-
1
-
-
84893810714
-
Essential Cell Biology
-
2nd Ed., New York & London
-
Alberts, B.; Bray, D.; Hopkin, K.; Johnson, A.; Lewis, J.; Raff, M.; Roberts, K.; Walter, P. Essential Cell Biology, 2nd Ed. Garland Science, New York & London, 2004, pp 119-159.
-
(2004)
Garland Science
, pp. 119-159
-
-
Alberts, B.1
Bray, D.2
Hopkin, K.3
Johnson, A.4
Lewis, J.5
Raff, M.6
Roberts, K.7
Walter, P.8
-
2
-
-
0003717374
-
-
5th Ed. W.H.Freeman & Company: New York
-
Berg, J. M.; Tymoczko, J. L.; Stryer, L. Biochemistry, 5th Ed. W.H.Freeman & Company: New York, 2002, pp 41-73.
-
(2002)
Biochemistry
, pp. 41-73
-
-
Berg, J.M.1
Tymoczko, J.L.2
Stryer, L.3
-
4
-
-
0033117830
-
Protein dynamics simulations from nanosecondsto microseconds
-
Doniach, S.; Eastman, P. Protein dynamics simulations from nanosecondsto microseconds. Curr. Opin. Struct. Biol., 1999, 9, 157-163.
-
(1999)
Curr. Opin. Struct. Biol.
, vol.9
, pp. 157-163
-
-
Doniach, S.1
Eastman, P.2
-
5
-
-
65349192770
-
Probing the flexibility of large conformationalchanges in protein structures through local perturbations
-
Ho, B. K.; Agard, D. A. Probing the flexibility of large conformationalchanges in protein structures through local perturbations.PLoS Comput. Biol., 2009, 5, 1-13.
-
(2009)
PLoS Comput. Biol.
, vol.5
, pp. 1-13
-
-
Ho, B.K.1
Agard, D.A.2
-
6
-
-
36849039429
-
A hierarchy of timescales in protein dynamics islinked to enzyme catalysis
-
Henzler-Wildman, K. A.; Lei, M.; Thai, V.; Kerns, S. J.; Karplus, M.; Kern, D. A hierarchy of timescales in protein dynamics islinked to enzyme catalysis. Nature, 2007, 450, 913-916.
-
(2007)
Nature
, vol.450
, pp. 913-916
-
-
Henzler-Wildman, K.A.1
Lei, M.2
Thai, V.3
Kerns, S.J.4
Karplus, M.5
Kern, D.6
-
7
-
-
0030773824
-
Molecular motors: Structural adaptations in cellularfunctions
-
Howard, J. Molecular motors: structural adaptations in cellularfunctions. Nature, 1997, 389, 561-567.
-
(1997)
Nature
, vol.389
, pp. 561-567
-
-
Howard, J.1
-
9
-
-
54549098184
-
Target flexibility: An emerging consideration in drug discovery and design
-
Cozzini, P.; Kellogg, G. E.; Spyrakis, F.; Abraham, D. J.; Costantino, G.; Emerson, A.; Fanelli, F.; Gohlke, H.; Kuhn, L. A.; Morris, G. M.; Orozco, M.; Pertinhez, T. A.; Rizzi, M.; Sotriffer, C. A.Target flexibility: an emerging consideration in drug discovery and design. J. Med. Chem., 2008, 51, 6237-6255.
-
(2008)
J. Med. Chem.
, vol.51
, pp. 6237-6255
-
-
Cozzini, P.1
Kellogg, G.E.2
Spyrakis, F.3
Abraham, D.J.4
Costantino, G.5
Emerson, A.6
Fanelli, F.7
Gohlke, H.8
Kuhn, L.A.9
Morris, G.M.10
Orozco, M.11
Pertinhez, T.A.12
Rizzi, M.13
Sotriffer, C.A.14
-
10
-
-
29144478787
-
Target flexibility in molecular recognition
-
McCammon, J. A. Target flexibility in molecular recognition.Biochim. Biophys. Acta, 2005, 1754, 221-224.
-
(2005)
Biochim. Biophys. Acta
, vol.1754
, pp. 221-224
-
-
McCammon, J.A.1
-
11
-
-
0037157153
-
Computational drug design accomodating receptor flexibility: Therelaxed complex scheme
-
Lin, J.-H.; Perryman, A. L.; Schames, J. R.; McCammon, J. A.Computational drug design accomodating receptor flexibility: Therelaxed complex scheme. J. Am. Chem. Soc., 2002, 124, 5632-5633.
