-
2
-
-
0035039453
-
The birth of computational structural biology
-
Levitt M (2001) The birth of computational structural biology. Nat Struct Biol 8:392-393
-
(2001)
Nat Struct Biol
, vol.8
, pp. 392-393
-
-
Levitt, M.1
-
3
-
-
84856899929
-
Consistent force field for calculations of conformations vibrational spectra and enthalpies of cycloalkane and n-Alkane molecules
-
Lifson S, Warshel A (1968) Consistent force field for calculations of conformations vibrational spectra and enthalpies of cycloalkane and n-Alkane molecules. J Chem Phys 49:5116
-
(1968)
J Chem Phys
, vol.49
, pp. 5116
-
-
Lifson, S.1
Warshel, A.2
-
5
-
-
0016610491
-
Computer simulation of protein folding
-
Levitt M, Warshel A (1975) Computer simulation of protein folding. Nature 253:694-698
-
(1975)
Nature
, vol.253
, pp. 694-698
-
-
Levitt, M.1
Warshel, A.2
-
6
-
-
0017100947
-
Theoretical studies of enzymic reactions: Dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme
-
Warshel A, Levitt M (1976) Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J Mol Biol 103:227-249
-
(1976)
J Mol Biol
, vol.103
, pp. 227-249
-
-
Warshel, A.1
Levitt, M.2
-
8
-
-
0242443693
-
Force fields for protein simulations
-
Ponder JW, Case DA (2003) Force fields for protein simulations. Adv Protein Chem 66:27-85
-
(2003)
Adv Protein Chem
, vol.66
, pp. 27-85
-
-
Ponder, J.W.1
Case, D.A.2
-
9
-
-
0021757436
-
A new force field for molecular mechanical simulation of nucleic acids and proteins
-
Weiner SJ, Kollman PA, Case DA, Singh UC, Ghio C, Alagona G, Profeta S,Weiner P (1984) A new force field for molecular mechanical simulation of nucleic acids and proteins. J Am Chem Soc 106:765-784
-
(1984)
J Am Chem Soc
, vol.106
, pp. 765-784
-
-
Weiner, S.J.1
Kollman, P.A.2
Case, D.A.3
Singh, U.C.4
Ghio, C.5
Alagona, G.6
Profeta, S.7
Weiner, P.8
-
10
-
-
84986492477
-
Atomic charges derived from semiempirical methods
-
Besler BH, Merz KM, Kollman PA (1990) Atomic charges derived from semiempirical methods. J Comput Chem 11:431-439
-
(1990)
J Comput Chem
, vol.11
, pp. 431-439
-
-
Besler, B.H.1
Merz, K.M.2
Kollman, P.A.3
-
11
-
-
0029011701
-
A 2nd generation force-field for the simulation of proteins, nucleic-Acids, and organic-molecules
-
Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA (1995) A 2nd generation force-field for the simulation of proteins, nucleic-Acids, and organic-molecules. J Am Chem Soc 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.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
12
-
-
33748538349
-
Automatic atom type and bond type perception in molecular mechanical calculations
-
Wang JM, Wang W, Kollman PA, Case DA (2006) Automatic atom type and bond type perception in molecular mechanical calculations. J Mol Graph Model 25:247-260
-
(2006)
J Mol Graph Model
, vol.25
, pp. 247-260
-
-
Wang, J.M.1
Wang, W.2
Kollman, P.A.3
Case, D.A.4
-
13
-
-
84986512474
-
Charmm: A program for macromolecular energy, minimisation, and dynamics calculations
-
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) CHARMM: a program for macromolecular energy, minimisation, and dynamics calculations. J Comput Chem 4:187-217
-
(1983)
J Comput Chem
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
14
-
-
4444351490
-
Empirical force fields for biological macromolecules: Overview and issues
-
Mackerell AD Jr. (2004) Empirical force fields for biological macromolecules: overview and issues. J Comput Chem 25:1584-1604
-
(2004)
J Comput Chem
, vol.25
, pp. 1584-1604
-
-
Mackerell Jr., A.D.1
-
15
-
-
0029912748
-
Development and testing of the opls all-Atom force field on conformational energetics and properties of organic liquids
