-
1
-
-
27344436659
-
Scalable molecular dynamics with namd
-
Phillips J C, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel R D, Kale L and Schulten K 2005 Scalable molecular dynamics with namd J. Comput. Chem. 26 1781-802
-
(2005)
J. Comput. Chem.
, vol.26
, Issue.16
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kale, L.9
Schulten, K.10
-
2
-
-
0026044754
-
Determination of the three-dimensional solution structure of barnase using nuclear magnetic resonance spectroscopy
-
Bycroft M, Ludvigsen S, Fersht A R and Poulsen F M 1991 Determination of the three-dimensional solution structure of barnase using nuclear magnetic resonance spectroscopy Biochemistry 30 8697-701
-
(1991)
Biochemistry
, vol.30
, Issue.35
, pp. 8697-8701
-
-
Bycroft, M.1
Ludvigsen, S.2
Fersht, A.R.3
Poulsen, F.M.4
-
3
-
-
0347357932
-
Solution structure of mycobacterium tuberculosis adenylate kinase
-
Miron S, Munier-Lehmann H and Craescu C T 2004 Solution structure of mycobacterium tuberculosis adenylate kinase Biochemistry 43 67-77
-
(2004)
Biochemistry
, vol.43
, Issue.1
, pp. 67-77
-
-
Miron, S.1
Munier-Lehmann, H.2
Craescu, C.T.3
-
4
-
-
11944256211
-
Experimental study of critical-mass fluctations in an evolving sandpile
-
Held G A, Solina D H II, Keane D T, Haag W J, Horn P M and Grinstein G 1990 Experimental study of critical-mass fluctations in an evolving sandpile Phys. Rev. Lett. 65 1120-3
-
(1990)
Phys. Rev. Lett.
, vol.65
, Issue.9
, pp. 1120-1123
-
-
Held, G.A.1
Solina, D.H.I.I.2
Keane, D.T.3
Haag, W.J.4
Horn, P.M.5
Grinstein, G.6
-
5
-
-
25344440586
-
Scaling laws and simulation results for the self-organized critical forest-fire model
-
Clar S, Drossel B and Schwabl F 1994 Scaling laws and simulation results for the self-organized critical forest-fire model Phys. Rev. E 50 1009-18
-
(1994)
Phys. Rev.
, vol.50
, Issue.2
, pp. 1009-1018
-
-
Clar, S.1
Drossel, B.2
Schwabl, F.3
-
6
-
-
0007648124
-
Forest fires as critical phenomena
-
MacKay G and Jan N 1984 Forest fires as critical phenomena J. Phys. A: Math. Gen. 17 L757-60
-
(1984)
J. Phys. A: Math. Gen.
, vol.17
, Issue.14
-
-
MacKay, G.1
Jan, N.2
-
7
-
-
0001413916
-
Superconducting vortex avalanches
-
Field S, Witt J and Nori F 1995 Superconducting vortex avalanches Phys. Rev. Lett. 74 1206-9
-
(1995)
Phys. Rev. Lett.
, vol.74
, Issue.7
, pp. 1206-1209
-
-
Field, S.1
Witt, J.2
Nori, F.3
-
8
-
-
0034250180
-
One- and two-particle microrheology
-
Levine A J and Lubensky T C 2000 One- and two-particle microrheology Phys. Rev. Lett. 85 1774-7
-
(2000)
Phys. Rev. Lett.
, vol.85
, Issue.8
, pp. 1774-1777
-
-
Levine, A.J.1
Lubensky, T.C.2
-
9
-
-
0038137166
-
Rheological microscopy: Local mechanical properties from microrheology
-
Chen D T, Weeks E R, Crocker J C, Islam M F, Verma R, Gruber J, Levine A J, Lubensky T C and Yodh A G 2003 Rheological microscopy: local mechanical properties from microrheology Phys. Rev. Lett. 90 108301-5
-
(2003)
Phys. Rev. Lett.
, vol.90
, Issue.10
, pp. 108301-108305
-
-
Chen, D.T.1
Weeks, E.R.2
Crocker, J.C.3
Islam, M.F.4
Verma, R.5
Gruber, J.6
Levine, A.J.7
Lubensky, T.C.8
Yodh, A.G.9
-
10
-
-
10244241008
-
Response function of a sphere in a viscoelastic two-fluid medium
-
Levine A J and Lubensky T C 2001 Response function of a sphere in a viscoelastic two-fluid medium Phys. Rev. E 63 041510
-
(2001)
Phys. Rev.