-
(2002)
J. Am. Chem. Soc.
, vol.124
, pp. 5632-5633
-
-
Lin, J.-H.1
Perryman, A.L.2
Schames, J.R.3
McCammon, J.A.4
-
12
-
-
68149131990
-
General library-based monte carlo technique enables equilibriumsampling of semi-atomistic protein models
-
Mamonov, A. B.; Bhatt, D.; Cashman, D. J.; Ding, Y.; Zuckerman, D. M. General library-based monte carlo technique enables equilibriumsampling of semi-atomistic protein models. J. Phys. Chem. B, 2009, 113, 10891-10904.
-
(2009)
J. Phys. Chem. B
, vol.113
, pp. 10891-10904
-
-
Mamonov, A.B.1
Bhatt, D.2
Cashman, D.J.3
Ding, Y.4
Zuckerman, D.M.5
-
13
-
-
0024237631
-
Sugar and signaltransducerbinding sites of the Escherichia coli galactose chemoreceptorprotein
-
Vyas, N. K.; Vyas, M. N.; Quiocho, F. A. Sugar and signaltransducerbinding sites of the Escherichia coli galactose chemoreceptorprotein. Science, 1988, 242, 1290-1305.
-
(1988)
Science
, vol.242
, pp. 1290-1305
-
-
Vyas, N.K.1
Vyas, M.N.2
Quiocho, F.A.3
-
14
-
-
35648996014
-
Engineering and rapid selection of a low-affinity glucose/galactose-binding protein for a glucose biosensor
-
Amiss, T. J.; Sherman, D. B.; Nycz, C. M.; Andaluz, S. A.; Pitner, J. B. Engineering and rapid selection of a low-affinity glucose/galactose-binding protein for a glucose biosensor. ProteinSci., 2007, 16, 1-10.
-
(2007)
ProteinSci.
, vol.16
, pp. 1-10
-
-
Amiss, T.J.1
Sherman, D.B.2
Nycz, C.M.3
Andaluz, S.A.4
Pitner, J.B.5
-
15
-
-
0033081688
-
Glucose sensor for lowcostlifetime-based sensing using a genetically engineered protein
-
Tolosa, L.; Gryczynski, I.; Eichhorn, L. R.; Dattelbaum, J. D.; Castellano, F. N.; Rao, G.; Lakowicz, J. R. Glucose sensor for lowcostlifetime-based sensing using a genetically engineered protein.Anal. Biochem., 1999, 267, 114-1120.
-
(1999)
Anal. Biochem.
, vol.267
, pp. 114-1120
-
-
Tolosa, L.1
Gryczynski, I.2
Eichhorn, L.R.3
Dattelbaum, J.D.4
Castellano, F.N.5
Rao, G.6
Lakowicz, J.R.7
-
16
-
-
68049131211
-
The construction of a glucose-sensing luciferase
-
Taneoka, T.; Sakaguchi-Mikami, A.; Yamazaki, T.; Tsugawa, W.; Sode, K. The construction of a glucose-sensing luciferase. Biosens.Bioelectron., 2009, 25, 76-81.
-
(2009)
Biosens.Bioelectron.
, vol.25
, pp. 76-81
-
-
Taneoka, T.1
Sakaguchi-Mikami, A.2
Yamazaki, T.3
Tsugawa, W.4
Sode, K.5
-
17
-
-
0026489631
-
Thermal motions of surface alphahelicesin the D-galactose chemosensory receptor. Detection by disulfidetrapping
-
Careaga, C. L.; Falke, J. J. Thermal motions of surface alphahelicesin the D-galactose chemosensory receptor. Detection by disulfidetrapping. J. Mol. Biol., 1992, 226, 1219-1235.
-
(1992)
J. Mol. Biol.
, vol.226
, pp. 1219-1235
-
-
Careaga, C.L.1
Falke, J.J.2
-
18
-
-
0028929925
-
Large amplitudetwisting motions of an interdomain hinge: A disulfide trappingstudy of the galactose-glucose binding protein
-
Careaga, C. L.; Sutherland, J.; Sabeti, J.; Falke, J. J. Large amplitudetwisting motions of an interdomain hinge: a disulfide trappingstudy of the galactose-glucose binding protein. Biochemistry, 1995, 34, 3048-3055.
-
(1995)
Biochemistry
, vol.34
, pp. 3048-3055
-
-
Careaga, C.L.1
Sutherland, J.2
Sabeti, J.3
Falke, J.J.4
-
19
-
-
0029912748
-
Developmentand testing of the OPLS all-atom force field on conformational energeticsand properties of organic liquids
-
Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. Developmentand testing of the OPLS all-atom force field on conformational energeticsand properties of organic liquids. J. Am. Chem. Soc., 1996, 118, 11225-11236.
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 11225-11236
-
-
Jorgensen, W.L.1
Maxwell, D.S.2
Tirado-Rives, J.3
-
20
-
-
27344436659
-
Scalablemolecular dynamics with NAMD
-
Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kale, L.; Schulten, K. Scalablemolecular dynamics with NAMD. J. Comput. Chem., 2005, 26, 1781-1802.