-
Jorgensen WL, Maxwell DS, TiradoRives J (1996) Development and testing of the OPLS all-Atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 118:11225-11236
-
(1996)
J Am Chem Soc
, vol.118
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
TiradoRives, J.3
-
16
-
-
0021515659
-
Optimized intermolecular potential functions for liquid hydrocarbons
-
Jorgensen WL, Madura JD, Swenson CJ (1984) Optimized intermolecular potential functions for liquid hydrocarbons. J Am Chem Soc 106:6638-6646
-
(1984)
J Am Chem Soc
, vol.106
, pp. 6638-6646
-
-
Jorgensen, W.L.1
Madura, J.D.2
Swenson, C.J.3
-
17
-
-
33645858780
-
Transferable intermolecular potential functions for water, alcohols and ethers. Application to liquid water
-
Jorgensen WL (1981) Transferable intermolecular potential functions for water, alcohols and ethers. Application to liquid water. J Am Chem Soc 103:335-340
-
(1981)
J Am Chem Soc
, vol.103
, pp. 335-340
-
-
Jorgensen, W.L.1
-
18
-
-
0008819754
-
The gromos biomolecular simulation program package
-
Scott WRP, Hunenberger PH, Tironi IG, Mark AE, Billeter SR, Fennen J, Torda AE, Huber T, Kruger P, van Gunsteren WF (1999) The GROMOS biomolecular simulation program package. J Phys Chem A 103:3596-3607
-
(1999)
J Phys Chem A
, vol.103
, pp. 3596-3607
-
-
Scott, W.R.P.1
Hunenberger, P.H.2
Tironi, I.G.3
Mark, A.E.4
Billeter, S.R.5
Fennen, J.6
Torda, A.E.7
Huber, T.8
Kruger, P.9
Van Gunsteren, W.F.10
-
19
-
-
4444282928
-
A biomolecular force field based on the free enthalpy of hydration and solvation: The gromos force-field parameter sets 53a5 and 53a6
-
Oostenbrink C, Villa A, Mark AE, Van Gunsteren WF (2004) A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6. J Comput Chem 25:1656-1676
-
(2004)
J Comput Chem
, vol.25
, pp. 1656-1676
-
-
Oostenbrink, C.1
Villa, A.2
Mark, A.E.3
Van Gunsteren, W.F.4
-
20
-
-
0029633167
-
Potential-energy function and parameters for simulations of the moleculardynamics of proteins and nucleic-Acids in solution
-
Levitt M, Hirshberg M, Sharon R, Daggett V (1995) Potential-energy function and parameters for simulations of the moleculardynamics of proteins and nucleic-Acids in solution. Comput Phys Commun 91:215-231
-
(1995)
Comput Phys Commun
, vol.91
, pp. 215-231
-
-
Levitt, M.1
Hirshberg, M.2
Sharon, R.3
Daggett, V.4
-
21
-
-
0036140611
-
Determining the shear viscosity of model liquids from molecular dynamics simulations
-
Hess B (2002) Determining the shear viscosity of model liquids from molecular dynamics simulations. J Chem Phys 116:209-217
-
(2002)
J Chem Phys
, vol.116
, pp. 209-217
-
-
Hess, B.1
-
22
-
-
26744440015
-
Structural and energetic effects of truncating long ranged interactions in ionic and polar fluids
-
Brooks CL, Pettitt BM, Karplus M (1985) Structural and energetic effects of truncating long ranged interactions in ionic and polar fluids. J Chem Phys 83:5897-5908
-
(1985)
J Chem Phys
, vol.83
, pp. 5897-5908
-
-
Brooks, C.L.1
Pettitt, B.M.2
Karplus, M.3
-
23
-
-
84859621720
-
-
version 4.5.4
-
Apol E, Apostolov R, Berendsen HJC, Van Buuren A, Bjelkmar P, Van Drunen R, Feenstra A, Groenhof G,Kasson P, Larsson P,Meulenhoff P, Murtola T, Pall S, Pronk S, Schulz R, ShirtsMR, SijbersA,TielemanDP, Hess B, van der SpoelD, Lindahl E (2010) GROMACS user manual version 4.5.4, http://www.gromacs.org
-
(2010)
GROMACS user manual
-
-
Apol, E.1
Apostolov, R.2
Berendsen, H.J.C.3
Van Buuren, A.4
Bjelkmar, P.5
Van Drunen, R.6
Feenstra, A.7
Groenhof, G.8
Kasson, P.9
Larsson, P.10
Meulenhoff, P.11
Murtola, T.12
Pall, S.13
Pronk, S.14
Schulz, R.15
Shirts, M.R.16
Sijbers, A.17
Tieleman, D.P.18
Hess, B.19
Van Der Spoel, D.20
Lindahl, E.21
more..
