. Available online: http://www.gromacs.org (accessed on 29 June 2014).
-
(2001)
Gromacs User Manual Version 3.0
-
-
Van Der Spoel, D.1
Van Buuren, A.R.2
Apol, E.3
Meulenhoff, P.J.4
Tieleman, D.P.5
Sijbers, A.L.T.M.6
Hess, B.7
Feenstra, K.A.8
Lindahl, E.9
Van Drunen, R.10
Berendsen, H.J.C.11
-
65
-
-
69349100797
-
PLUMED: A portable plugin for free-energy calculations with molecular dynamics
-
Bonomi, M.; Branduardi, D.; Bussi, G.; Camilloni, C.; Provasi, D.; Raiteri, P.; Donadio, D.; Marinelli, F.; Pietrucci, F.; Broglia, R.A.; Parrinello, M. PLUMED: A portable plugin for free-energy calculations with molecular dynamics. Comput. Phys. Comm. 2009, 180, 1961-1972.
-
(2009)
Comput. Phys. Comm
, vol.180
, pp. 1961-1972
-
-
Bonomi, M.1
Branduardi, D.2
Bussi, G.3
Camilloni, C.4
Provasi, D.5
Raiteri, P.6
Donadio, D.7
Marinelli, F.8
Pietrucci, F.9
Broglia, R.A.10
Parrinello, M.11
-
66
-
-
0001684030
-
Shape of unperturbed linear polymers: Polypropylene
-
Theodorou, D.N.; Suter, U.W. Shape of unperturbed linear polymers: Polypropylene. Macromolecules 1985, 18, 1206-1214.
-
(1985)
Macromolecules
, vol.18
, pp. 1206-1214
-
-
Theodorou, D.N.1
Suter, U.W.2
-
67
-
-
80053512597
-
Open Babel: An open chemical toolbox
-
O'Boyle, N.; Banck, M.; James, C.; Morley, C.; Vandermeersch, T.; Hutchison, G. Open Babel: An open chemical toolbox. J. Cheminf. 2011, 3, doi:10.1186/1758-2946-3-33.
-
(2011)
J. Cheminf
, pp. 3
-
-
O'Boyle, N.1
Banck, M.2
James, C.3
Morley, C.4
Vandermeersch, T.5
Hutchison, G.6
-
68
-
-
79955574923
-
-
Version 1.3r1. The PyMOL Molecular Graphics System, Version 1.3, Schrödinger, LLC, Mannheim, Germany
-
The PyMOL Molecular Graphics System, Version 1.3r1. The PyMOL Molecular Graphics System, Version 1.3, Schrödinger, LLC, Mannheim, Germany.
-
The PyMOL Molecular Graphics System
-
-
-
69
-
-
0029878720
-
VMD - Visual Molecular Dynamics
-
Humphrey, W.; Dalke, A.; Schulten, K. VMD - Visual Molecular Dynamics. J. Mol. Graph. 1996, 14, 33-38.
-
(1996)
J. Mol. Graph
, vol.14
, pp. 33-38
-
-
Humphrey, W.1
Dalke, A.2
Schulten, K.3
-
70
-
-
77954911184
-
Molecular simulations reveal the mechanism and the determinants for ampicillin translocation through OmpF
-
Kumar, A.; Hajjar, E.; Ruggerone, P.; Ceccarelli, M. Molecular simulations reveal the mechanism and the determinants for ampicillin translocation through OmpF. J. Phys. Chem. B 2010, 114, 9608-9616.
-
(2010)
J. Phys. Chem. B
, vol.114
, pp. 9608-9616
-
-
Kumar, A.1
Hajjar, E.2
Ruggerone, P.3
Ceccarelli, M.4
-
71
-
-
77955564233
-
Toward screening for antibiotics with enhanced permeation properties through bacterial porins
-
Hajjar, E.; Bessonov, A.; Molitor, A.; Kumar, A.; Mahendran, K.R.;Winterhalter, M.; Pagès, J.M.; Ruggerone, P.; Ceccarelli, M. Toward screening for antibiotics with enhanced permeation properties through bacterial porins. Biochemistry 2010, 49, 6928-6935.
-
(2010)
Biochemistry
, vol.49
, pp. 6928-6935
-
-
Hajjar, E.1
Bessonov, A.2
Molitor, A.3
Kumar, A.4
Mahendran, K.R.5
Winterhalter, M.6
Pagès, J.M.7
Ruggerone, P.8
Ceccarelli, M.9
-
72
-
-
80055047308
-
Altered Antibiotic Transport in OmpC Mutants Isolated from a Series of Clinical Strains of Multi-Drug Resistant e coli
-
Lou, H.; Chen, M.; Black, S.S.; Bushell, S.R.; Ceccarelli, M.; Mach, T.; Beis, K.; Low, A.S.; Bamford, V.A.; Booth, I.R.; Bayley, H.; Naismith, J.H. Altered Antibiotic Transport in OmpC Mutants Isolated from a Series of Clinical Strains of Multi-Drug Resistant E. coli. PLoS ONE 2011, 6, e25825.
