-
1
-
-
0031910020
-
Locally accessible conformations of proteins: Multiple molecular dynamics simulations of crambin
-
Caves LSD, Evanseck JD, Karplus M. Locally accessible conformations of proteins: Multiple molecular dynamics simulations of crambin. Protein Science 1998;7:649-666.
-
(1998)
Protein Science
, vol.7
, pp. 649-666
-
-
Caves, L.S.D.1
Evanseck, J.D.2
Karplus, M.3
-
2
-
-
0001060458
-
A Monte Carlo method for obtaining the interionic potential of mean force in ionic solution
-
Patey GN, Valeau JP. A Monte Carlo method for obtaining the interionic potential of mean force in ionic solution. J Chem Phys 1975;63:2334-2339.
-
(1975)
J Chem Phys
, vol.63
, pp. 2334-2339
-
-
Patey, G.N.1
Valeau, J.P.2
-
3
-
-
33847416519
-
Manipulating proteins by steered molecular dynamics
-
Schulten K. Manipulating proteins by steered molecular dynamics. J Mol Graph Mod 1998;16:289.
-
(1998)
J Mol Graph Mod
, vol.16
, pp. 289
-
-
Schulten, K.1
-
4
-
-
0029633155
-
The calculation of the potential of mean force using computer simulation
-
Roux B. The calculation of the potential of mean force using computer simulation. Comp Phys Comm 1995;91:275-282.
-
(1995)
Comp Phys Comm
, vol.91
, pp. 275-282
-
-
Roux, B.1
-
5
-
-
0042885340
-
Free energy calculation from steered molecular dynamics simulations using jarzynski's equality
-
Park S, Khalili-Araghi F, Tajkhorshid E, Schulten K. Free energy calculation from steered molecular dynamics simulations using jarzynski's equality. J Chem Phys 2003;119:3559-3566.
-
(2003)
J Chem Phys
, vol.119
, pp. 3559-3566
-
-
Park, S.1
Khalili-Araghi, F.2
Tajkhorshid, E.3
Schulten, K.4
-
6
-
-
4143087050
-
Calculating potentials of mean force from steered molecular dynamics simulations
-
Park S, Schulten K. Calculating potentials of mean force from steered molecular dynamics simulations. J Chem Phys 2004;120:5946-5961.
-
(2004)
J Chem Phys
, vol.120
, pp. 5946-5961
-
-
Park, S.1
Schulten, K.2
-
8
-
-
1542366657
-
Role of solvent in deteriming conformational preferences of alanine dipeptide in water
-
Drozdov AN, Grossfield A, Pappu RV. Role of solvent in deteriming conformational preferences of alanine dipeptide in water. J Am Chem Soc 2004;126:2574-2581.
-
(2004)
J Am Chem Soc
, vol.126
, pp. 2574-2581
-
-
Drozdov, A.N.1
Grossfield, A.2
Pappu, R.V.3
-
9
-
-
0036930078
-
Molecular dynamics investigation of primary photoinduced events in the activation of rhodopsin
-
Saam J, Tajkhorshid E, Hayashi S, Schulten K. Molecular dynamics investigation of primary photoinduced events in the activation of rhodopsin. Biophys J 2002;83:3097-3112.
-
(2002)
Biophys J
, vol.83
, pp. 3097-3112
-
-
Saam, J.1
Tajkhorshid, E.2
Hayashi, S.3
Schulten, K.4
-
10
-
-
0036467163
-
Structure of met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics
-
Sanbonmatsu KY, Garcia AE. Structure of met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics. Proteins: Struc Func Gen 2002;46:225-234.
-
(2002)
Proteins: Struc Func Gen
, vol.46
, pp. 225-234
-
-
Sanbonmatsu, K.Y.1
Garcia, A.E.2
-
11
-
-
0344824394
-
Trp-cage: Folding free energy landscape in explicit water
-
Zhou R. Trp-cage: folding free energy landscape in explicit water. Proc Nat Acad Sci USA 2003;100:13280-13285.
-
(2003)
Proc Nat Acad Sci USA
, vol.100
, pp. 13280-13285
-
-
Zhou, R.1
-
12
-
-
0037109535
-
On the acceptance probability of replica-exchange Monte Carlo trials
-
Kofke DA. On the acceptance probability of replica-exchange Monte Carlo trials. J Chem Phys 2002;117:6911-6914.