, vol.63
, Issue.4
, pp. 041510
-
-
Levine, A.J.1
Lubensky, T.C.2
-
11
-
-
41349103607
-
Two-point microrheology and the electrostatic analogy
-
Levine A J and Lubensky T C 2001 Two-point microrheology and the electrostatic analogy Phys. Rev. E 65 011501
-
(2001)
Phys. Rev.
, vol.65
, Issue.1
, pp. 011501
-
-
Levine, A.J.1
Lubensky, T.C.2
-
12
-
-
0034214831
-
Two-point microrheology of inhomogenous soft materials
-
Crocker J C, Valentine M T, Weeks E R, Gisler T, Kaplan P D, Yodh A G and Weitz D A 2000 Two-point microrheology of inhomogenous soft materials Phys. Rev. Lett. 85 888-91
-
(2000)
Phys. Rev. Lett.
, vol.85
, Issue.4
, pp. 888-891
-
-
Crocker, J.C.1
Valentine, M.T.2
Weeks, E.R.3
Gisler, T.4
Kaplan, P.D.5
Yodh, A.G.6
Weitz, D.A.7
-
13
-
-
5344221031
-
Bunching of cars in asymmetric exclusion models for freeway traffic
-
Nagatani T 1995 Bunching of cars in asymmetric exclusion models for freeway traffic Phys. Rev. E 51 922-8
-
(1995)
Phys. Rev.
, vol.51
, Issue.2
, pp. 922-928
-
-
Nagatani, T.1
-
14
-
-
0000633922
-
Stochastic master-equation approach to aggregation in freeway traffic
-
Mahnke R and Pieret N 1997 Stochastic master-equation approach to aggregation in freeway traffic Phys. Rev. E 56 2666-71
-
(1997)
Phys. Rev.
, vol.56
, Issue.3
, pp. 2666-2671
-
-
Mahnke, R.1
Pieret, N.2
-
15
-
-
28244476619
-
Emergent traffic jams
-
Nagel K and Paczuski M 1995 Emergent traffic jams Phys. Rev. E 51 2909-18
-
(1995)
Phys. Rev.
, vol.51
, Issue.4
, pp. 2909-2918
-
-
Nagel, K.1
Paczuski, M.2
-
16
-
-
11744273781
-
Deterministic spontaneous appearance of traffic jams in slightly inhomogeneous traffic flow
-
Kerner B S, Konhäuser P and Schilke M 1995 Deterministic spontaneous appearance of traffic jams in slightly inhomogeneous traffic flow Phys. Rev. E 51 6243-6
-
(1995)
Phys. Rev.
, vol.51
, Issue.6
, pp. 6243-6246
-
-
Kerner, B.S.1
Konhäuser, P.2
Schilke, M.3
-
17
-
-
0001087706
-
Phase transition in a computer network traffic model
-
Ohira T and Sawatari R 1998 Phase transition in a computer network traffic model Phys. Rev. E 58 193-5
-
(1998)
Phys. Rev.
, vol.58
, Issue.1
, pp. 193-195
-
-
Ohira, T.1
Sawatari, R.2
-
18
-
-
0034321182
-
Origin of critical behavior in ethernet traffic
-
Fukuda K, Takayasu H and Takayasu M 2000 Origin of critical behavior in ethernet traffic Physica A 287 289-301
-
(2000)
Physica
, vol.287
, Issue.1-2
, pp. 289-301
-
-
Fukuda, K.1
Takayasu, H.2
Takayasu, M.3
-
19
-
-
5844290410
-
Self-organized criticality: An explanation of 1/f noise
-
Bak P, Tang C and Wiesenfeld K 1987 Self-organized criticality: an explanation of 1/f noise Phys. Rev. Lett. 59 381-4
-
(1987)
Phys. Rev. Lett.
, vol.59
, Issue.4
, pp. 381-384
-
-
Bak, P.1
Tang, C.2
Wiesenfeld, K.3
-
21
-
-
0016973661
-
Pattern recognition by means of disjoint principal components models
-
Wold S 1976 Pattern recognition by means of disjoint principal components models Pattern Recognit. 8 127-39
-
(1976)
Pattern Recognit.