-
(2011)
PLoS ONE
, vol.6
, pp. e25825
-
-
Lou, H.1
Chen, M.2
Black, S.S.3
Bushell, S.R.4
Ceccarelli, M.5
Mach, T.6
Beis, K.7
Low, A.S.8
Bamford, V.A.9
Booth, I.R.10
Bayley, H.11
Naismith, J.H.12
-
73
-
-
84869433336
-
Recognition of Imipenem and Meropenem by the RND-Transporter MexB Studied by Computer Simulations
-
Collu, F.; Vargiu, A.V.; Dreier, J.; Cascella, M.; Ruggerone, P. Recognition of Imipenem and Meropenem by the RND-Transporter MexB Studied by Computer Simulations. J. Am. Chem. Soc. 2012, 134, 19146-19158.
-
(2012)
J. Am. Chem. Soc
, vol.134
, pp. 19146-19158
-
-
Collu, F.1
Vargiu, A.V.2
Dreier, J.3
Cascella, M.4
Ruggerone, P.5
-
74
-
-
84874431455
-
Multidrug binding properties of the AcrB efflux pump characterized by molecular dynamics simulations
-
Vargiu, A.V.; Nikaido, H. Multidrug binding properties of the AcrB efflux pump characterized by molecular dynamics simulations. Proc. Natl. Acad. Sci. USA 2012, 109, 20637-20642.
-
(2012)
Proc. Natl. Acad. Sci. USA
, vol.109
, pp. 20637-20642
-
-
Vargiu, A.V.1
Nikaido, H.2
-
75
-
-
84907267776
-
Molecular Mechanism of MBX2319 Inhibition of Escherichia coli AcrB Multidrug Efflux Pump and Comparison with Other Inhibitors
-
Vargiu, A.V.; Ruggerone, P.; Opperman, T.J.; Nguyen, S.T.; Nikaido, H. Molecular Mechanism of MBX2319 Inhibition of Escherichia coli AcrB Multidrug Efflux Pump and Comparison with Other Inhibitors. Antimicrob. Agents Chemother. 2014, 58, 6224-6234.
-
(2014)
Antimicrob. Agents Chemother
, vol.58
, pp. 6224-6234
-
-
Vargiu, A.V.1
Ruggerone, P.2
Opperman, T.J.3
Nguyen, S.T.4
Nikaido, H.5
-
77
-
-
84901363730
-
RDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids
-
Ruiz-Carmona, S.; Alvarez-Garcia, D.; Foloppe, N.; Garmendia-Doval, A.B.; Juhos, S.; Schmidtke, P.; Barril, X.; Hubbard, R.E.; Morley, S.D. rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids. PLoS Comput. Biol. 2014, 10, e1003571.
-
(2014)
PLoS Comput. Biol
, vol.10
, pp. e1003571
-
-
Ruiz-Carmona, S.1
Alvarez-Garcia, D.2
Foloppe, N.3
Garmendia-Doval, A.B.4
Juhos, S.5
Schmidtke, P.6
Barril, X.7
Hubbard, R.E.8
Morley, S.D.9
-
78
-
-
76149120388
-
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
-
Trott, O.; Olson, A.J. AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J. Comput. Chem. 2010, 31, 455-461.
-
(2010)
J. Comput. Chem
, vol.31
, pp. 455-461
-
-
Trott, O.1
Olson, A.J.2
-
79
-
-
0038583687
-
Protein-protein docking with a reduced protein model accounting for side-chain flexibility
-
Zacharias, M. Protein-protein docking with a reduced protein model accounting for side-chain flexibility. Protein Sci. 2003, 12, 1271-1282.
-
(2003)
Protein Sci
, vol.12
, pp. 1271-1282
-
-
Zacharias, M.1
-
80
-
-
77951297973
-
Accounting for conformational changes during protein-protein docking
-
Zacharias, M. Accounting for conformational changes during protein-protein docking. Curr. Opin. Struct. Biol. 2010, 20, 180-186.
-
(2010)
Curr. Opin. Struct. Biol
, vol.20
, pp. 180-186
-
-
Zacharias, M.1
-
81
-
-
33645961330
-
Flexible protein-protein docking
-
Bonvin, A. Flexible protein-protein docking. Curr. Opin. Struct. Biol. 2006, 16, 194-200.