-
(2002)
J Chem Phys
, vol.117
, pp. 6911-6914
-
-
Kofke, D.A.1
-
13
-
-
18544381108
-
Modified replica exchange simulation methods for local structure refinement
-
Cheng X, Cui G, Hornak V, Simmerling C. Modified replica exchange simulation methods for local structure refinement. J Phys Chem B 2005;109:8220-8230.
-
(2005)
J Phys Chem B
, vol.109
, pp. 8220-8230
-
-
Cheng, X.1
Cui, G.2
Hornak, V.3
Simmerling, C.4
-
14
-
-
25444481354
-
Replica exchange with solute tempering: A method for sampling biological systems in explicit water
-
Liu P, Kim B, Friesner RA, Berne BJ. Replica exchange with solute tempering: a method for sampling biological systems in explicit water. Proc Nat Acad Sci USA 2005;102:13749-13754.
-
(2005)
Proc Nat Acad Sci USA
, vol.102
, pp. 13749-13754
-
-
Liu, P.1
Kim, B.2
Friesner, R.A.3
Berne, B.J.4
-
15
-
-
0001497502
-
On monte carlo and molecular dynamics methods inspired by Tsallis statistics: Methodology, optimization, and application to atomic clusters
-
Andricioaei I, Straub JE. On monte carlo and molecular dynamics methods inspired by Tsallis statistics: methodology, optimization, and application to atomic clusters. J Chem Phys 1997;107:9117-9124.
-
(1997)
J Chem Phys
, vol.107
, pp. 9117-9124
-
-
Andricioaei, I.1
Straub, J.E.2
-
16
-
-
1942455272
-
Generalize-ensemble algorithms: Enhanced sampling techniques for Monte Carlo .and molecular dynamics simulations
-
Okamoto Y. Generalize-ensemble algorithms: enhanced sampling techniques for Monte Carlo .and molecular dynamics simulations. J Mol Graph Model 2004;22:425-439.
-
(2004)
J Mol Graph Model
, vol.22
, pp. 425-439
-
-
Okamoto, Y.1
-
17
-
-
0031648813
-
Probability distributions for complex systems: Adaptive umbrella sampling of the potential energy
-
Bartels C, Karplus M. Probability distributions for complex systems: adaptive umbrella sampling of the potential energy. J Phys Chem B 1998;102:865-880.
-
(1998)
J Phys Chem B
, vol.102
, pp. 865-880
-
-
Bartels, C.1
Karplus, M.2
-
18
-
-
4344606960
-
Multidimensional adaptive umbrella sampling: Applications to main chain and side chain peptide conformations
-
Bartels C, Karplus M. Multidimensional adaptive umbrella sampling: applications to main chain and side chain peptide conformations. J Comput Chem 1997;18:1450-1462.
-
(1997)
J Comput Chem
, vol.18
, pp. 1450-1462
-
-
Bartels, C.1
Karplus, M.2
-
19
-
-
0344118922
-
Configurational temperature density of states simulations of proteins
-
Rathore N, Knotts IVTA, de Pablo JJ. Configurational temperature density of states simulations of proteins. Biophys J 2003;85:3963-3968.
-
(2003)
Biophys J
, vol.85
, pp. 3963-3968
-
-
Rathore, N.1
Knotts, I.V.T.A.2
de Pablo, J.J.3
-
20
-
-
17444413356
-
-
Mastny EA, de Pablo JJ. Direct calculations of solid-liquid equilibria density-of-states Monte Carlo simulations. J Chem Phys 2005;122:124109-1-124109- 6.
-
Mastny EA, de Pablo JJ. Direct calculations of solid-liquid equilibria density-of-states Monte Carlo simulations. J Chem Phys 2005;122:124109-1-124109- 6.
-
-
-
-
21
-
-
4344612164
-
Replica-exchange extensions of simulated tempering method
-
Mitsutake A, Okamoto Y. Replica-exchange extensions of simulated tempering method. J Chem Phys 2004;121:2491-2504.
-
(2004)
J Chem Phys
, vol.121
, pp. 2491-2504
-
-
Mitsutake, A.1
Okamoto, Y.2
-
22
-
-
34547853580
-
Order-parameter-based Monte Carlo simulations of crystallization
-
Chopra M, Muller M, de Pablo JJ. Order-parameter-based Monte Carlo simulations of crystallization. J Chem Phys 2006;124:134102-1-134102-8.