-
24
-
-
4544369164
-
A generalized reaction field method for molecular-dynamics simulations
-
Tironi IG, Sperb R, Smith PE, Vangunsteren WF (1995) A generalized reaction field method for molecular-dynamics simulations. J Chem Phys 102:5451-5459
-
(1995)
J Chem Phys
, vol.102
, pp. 5451-5459
-
-
Tironi, I.G.1
Sperb, R.2
Smith, P.E.3
Vangunsteren, W.F.4
-
25
-
-
73949107784
-
Scaling of multimillion-Atom biological molecular dynamics simulation on a petascale supercomputer
-
Schulz R, Lindner B, Petridis L, Smith JC (2009) Scaling of multimillion-Atom biological molecular dynamics simulation on a petascale supercomputer. J Chem Theory Comput 5:2798-2808
-
(2009)
J Chem Theory Comput
, vol.5
, pp. 2798-2808
-
-
Schulz, R.1
Lindner, B.2
Petridis, L.3
Smith, J.C.4
-
26
-
-
33645310406
-
Assessing the influence of electrostatic schemes on molecular dynamics simulations of secondary structure forming peptides
-
Monticelli L, Simoes C, Belvisi L, Colombo G (2006) Assessing the influence of electrostatic schemes on molecular dynamics simulations of secondary structure forming peptides. J Phys Condens Matter 18:S329-S345
-
(2006)
J Phys Condens Matter
, vol.18
-
-
Monticelli, L.1
Simoes, C.2
Belvisi, L.3
Colombo, G.4
-
27
-
-
17144471008
-
Comparison of different schemes to treat long-range electrostatic interactions in molecular dynamics simulations of a protein crystal
-
Walser R, Hunenberger PH, van Gunsteren WF (2001) Comparison of different schemes to treat long-range electrostatic interactions in molecular dynamics simulations of a protein crystal. Proteins 43:509-519
-
(2001)
Proteins
, vol.43
, pp. 509-519
-
-
Walser, R.1
Hunenberger, P.H.2
Van Gunsteren, W.F.3
-
28
-
-
4143138518
-
Methodogical issues in lipid bilayer simulations
-
Anezo C, Vries AHD, Holtje H-D, Tieleman DP, Marrink S-J (2003) Methodogical issues in lipid bilayer simulations. J Phys Chem B 107:9424-9433
-
(2003)
J Phys Chem B
, vol.107
, pp. 9424-9433
-
-
Anezo, C.1
Vries, A.H.D.2
Holtje, H.-D.3
Tieleman, D.P.4
Marrink, S.-J.5
-
29
-
-
45949090963
-
Explicitsolvent molecular dynamics simulations of a dna tetradecanucleotide duplex: Lattice-sum versus reaction-field electrostatics
-
Krautler V, Hunenberger PH (2008) Explicitsolvent molecular dynamics simulations of a DNA tetradecanucleotide duplex: lattice-sum versus reaction-field electrostatics. Mol Simulat 34:491-499
-
(2008)
Mol Simulat
, vol.34
, pp. 491-499
-
-
Krautler, V.1
Hunenberger, P.H.2
-
30
-
-
0029170114
-
Molecular-dynamics simulations on solvated biomolecular systems -The particle mesh ewald method leads to stable trajectories of dna, rna, and proteins
-
Cheatham TE, Miller JL, Fox T, Darden TA, Kollman PA (1995) Molecular-dynamics simulations on solvated biomolecular systems -the particle mesh Ewald method leads to stable trajectories of DNA, RNA, and proteins. J Am Chem Soc 117:4193-4194
-
(1995)
J Am Chem Soc
, vol.117
, pp. 4193-4194
-
-
Cheatham, T.E.1
Miller, J.L.2
Fox, T.3
Darden, T.A.4
Kollman, P.A.5
-
31
-
-
33846823909
-
Particle mesh ewald: An n-log(n) method for ewald sums in large systems
-
Darden T, York D, Pedersen L (1993) Particle mesh Ewald: an N-log(N) method for Ewald sums in large systems. J Chem Phys 98:10089-10092
-
(1993)
J Chem Phys
, vol.98
, pp. 10089-10092
-
-
Darden, T.1
York, D.2
Pedersen, L.3
-
32
-
-
33645961739
-
A smooth particle mesh ewald potential
-
Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG (1995) A smooth particle mesh Ewald potential. J Chem Phys 103:8577-8592
-
(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
-
34
-
-
33745155379
-
Computation of methodology-independent ionic solvation free energies from molecular simulations. I. The electrostatic potential in molecular liquids
-
Kastenholz MA, Hunenberger PH (2006) Computation of methodology- independent ionic solvation free energies from molecular simulations. I. The electrostatic potential in molecular liquids. J Chem Phys 124 224501