-
(2006)
Curr. Opin. Struct. Biol
, vol.16
, pp. 194-200
-
-
Bonvin, A.1
-
82
-
-
41949132916
-
Flexible ligand docking to multiple receptor conformations: A practical alternative
-
Totrov, M.; Abagyan, R. Flexible ligand docking to multiple receptor conformations: A practical alternative. Curr. Opin. Struct. Biol. 2008, 18, 178-184.
-
(2008)
Curr. Opin. Struct. Biol
, vol.18
, pp. 178-184
-
-
Totrov, M.1
Abagyan, R.2
-
83
-
-
52249122794
-
Principles of flexible protein-protein docking
-
Andrusier, N.; Mashiach, E.; Nussinov, R.; Wolfson, H.J. Principles of flexible protein-protein docking. Proteins 2008, 73, 271-289.
-
(2008)
Proteins
, vol.73
, pp. 271-289
-
-
Andrusier, N.1
Mashiach, E.2
Nussinov, R.3
Wolfson, H.J.4
-
84
-
-
63149162777
-
Managing protein flexibility in docking and its applications
-
B-Rao, C.; Subramanian, J.; Sharma, S.D. Managing protein flexibility in docking and its applications. Drug Discov. Today 2009, 14, 394-400.
-
(2009)
Drug Discov. Today
, vol.14
, pp. 394-400
-
-
B-Rao, C.1
Subramanian, J.2
Sharma, S.D.3
-
85
-
-
79952181220
-
Challenges and advances in computational docking: 2009 in review
-
Yuriev, E.; Agostino, M.; Ramsland, P.A. Challenges and advances in computational docking: 2009 in review. J. Mol. Recognit. 2011, 24, 149-164.
-
(2011)
J. Mol. Recognit
, vol.24
, pp. 149-164
-
-
Yuriev, E.1
Agostino, M.2
Ramsland, P.A.3
-
86
-
-
84871381838
-
Accounting for Receptor Flexibility and Enhanced Sampling Methods in Computer-Aided Drug Design
-
Sinko, W.; Lindert, S.; McCammon, J.A. Accounting for Receptor Flexibility and Enhanced Sampling Methods in Computer-Aided Drug Design. Chem. Biol. Drug Des. 2013, 81, 41-49.
-
(2013)
Chem. Biol. Drug des
, vol.81
, pp. 41-49
-
-
Sinko, W.1
Lindert, S.2
McCammon, J.A.3
-
87
-
-
34447275949
-
Ligand docking and structure-based virtual screening in drug discovery
-
Cavasotto, C.N.; Orry, A.J.W. Ligand docking and structure-based virtual screening in drug discovery. Curr. Opin. Struct. Biol. 2007, 7, 1006-1014.
-
(2007)
Curr. Opin. Struct. Biol
, vol.7
, pp. 1006-1014
-
-
Cavasotto, C.N.1
Orry, A.J.W.2
-
88
-
-
50249114683
-
An improved relaxed complex scheme for receptor flexibility in computer-aided drug design
-
Amaro, R.E.; Baron, R.; McCammon, J.A. An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. J. Comput. -Aided Mol. Des. 2008, 22, 693-705.
-
(2008)
J. Comput. -Aided Mol. des
, vol.22
, pp. 693-705
-
-
Amaro, R.E.1
Baron, R.2
McCammon, J.A.3
-
89
-
-
79960204167
-
Effect of the F610A Mutation on Substrate Extrusion in the AcrB Transporter: Explanation and Rationale by Molecular Dynamics Simulations
-
Vargiu, A.V.; Collu, F.; Schulz, R.; Pos, K.M.; Zacharias, M.; Kleinekathöfer, U.; Ruggerone, P. Effect of the F610A Mutation on Substrate Extrusion in the AcrB Transporter: Explanation and Rationale by Molecular Dynamics Simulations. J. Am. Chem. Soc. 2011, 133, 10704-10707.
-
(2011)
J. Am. Chem. Soc
, vol.133
, pp. 10704-10707
-
-
Vargiu, A.V.1
Collu, F.2
Schulz, R.3
Pos, K.M.4
Zacharias, M.5
Kleinekathöfer, U.6
Ruggerone, P.7
-
90
-
-
84909641215
-
Molecular Mechanism of Viral Resistance to a Potent Non-nucleoside Inhibitor Unveiled by Molecular Simulations
-
Asthana, S.; Shukla, S.; Ruggerone, P.; Vargiu, A.V. Molecular Mechanism of Viral Resistance to a Potent Non-nucleoside Inhibitor Unveiled by Molecular Simulations. Biochemistry 2014, 53, 6941-6953.
-
(2014)
Biochemistry
, vol.53
, pp. 6941-6953
-
-
Asthana, S.1
Shukla, S.2
Ruggerone, P.3
Vargiu, A.V.4
-
91
-
-
84905399186
-
Switch-Loop Flexibility Affects Transport of Large Drugs by the Promiscuous AcrB Multidrug Efflux Transporter
-
Cha, H.J.; Müller, R.T.; Pos, K.M. Switch-Loop Flexibility Affects Transport of Large Drugs by the Promiscuous AcrB Multidrug Efflux Transporter. Antimicrob. Agents Chemother. 2014, 58, 4767-4772.