-
(2006)
J Chem Phys
, vol.124
-
-
Chopra, M.1
Muller, M.2
de Pablo, J.J.3
-
23
-
-
25444449847
-
Probing specific lipid-protein interaction by saturation transfer difference NMR spectroscopy
-
Soubias O, Gawrisch K. Probing specific lipid-protein interaction by saturation transfer difference NMR spectroscopy. J Am Chem Soc 2005;127:13110-13111.
-
(2005)
J Am Chem Soc
, vol.127
, pp. 13110-13111
-
-
Soubias, O.1
Gawrisch, K.2
-
24
-
-
0034958341
-
-
Allen F, Almasi G, Andreoni W, Beece D, Berne BJ, Bright A, Brunheroto J, Cascaval C, Castanos J, Coteus P, Crumley P, Curioni A, Denneau M, Donath W, Eleftheriou M, Fitch B, Fleisher B, Georgiou CJ, Germain R, Giampapa M, Gresh D, Gupta M, Haring R, Ho H, Hochschild P, Hummel S, Jonas T, Lieber D, Martyna G, Maturu K, Moreira J, Newns D, Newton M, Philhower R, Picunko T, Pitera J, Pitman M, Rand R, Royyuru A, Salapura V, Sanomiya A, Shah R, Sham Y, Singh S, Snir M, Suits F, Swetz R, Swope WC, Vishnumurthy N, Ward TJC, Warren H, Zhou R. Blue Gene: a vision for protein science using a petaflop supercomputer. IBM Syst J 2001;40:310.
-
Allen F, Almasi G, Andreoni W, Beece D, Berne BJ, Bright A, Brunheroto J, Cascaval C, Castanos J, Coteus P, Crumley P, Curioni A, Denneau M, Donath W, Eleftheriou M, Fitch B, Fleisher B, Georgiou CJ, Germain R, Giampapa M, Gresh D, Gupta M, Haring R, Ho H, Hochschild P, Hummel S, Jonas T, Lieber D, Martyna G, Maturu K, Moreira J, Newns D, Newton M, Philhower R, Picunko T, Pitera J, Pitman M, Rand R, Royyuru A, Salapura V, Sanomiya A, Shah R, Sham Y, Singh S, Snir M, Suits F, Swetz R, Swope WC, Vishnumurthy N, Ward TJC, Warren H, Zhou R. Blue Gene: a vision for protein science using a petaflop supercomputer. IBM Syst J 2001;40:310.
-
-
-
-
25
-
-
0142010565
-
Blue Matter, an application framework for molecular simulation on blue gene
-
Fitch BG, Germain RS, Mendell M, Pitera J, Pitman M, Rayshubskiy A, Sham Y, Suits F, Swope WC, Ward TJC, Zhestkov Y, Zhou R. Blue Matter, an application framework for molecular simulation on blue gene. J Para Distrib Comp 2003;63:759-773.
-
(2003)
J Para Distrib Comp
, vol.63
, pp. 759-773
-
-
Fitch, B.G.1
Germain, R.S.2
Mendell, M.3
Pitera, J.4
Pitman, M.5
Rayshubskiy, A.6
Sham, Y.7
Suits, F.8
Swope, W.C.9
Ward, T.J.C.10
Zhestkov, Y.11
Zhou, R.12
-
26
-
-
33645519597
-
A role for direct interactions in the modulation of rhodopsin by omega-3 polyunsaturated lipids
-
Grossfield A, Feller SE, Pitman MC. A role for direct interactions in the modulation of rhodopsin by omega-3 polyunsaturated lipids. Proc Nat Acad Sci USA 2006;103:4888-4893.
-
(2006)
Proc Nat Acad Sci USA
, vol.103
, pp. 4888-4893
-
-
Grossfield, A.1
Feller, S.E.2
Pitman, M.C.3
-
27
-
-
33744803716
-
Contribution of omega-3 fatty acids to the thermodynamics of membrane protein solvation
-
Grossfield A, Feller SE, Pitman MC. Contribution of omega-3 fatty acids to the thermodynamics of membrane protein solvation. J Phys Chem B 2006;110:8907-8909.