, vol.8
, Issue.3
, pp. 127-139
-
-
Wold, S.1
-
22
-
-
58149421595
-
Analysis of a complex of statistical variables into principal components
-
Hotelling H 1933 Analysis of a complex of statistical variables into principal components J. Educ. Psychol. 24 417-41
-
(1933)
J. Educ. Psychol.
, vol.24
, Issue.6
, pp. 417-441
-
-
Hotelling, H.1
-
23
-
-
0001295503
-
Principal component analysis and long time protein dynamics
-
Balsera M A, Wriggers W, Oono Y and Schulten K 1996 Principal component analysis and long time protein dynamics J. Phys. Chem. 100 2567-72
-
(1996)
J. Phys. Chem.
, vol.100
, Issue.7
, pp. 2567-2572
-
-
Balsera, M.A.1
Wriggers, W.2
Oono, Y.3
Schulten, K.4
-
24
-
-
0030888546
-
Model-free methods of analyzing domain motions in proteins from simulation: A comparison of normal mode analysis and molecular dynamics simulation of lysozyme
-
Hayward S, Kitao A and Berndsen H J C 1997 Model-free methods of analyzing domain motions in proteins from simulation: a comparison of normal mode analysis and molecular dynamics simulation of lysozyme Proteins 27 425-37
-
(1997)
Proteins
, vol.27
, Issue.3
, pp. 425-437
-
-
Hayward, S.1
Kitao, A.2
Berndsen, H.J.C.3
-
25
-
-
0032006209
-
Systematic analysis of domain motions in proteins from conformational change: New results on citrate synthase and t4 lysozyme
-
Hayward S and Berendsen H J C 1998 Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and t4 lysozyme Proteins 30 144-54
-
(1998)
Proteins
, vol.30
, Issue.2
, pp. 144-154
-
-
Hayward, S.1
Berendsen, H.J.C.2
-
26
-
-
0024621473
-
Chain dimensions and fluctuations in random elastomeric networks: I. Phantom Gaussian networks in the undeformed state
-
Kloczkowski A, Mark J E and Erman B 1989 Chain dimensions and fluctuations in random elastomeric networks: I. Phantom Gaussian networks in the undeformed state Macromolecules 22 1423-32
-
(1989)
Macromolecules
, vol.22
, Issue.3
, pp. 1423-1432
-
-
Kloczkowski, A.1
Mark, J.E.2
Erman, B.3
-
27
-
-
0036888379
-
Identifying protein folding cores from the evolution of flexible regions during unfolding
-
Hespenheide B M, Rader A J, Thorpe M F and Kuhn L A 2002 Identifying protein folding cores from the evolution of flexible regions during unfolding J. Mol. Graph. Model. 21 195-207
-
(2002)
J. Mol. Graph. Model.
, vol.21
, Issue.3
, pp. 195-207
-
-
Hespenheide, B.M.1
Rader, A.J.2
Thorpe, M.F.3
Kuhn, L.A.4
-
28
-
-
0028912595
-
A sampling problem in molecular dynamics simulations of macromolecules
-
Clarage J B, Romo T, Andrews B K, Pettitt B M and Phillips G N Jr 1995 A sampling problem in molecular dynamics simulations of macromolecules Proc. Natl Acad. Sci. 92 3288-92
-
(1995)
Proc. Natl Acad. Sci.
, vol.92
, Issue.8
, pp. 3288-3292
-
-
Clarage, J.B.1
Romo, T.2
Andrews, B.K.3
Pettitt, B.M.4
Phillips, G.N.5
-
31
-
-
22944467757
-
Computer experiments on classical fluids: I. Thermodynamical properties of Lennard-Jones molecules
-
Verlet L 1967 Computer experiments on classical fluids: I. Thermodynamical properties of Lennard-Jones molecules Phys. Rev. 159 98-103
-
(1967)
Phys. Rev.
, vol.159
, Issue.1
, pp. 98-103
-
-
Verlet, L.1
-
32
-
-
0032363602
-
Constant temperature simulations using the Langevin equation with velocity Verlet integration
-
Paterlini M G and Ferguson D M 1998 Constant temperature simulations using the Langevin equation with velocity Verlet integration Chem. Phys. 236 243-52
-
(1998)
Chem. Phys.
, vol.236
, Issue.1-3
, pp. 243-252
-
-
Paterlini, M.G.1
Ferguson, D.M.2
-
33
-
-
0028815464
-
Protein structure prediction: Recognition of primary, secondary, and tertiary structural features from amino acid sequence
-
Eisenhaber F, Persson B and Argos P 1995 Protein structure prediction: recognition of primary, secondary, and tertiary structural features from amino acid sequence Cirt. Rev. Biochem. Mol. Biol. 30 1-94
-
(1995)
Cirt. Rev. Biochem. Mol. Biol.