-
(2014)
Antimicrob. Agents Chemother
, vol.58
, pp. 4767-4772
-
-
Cha, H.J.1
Müller, R.T.2
Pos, K.M.3
-
92
-
-
84888251078
-
RND efflux pumps: Structural information translated into function and inhibition mechanisms
-
Ruggerone, P.; Murakami, S.; Pos, K.M.; Vargiu, A.V. RND efflux pumps: Structural information translated into function and inhibition mechanisms. Curr. Top. Med. Chem. 2013, 13, 3079-3100.
-
(2013)
Curr. Top. Med. Chem
, vol.13
, pp. 3079-3100
-
-
Ruggerone, P.1
Murakami, S.2
Pos, K.M.3
Vargiu, A.V.4
-
93
-
-
68949110351
-
Efflux-Mediated Drug Resistance in Bacteria An Update
-
Li, X.Z.; Nikaido, H. Efflux-Mediated Drug Resistance in Bacteria An Update. Drugs 2009, 69, 1555-1623.
-
(2009)
Drugs
, vol.69
, pp. 1555-1623
-
-
Li, X.Z.1
Nikaido, H.2
-
94
-
-
84911484514
-
Multidrug efflux pumps in Gram-negative bacteria and their role in antibiotic resistance
-
Blair, J.; Richmond, G.; Piddock, L. Multidrug efflux pumps in Gram-negative bacteria and their role in antibiotic resistance. Future Microbiol. 2014, 9, 1165-1177.
-
(2014)
Future Microbiol
, vol.9
, pp. 1165-1177
-
-
Blair, J.1
Richmond, G.2
Piddock, L.3
-
95
-
-
33845886664
-
Waltzing transporters and 'the dance macabre' between humans and bacteria
-
Lomovskaya, O.; Zgurskaya, H.I.; Totrov, M.;Watkins, W.J. Waltzing transporters and 'the dance macabre' between humans and bacteria. Nat. Rev. Drug Discov. 2007, 6, 56-65.
-
(2007)
Nat. Rev. Drug Discov
, vol.6
, pp. 56-65
-
-
Lomovskaya, O.1
Zgurskaya, H.I.2
Totrov, M.3
Watkins, W.J.4
-
96
-
-
24044514016
-
Efflux-mediated antimicrobial resistance
-
Poole, K. Efflux-mediated antimicrobial resistance. J. Antimicrob. Chemother. 2005, 56, 20-51.
-
(2005)
J. Antimicrob. Chemother
, vol.56
, pp. 20-51
-
-
Poole, K.1
-
97
-
-
84856729230
-
Broad-specificity efflux pumps and their role in multidrug resistance of Gram-negative bacteria
-
Nikaido, H.; Pagés, J.M. Broad-specificity efflux pumps and their role in multidrug resistance of Gram-negative bacteria. FEMS Microbiol. Rev. 2012, 36, 340-363.
-
(2012)
FEMS Microbiol. Rev
, vol.36
, pp. 340-363
-
-
Nikaido, H.1
Pagés, J.M.2
-
98
-
-
84941235456
-
-
(accessed on 29 January 2014).
-
Chemicalize. ChemAxon 2014. Available online: http://www.chemicalize.org (accessed on 29 January 2014).
-
ChemAxon 2014
-
-
-
99
-
-
3142716857
-
Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules
-
Hamelberg, D.; Mongan, J.; McCammon, J.A. Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules. J. Chem. Phys. 2004, 120, 11919-11929.
-
(2004)
J. Chem. Phys
, vol.120
, pp. 11919-11929
-
-
Hamelberg, D.1
Mongan, J.2
McCammon, J.A.3
-
100
-
-
0001616080
-
Replica-exchange molecular dynamics method for protein folding
-
Sugita, Y.; Okamoto, Y. Replica-exchange molecular dynamics method for protein folding. Chem. Phys. Lett. 1999, 314, 141-151.
-
(1999)
Chem. Phys. Lett
, vol.314
, pp. 141-151
-
-
Sugita, Y.1
Okamoto, Y.2
-
101
-
-
0037157317
-
On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction
-
Fukunishi, H.;Watanabe, O.; Takada, S. On the Hamiltonian replica exchange method for efficient sampling of biomolecular systems: Application to protein structure prediction. J. Chem. Phys. 2002, 116, 9058-9067.
-
(2002)
J. Chem. Phys
, vol.116
, pp. 9058-9067
-
-
Fukunishi, H.1
Watanabe, O.2
Takada, S.3
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