-
(2006)
J Phys Chem B
, vol.110
, pp. 8907-8909
-
-
Grossfield, A.1
Feller, S.E.2
Pitman, M.C.3
-
28
-
-
0041784950
-
All-atom empirical potential for molecular modeling dynamics studies of proteins
-
MacKerell AD Jr, Bashford D, Bellott M, Dunbrack JrR, Evanseck J, Field M, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau F, Mattos C, Michnick S, Ngo T, Nguyen D, Prodhom B, Reiher W III, Roux B, Schlenkrich M, Smith J, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M. All-atom empirical potential for molecular modeling dynamics studies of proteins. J Phys Chem B 1998;102:3586-3616.
-
(1998)
J Phys Chem B
, vol.102
, pp. 3586-3616
-
-
MacKerell Jr, A.D.1
Bashford, D.2
Bellott, M.3
JrR, D.4
Evanseck, J.5
Field, M.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-McCarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.18
Prodhom, B.19
Reiher III, W.20
Roux, B.21
Schlenkrich, M.22
Smith, J.23
Stote, R.24
Straub, J.25
Watanabe, M.26
Wiorkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
29
-
-
15744368593
-
An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer
-
Klauda JB, Brooks BR, MacKerell Jr AD, Venable RM, Pastor RW. An ab initio study on the torsional surface of alkanes and its effect on molecular simulations of alkanes and a DPPC bilayer. J Phys Chem B 2005;109:5300-5311.
-
(2005)
J Phys Chem B
, vol.109
, pp. 5300-5311
-
-
Klauda, J.B.1
Brooks, B.R.2
MacKerell Jr, A.D.3
Venable, R.M.4
Pastor, R.W.5
-
30
-
-
0037116518
-
Polyunsaturated fatty acids in lipid bilayers: Intrinsic and environmental contributions to their unique physical properties
-
Feller SE, Gawrisch K, MacKerell AD, Jr. Polyunsaturated fatty acids in lipid bilayers: Intrinsic and environmental contributions to their unique physical properties. J Amer Chem Soc 2002;124:318-326.
-
(2002)
J Amer Chem Soc
, vol.124
, pp. 318-326
-
-
Feller, S.E.1
Gawrisch, K.2
MacKerell Jr., A.D.3
-
31
-
-
10644227774
-
Molecular-level organization saturated and polyunsaturated fatty acids in a phosphatidylcholine bilayer containing cholesterol
-
Pitman M, Suits F, MacKerell J AD, Feller SE. Molecular-level organization saturated and polyunsaturated fatty acids in a phosphatidylcholine bilayer containing cholesterol. Biochem 2004;43:15318-15328.
-
(2004)
Biochem
, vol.43
, pp. 15318-15328
-
-
Pitman, M.1
Suits, F.2
MacKerell, J.A.3
Feller, S.E.4
-
32
-
-
0033954256
-
The protein data bank
-
Available at
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The protein data bank. Nucleic Acids Res 2000;28:235-242. Available at http://www.rcsb.org/pdb.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
33
-
-
4344581120
-
The retinal conformation and its environment in rhodopsin in light of a new 2.2 a crystal structure
-
Okada T, Sugihara M, Bondar AN, Elstner M, Entel P, Buss V. The retinal conformation and its environment in rhodopsin in light of a new 2.2 a crystal structure. J Mol Biol 2004;342:571-583.
-
(2004)
J Mol Biol
, vol.342
, pp. 571-583
-
-
Okada, T.1
Sugihara, M.2
Bondar, A.N.3
Elstner, M.4
Entel, P.5
Buss, V.6
-
34
-
-
84986512474
-
-
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: A program for macromolecular energy minimization and dynamics calculations. J Comput Chem 1983;4:187-217.
-
Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: A program for macromolecular energy minimization and dynamics calculations. J Comput Chem 1983;4:187-217.
-
-
-
-
35
-
-
33847395277
-
-
Ponder JW. TINKER: Software Tools for Molecular Design 2004; 4.2: http://dasher.wustl.edu/tinker/.
-
Ponder JW. TINKER: Software Tools for Molecular Design 2004; 4.2: http://dasher.wustl.edu/tinker/.
-
-
-
-
37
-
-
0029811307
-
-
deGroot BL, Amadei A, Scheek RM, van Nuland NAJ, Berendsen HJC. An extended sampling of the configurational space of HPr from E. coli. Proteins: Struc Func Gen 1996;26:314-322.