-
(2006)
J Chem Phys
, vol.124
, pp. 224501
-
-
Kastenholz, M.A.1
Hunenberger, P.H.2
-
35
-
-
1642525904
-
Influence of artificial periodicity and ionic strength in molecular dynamics simulations of charged biomolecules employing lattice-sum methods
-
Kastenholz MA, Hunenberger PH (2004) Influence of artificial periodicity and ionic strength in molecular dynamics simulations of charged biomolecules employing lattice-sum methods. J Phys Chem B 108:774-788
-
(2004)
J Phys Chem B
, vol.108
, pp. 774-788
-
-
Kastenholz, M.A.1
Hunenberger, P.H.2
-
36
-
-
0347089020
-
Energetics of ion conduction through the gramicidin channel
-
Allen TW, Andersen OS, Roux B (2004) Energetics of ion conduction through the gramicidin channel. Proc Natl Acad Sci USA 101:117-122
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 117-122
-
-
Allen, T.W.1
Andersen, O.S.2
Roux, B.3
-
37
-
-
0000242569
-
A comparison of algorithms for long-range interactions
-
Esselink K (1995) A comparison of algorithms for long-range interactions. Comput Phys Commun 87:375-395
-
(1995)
Comput Phys Commun
, vol.87
, pp. 375-395
-
-
Esselink, K.1
-
38
-
-
36649007647
-
Accurate and efficient corrections for missing dispersion interactions in molecular simulations
-
Shirts MR, Mobley DL, Chodera JD, Pande VS (2007) Accurate and efficient corrections for missing dispersion interactions in molecular Simulations. J Phys Chem B 111:13052-13063
-
(2007)
J Phys Chem B
, vol.111
, pp. 13052-13063
-
-
Shirts, M.R.1
Mobley, D.L.2
Chodera, J.D.3
Pande, V.S.4
-
40
-
-
66349128874
-
Comparison of the extended isotropic periodic sum and particle mesh ewald methods for simulations of lipid bilayers and monolayers
-
Venable RM, Chen LE, Pastor RW (2009) Comparison of the extended isotropic periodic sum and particle mesh ewald methods for simulations of lipid bilayers and monolayers. J Phys Chem B 113:5855-5862
-
(2009)
J Phys Chem B
, vol.113
, pp. 5855-5862
-
-
Venable, R.M.1
Chen, L.E.2
Pastor, R.W.3
-
41
-
-
35248830820
-
Application of ewald summations to long-range dispersion forces
-
Veld PJ, Ismail AE, Grest GS (2007) Application of Ewald summations to long-range dispersion forces. J Chem Phys 127(14):144711
-
(2007)
J Chem Phys
, vol.127
, Issue.14
, pp. 144711
-
-
Veld, P.J.1
Ismail, A.E.2
Grest, G.S.3
-
42
-
-
33745630723
-
Membrane protein simulations with a united-Atom lipid and all-Atom protein model: Lipid-protein interactions, side chain transfer free energies and model proteins
-
Tieleman DP, MacCallum JL, Ash WL, Kandt C, Xu ZT, Monticelli L (2006) Membrane protein simulations with a united-Atom lipid and all-Atom protein model: lipid-protein interactions, side chain transfer free energies and model proteins. J Phys Condens Matter 18: S1221-S1234
-
(2006)
J Phys Condens Matter
, vol.18
-
-
Tieleman, D.P.1
MacCallum, J.L.2
Ash, W.L.3
Kandt, C.4
Xu, Z.T.5
Monticelli, L.6
-
43
-
-
0001349174
-
Validation of molecular dynamics simulation
-
van Gunsteren WF, Mark AE (1998) Validation of molecular dynamics simulation. J Chem Phys 108:6109-6116
-
(1998)
J Chem Phys
, vol.108
, pp. 6109-6116
-
-
Van Gunsteren, W.F.1
Mark, A.E.2
-
44
-
-
33746271105
-
Biomolecular modeling: Goals, problems, perspectives
-
vanGunsterenWF,BakowiesD,Baron R,Chandrasekhar I,ChristenM,Daura X, Gee P,Geerke DP, Glattli A, Hunenberger PH, Kastenholz MA, Ostenbrink C, Schenk M, Trzesniak D, van der Vegt NFA, Yu HB (2006) Biomolecular modeling: goals, problems, perspectives. Angew Chem Int Ed 45:4064-4092
-
(2006)
Angew Chem Int Ed
, vol.45
, pp. 4064-4092
-
-
VanGunsteren, 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
Glattli, A.9
Hunenberger, P.H.10
Kastenholz, M.A.11
Ostenbrink, C.12
Schenk, M.13
Trzesniak, D.14
Van Der Vegt, N.F.A.15
Yu, H.B.16
|