, vol.30
, Issue.1
, pp. 1-94
-
-
Eisenhaber, F.1
Persson, B.2
Argos, P.3
-
34
-
-
0030963424
-
Fast events in protein folding: Relaxation dynamics of secondary and tertiary structure in native apomyoglobin
-
DOI 10.1073/pnas.94.8.3709
-
Gilmanshin R, Williams S, Callender R H, Woodruff W H and Dyer R B 1997 Fast events in protein folding: relaxation dynamics of secondary and tertiary structure in native apomyoglobin Proc. Natl Acad. Sci. 94 3709-13 (Pubitemid 27180437)
-
(1997)
Proceedings of the National Academy of Sciences of the United States of America
, vol.94
, Issue.8
, pp. 3709-3713
-
-
Gilmanshin, R.1
Williams, S.2
Callender, R.H.3
Woodruff, W.H.4
Dyer, R.B.5
-
36
-
-
0037338365
-
Proteomic analysis of post-translational modifications
-
Mann M and Jensen O N 2003 Proteomic analysis of post-translational modifications Nat. Biotechnol. 21 255-61
-
(2003)
Nat. Biotechnol.
, vol.21
, Issue.3
, pp. 255-261
-
-
Mann, M.1
Jensen, O.N.2
-
37
-
-
0036019907
-
Protein glycosylation: Nature, distribution, enzymatic formation, and disease implications of glycopeptide bonds
-
Spiro R G 2002 Protein glycosylation: nature, distribution, enzymatic formation, and disease implications of glycopeptide bonds Glycobiology 12 43R-56R
-
(2002)
Glycobiology
, vol.12
, Issue.4
-
-
Spiro, R.G.1
-
38
-
-
0034677966
-
Drug discovery: A historical perspective
-
Drews J 2000 Drug discovery: a historical perspective Science 287 1960-4
-
(2000)
Science
, vol.287
, Issue.5460
, pp. 1960-1964
-
-
Drews, J.1
-
39
-
-
0027480452
-
Structure-based inhibitor design by using protein models for the development of antiparasitic agents
-
Ring C S, Sun E, Mckerrow J H, Lee G K, Rosenthal P J, Kuntz I D and Cohen F E 1993 Structure-based inhibitor design by using protein models for the development of antiparasitic agents Proc. Natl Acad. Sci. 90 3583-7
-
(1993)
Proc. Natl Acad. Sci.
, vol.90
, Issue.8
, pp. 3583-3587
-
-
Ring, C.S.1
Sun, E.2
McKerrow, J.H.3
Lee, G.K.4
Rosenthal, P.J.5
Kuntz, I.D.6
Cohen, F.E.7
-
40
-
-
0035342428
-
Ligand-protein inverse docking and its potential use in the computer search of protein targets of a small molecule
-
Chen Y Z and Zhi D G 2001 Ligand-protein inverse docking and its potential use in the computer search of protein targets of a small molecule Proteins 43 217-26
-
(2001)
Proteins
, vol.43
, Issue.2
, pp. 217-226
-
-
Chen, Y.Z.1
Zhi, D.G.2
-
41
-
-
0037666888
-
Implications of protein flexibility for drug discovery
-
Teague S J 2003 Implications of protein flexibility for drug discovery Nat. Rev. 2 527-41
-
(2003)
Nat. Rev.
, vol.2
, pp. 527-541
-
-
Teague, S.J.1
-
42
-
-
0033915678
-
Recent developments in structure-based drug design
-
Klebe G 2000 Recent developments in structure-based drug design J. Mol. Med. 78 1432-40
-
(2000)