-
deGroot BL, Amadei A, Scheek RM, van Nuland NAJ, Berendsen HJC. An extended sampling of the configurational space of HPr from E. coli. Proteins: Struc Func Gen 1996;26:314-322.
-
-
-
-
38
-
-
0344702698
-
Simulation of the folding equilibrium of α-helical peptides: A comparison of the generalized Born approximation with explicit solvent
-
Nymeyer H, Garcia AE. Simulation of the folding equilibrium of α-helical peptides: a comparison of the generalized Born approximation with explicit solvent. Proc Nat Acad Sci USA 2003;100:13934-13939.
-
(2003)
Proc Nat Acad Sci USA
, vol.100
, pp. 13934-13939
-
-
Nymeyer, H.1
Garcia, A.E.2
-
39
-
-
33645722974
-
Convergence of replica exchange molecular dynamics
-
Zhang W, Wu C, Duan Y. Convergence of replica exchange molecular dynamics. J Chem Phys 2005;123:154105-1-154105-9.
-
(2005)
J Chem Phys
, vol.123
-
-
Zhang, W.1
Wu, C.2
Duan, Y.3
-
40
-
-
0034500645
-
Similarities between principal components of protein dynamics and random diffusion
-
Hess B. Similarities between principal components of protein dynamics and random diffusion. Phys Rev E 2000;62:8438-8448.
-
(2000)
Phys Rev E
, vol.62
, pp. 8438-8448
-
-
Hess, B.1
-
41
-
-
10344261477
-
Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations
-
Faraldo-Gomez JD, Forrest LR, Baaden M, Bond PJ, Domene C, Patargias G, Cutherbertson J, Sansom MSP. Conformational sampling and dynamics of membrane proteins from 10-nanosecond computer simulations. Proteins 2004;57:783-791.
-
(2004)
Proteins
, vol.57
, pp. 783-791
-
-
Faraldo-Gomez, J.D.1
Forrest, L.R.2
Baaden, M.3
Bond, P.J.4
Domene, C.5
Patargias, G.6
Cutherbertson, J.7
Sansom, M.S.P.8
-
42
-
-
33745759471
-
Ensemble based convergence analysis of biomolecular trajectories
-
Lyman E, Zuckerman DM. Ensemble based convergence analysis of biomolecular trajectories. Biophys J 2006;91:164-172.
-
(2006)
Biophys J
, vol.91
, pp. 164-172
-
-
Lyman, E.1
Zuckerman, D.M.2
-
45
-
-
0034604451
-
Crystal structure of rhodopsin: A g protein-coupled receptor
-
Palczewski K, Kumasaka T, Hori T, Behnke CA, Motoshima H, Fox BJ, Le Trong I, Teller DC, Okada T, Stenkamp RE, Yamamoto M, Miyano M. Crystal structure of rhodopsin: a g protein-coupled receptor. Science 2000;289:739-745.
-
(2000)
Science
, vol.289
, pp. 739-745
-
-
Palczewski, K.1
Kumasaka, T.2
Hori, T.3
Behnke, C.A.4
Motoshima, H.5
Fox, B.J.6
Le Trong, I.7
Teller, D.C.8
Okada, T.9
Stenkamp, R.E.10
Yamamoto, M.11
Miyano, M.12
-
46
-
-
0035800032
-
Advances in determination of a high-resolution three-dimensional structure of rhodopsin, a model of g-protein-coupled receptors (gpcrs)
-
Teller DC, Okada T, Behnke CA, Palczewski K, Stenkamp RE. Advances in determination of a high-resolution three-dimensional structure of rhodopsin, a model of g-protein-coupled receptors (gpcrs). Biochem 2001;40:7761-7772.
-
(2001)
Biochem
, vol.40
, pp. 7761-7772
-
-
Teller, D.C.1
Okada, T.2
Behnke, C.A.3
Palczewski, K.4
Stenkamp, R.E.5
-
47
-
-
6344248639
-
Structure of bovine rhodopsin in a trigonal crystal form
-
Li J, Edwards PC, Burghammer M, Villa C, Schertler GFX. Structure of bovine rhodopsin in a trigonal crystal form. J Mol Biol 2004;343:1409-1438.
-
(2004)
J Mol Biol
, vol.343
, pp. 1409-1438
-
-
Li, J.1
Edwards, P.C.2
Burghammer, M.3
Villa, C.4
Schertler, G.F.X.5
-
48
-
-
0037197848
-
Functional role of internal water molecules in rhodopsin revealed by X-ray crystallography
-
Okada T, Fujiyoshi Y, Silow M, Navarro J, Landau EM, Shichida Y. Functional role of internal water molecules in rhodopsin revealed by X-ray crystallography. Proc Natl Acad Sci U S A 2002;99:5982-5987.
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, pp. 5982-5987
-
-
Okada, T.1
Fujiyoshi, Y.2
Silow, M.3
Navarro, J.4
Landau, E.M.5
Shichida, Y.6
-
49
-
-
0001295503
-
Principal component analysis and long time protein dynamics
-
Balsera MA, Wriggers W, Oono Y, Schulten K. Principal component analysis and long time protein dynamics. J Phys Chem 1996;100:2567-2572.
-
(1996)
J Phys Chem
, vol.100
, pp. 2567-2572
-
-
Balsera, M.A.1
Wriggers, W.2
Oono, Y.3
Schulten, K.4
-
51
-
-
0018790701
-
Protein structural fluctuations during a period of 100 ps
-
Karplus M, McCammon JA. Protein structural fluctuations during a period of 100 ps. Nature 1979;277:578-578.
-
(1979)
Nature
, vol.277
, pp. 578-578
-
-
Karplus, M.1
McCammon, J.A.2
-
53
-
-
0012181565
-
Measures of effective ergodic convergence in liquids
-
Mountain RD, Thirumalai D. Measures of effective ergodic convergence in liquids. J Phys Chem 1989;93:6975-6979.
-
(1989)
J Phys Chem
, vol.93
, pp. 6975-6979
-
-
Mountain, R.D.1
Thirumalai, D.2
-
54
-
-
36549102647
-
Error estimates on averages of correlated data
-
Flyvbjerg H, Petersen HG. Error estimates on averages of correlated data. J Chem Phys 1989;91:461-466.
-
(1989)
J Chem Phys
, vol.91
, pp. 461-466
-
-
Flyvbjerg, H.1
Petersen, H.G.2
-
55
-
-
33847194737
-
On energy estimators in path integral Monte Carlo simulations: Dependence of accuracy on algorithm
-
Cao J, Berne BJ. On energy estimators in path integral Monte Carlo simulations: dependence of accuracy on algorithm. J Chem Phys 1989;91:6359-6366.
-
(1989)
J Chem Phys
, vol.91
, pp. 6359-6366
-
-
Cao, J.1
Berne, B.J.2
-
56
-
-
0000127140
-
Method for estimating the configurational entropy of macromolecules
-
Karplus M, Kushick J. Method for estimating the configurational entropy of macromolecules. Macromolecules 1981;14:325-332.
-
(1981)
Macromolecules
, vol.14
, pp. 325-332
-
-
Karplus, M.1
Kushick, J.2
-
57
-
-
0035828630
-
On the calculation of entropy from covariance matrices of atomic fluctuations
-
Andricioaei I, Karplus M. On the calculation of entropy from covariance matrices of atomic fluctuations. J Chem Phys 2001;115:6289-6292.
-
(2001)
J Chem Phys
, vol.115
, pp. 6289-6292
-
-
Andricioaei, I.1
Karplus, M.2
-
58
-
-
0000577041
-
Large-amplitude nonlinear motions in proteins
-
Garcia AE. Large-amplitude nonlinear motions in proteins. Phys Rev Lett 1992;68:2696-2699.
-
(1992)
Phys Rev Lett
, vol.68
, pp. 2696-2699
-
-
Garcia, A.E.1
-
59
-
-
41349089279
-
Convergence of sampling in protein simulations
-
Hess B. Convergence of sampling in protein simulations. Phys Rev E 2002;65:031910-1-031910-10.
-
(2002)
Phys Rev E
, vol.65
-
-
Hess, B.1
-
60
-
-
2442548750
-
Identification of core amino acids stabilizing rhodopsin
-
Rader AJ, Anderson G, Isin B, Khorana HG, Bahar I, Klein-Seetharam J. Identification of core amino acids stabilizing rhodopsin. Proc Nat Acad Sci USA 2004;101:7246-7251.
-
(2004)
Proc Nat Acad Sci USA
, vol.101
, pp. 7246-7251
-
-
Rader, A.J.1
Anderson, G.2
Isin, B.3
Khorana, H.G.4
Bahar, I.5
Klein-Seetharam, J.6
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