J. Mol. Med.
, vol.78
, Issue.5
, pp. 269-1440
-
-
Klebe, G.1
-
43
-
-
36949091243
-
Structure of myoglobin: A three-dimensional Fourier synthesis at 2 resolution
-
Kendrew J C, Dickerson R E, Strandbertg B E, Hart R G, Daview D R, Phillips D C and Shore V C 1960 Structure of myoglobin: a three-dimensional Fourier synthesis at 2 resolution Nature 185 422-7
-
(1960)
Nature
, vol.185
, Issue.4711
, pp. 422-427
-
-
Kendrew, J.C.1
Dickerson, R.E.2
Strandbertg, B.E.3
Hart, R.G.4
Daview, D.R.5
Phillips, D.C.6
Shore, V.C.7
-
44
-
-
0001266102
-
A three-dimensional model of the myoglobin molecule obtained by x-ray analysis
-
Kendrew J C, Bodo G, Dintzis H M, Parrish R G, Wyckoff H and Phillip D C 1958 A three-dimensional model of the myoglobin molecule obtained by x-ray analysis Nature 181 662-6
-
(1958)
Nature
, vol.181
, Issue.4610
, pp. 662-666
-
-
Kendrew, J.C.1
Bodo, G.2
Dintzis, H.M.3
Parrish, R.G.4
Wyckoff, H.5
Phillip, D.C.6
-
45
-
-
0019889444
-
Combined use of proton-proton overhauser enhancements and a distance geometry algorithm for determination of polypeptide conformations. Application to micelle-bound glucagon
-
Brown W, Bosch C, Braun LR, Go N and Wuthrich K 1981 Combined use of proton-proton overhauser enhancements and a distance geometry algorithm for determination of polypeptide conformations. Application to micelle-bound glucagon Biochim. Biophys. Acta 667 377-96
-
(1981)
Biochim. Biophys. Acta
, vol.667
, pp. 377-396
-
-
Brown, W.1
Bosch, C.2
Braun, L.R.3
Go, N.4
Wuthrich, K.5
-
46
-
-
0023645325
-
Protein structures in solution by nuclear magnetic resonance and distance geometry. the polypeptide fold of the basic pancreatic trypsin inhibitor determined using two different algorithms, disgeo and disman
-
Wagner G, Braun W, Havel T F, Schaumann T, Go N and Wuthrich K 1987 Protein structures in solution by nuclear magnetic resonance and distance geometry. The polypeptide fold of the basic pancreatic trypsin inhibitor determined using two different algorithms, disgeo and disman J. Mol. Biol. 196 611-39
-
(1987)
J. Mol. Biol.
, vol.196
, Issue.3
, pp. 611-639
-
-
Wagner, G.1
Braun, W.2
Havel, T.F.3
Schaumann, T.4
Go, N.5
Wuthrich, K.6
-
47
-
-
0000785338
-
Generic rigidity percolation: The pebble game
-
Jacobs D J and Thorpe M F 1995 Generic rigidity percolation: the pebble game Phys. Rev. Lett. 75 4051-4
-
(1995)
Phys. Rev. Lett.
, vol.75
, Issue.22
, pp. 4051-4054
-
-
Jacobs, D.J.1
Thorpe, M.F.2
-
48
-
-
0035427398
-
Protein flexibility predictions using graph theory
-
Jacobs D J, Rader A J, Kuhn L A and Thorpe M F 2001 Protein flexibility predictions using graph theory Proteins 44 150-65
-
(2001)
Proteins
, vol.44
, Issue.2
, pp. 150-165
-
-
Jacobs, D.J.1
Rader, A.J.2
Kuhn, L.A.3
Thorpe, M.F.4
-
49
-
-
67349149129
-
Barnase wildtype structure at 1.5 angstroms resolution
-
Martin C, Richard V, Salem M, Hartley R W and Mauguen Y 1982 Barnase wildtype structure at 1.5 angstroms resolution Nature 297 162-4
-
(1982)
Nature
, vol.297
, pp. 162-164
-
-
Martin, C.1
Richard, V.2
Salem, M.3
Hartley, R.W.4
Mauguen, Y.5
-
50
-
-
0024453699
-
Barnase and barstar: Two small proteins to fold and fit together
-
Hartley R W 1989 Barnase and barstar: two small proteins to fold and fit together Trends Biochem. Sci. 14 450-4
-
(1989)
Trends Biochem. Sci.
, vol.14
, Issue.11
, pp. 450-454
-
-
Hartley, R.W.1
-
51
-
-
0029056922
-
Energetics of protein-protein interactions: Analysis of the barnase-barstar interface by single mutations and double mutant cycles
-
Schreiber G and Fersht A R 1995 Energetics of protein-protein interactions: analysis of the barnase-barstar interface by single mutations and double mutant cycles J. Mol. Biol. 248 478-86
-
(1995)
J. Mol. Biol.
, vol.248
, Issue.2
, pp. 478-486
-
-
Schreiber, G.1
Fersht, A.R.2
|