-
(2005)
J. Comput. Chem.
, vol.26
, 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
-
21
-
-
36248954429
-
On the structural convergence of biomolecular simulations by determination of the effective samplesize
-
Lyman, E.; Zuckerman, D. M. On the structural convergence of biomolecular simulations by determination of the effective samplesize. J. Phys. Chem. B, 2007, 111, 12876-12882.
-
(2007)
J. Phys. Chem. B
, vol.111
, pp. 12876-12882
-
-
Lyman, E.1
Zuckerman, D.M.2
-
22
-
-
34249781722
-
Conformationalchanges of glucose/galactose-binding protein illuminated by open, unliganded and ultra-high-resolution ligand-bound structures
-
Borrok, M. J.; Kiessling, L. L.; Forest, K. T. Conformationalchanges of glucose/galactose-binding protein illuminated by open, unliganded and ultra-high-resolution ligand-bound structures. ProteinSci., 2007, 16, 1032-1041.
-
(2007)
ProteinSci.
, vol.16
, pp. 1032-1041
-
-
Borrok, M.J.1
Kiessling, L.L.2
Forest, K.T.3
-
23
-
-
33846847773
-
Conformationaltransitions of adenylate kinase: Switching by cracking
-
Whitford, P. C.; Miyashita, O.; Levy, Y.; Onuchic, J. N. Conformationaltransitions of adenylate kinase: Switching by cracking. J.Mol. Biol., 2007, 366, 1661-1671.
-
(2007)
J.Mol. Biol.
, vol.366
, pp. 1661-1671
-
-
Whitford, P.C.1
Miyashita, O.2
Levy, Y.3
Onuchic, J.N.4
-
24
-
-
24344509845
-
The role of calcium in the conformational dynamics and thermal stability of theD-galactose/D-glucose-binding protein from escherichia coli
-
Herman, P.; Vecer, J.; Barvik, I.; Scognamiglio, V.; Staiano, M.; deChampdore, M.; Varriale, A.; Rossi, M.; D'Auria, S. The role of calcium in the conformational dynamics and thermal stability of theD-galactose/D-glucose-binding protein from escherichia coli. Proteins: Struct., Funct., Bioinf., 2005, 61, 184-195.
-
(2005)
Proteins: Struct., Funct., Bioinf.
, vol.61
, pp. 184-195
-
-
Herman, P.1
Vecer, J.2
Barvik, I.3
Scognamiglio, V.4
Staiano, M.5
deChampdore, M.6
Varriale, A.7
Rossi, M.8
D'Auria, S.9
-
25
-
-
0035478585
-
Macromolecular crowding: Obvious but underappreciated
-
Ellis, R. J. Macromolecular crowding: obvious but underappreciated.Trends Biochem. Sci., 2001, 26, 597-604.
-
(2001)
Trends Biochem. Sci.
, vol.26
, pp. 597-604
-
-
Ellis, R.J.1
-
26
-
-
84988112508
-
An efficient newton-like method formolecular mechanics energy minimization of large molecules
-
Ponder, J. W.; Richards, F. M. An efficient newton-like method formolecular mechanics energy minimization of large molecules. J.Comput. Chem., 1987, 8, 1016-1024.
-
(1987)
J.Comput. Chem.
, vol.8
, pp. 1016-1024
-
-
Ponder, J.W.1
Richards, F.M.2
-
27
-
-
33645941402
-
The OPLS [optimized potentialsfor liquid simulations] potential functions for proteins, energyminimizations for crystals of cyclic peptides and crambin
-
Jorgensen, W. L.; Tirado-Rives, J. The OPLS [optimized potentialsfor liquid simulations] potential functions for proteins, energyminimizations for crystals of cyclic peptides and crambin. J. Am.Chem. Soc., 1988, 110, 1657-1666.
-
(1988)
J. Am.Chem. Soc.
, vol.110
, pp. 1657-1666
-
-
Jorgensen, W.L.1
Tirado-Rives, J.2
-
28
-
-
0016696599
-
Studies on protein folding, unfolding and fluctuations by computer simulation
-
Taketomi, H.; Ueda, Y.; Nobuhiro, G. Studies on protein folding, unfolding and fluctuations by computer simulation. Int. J. Pept.Protein Res., 1975, 7, 445-459.
-
(1975)
Int. J. Pept.Protein Res.
, vol.7
, pp. 445-459
-
-
Taketomi, H.1
Ueda, Y.2
Nobuhiro, G.3
-
29
-
-
0017842051
-
Studies on protein folding, unfolding and fluctuations by computer simulation. II. A. Threedimensionallattice model of lysozyme
-
Ueda, Y.; Taketomi, H.; Nobuhiro, G. Studies on protein folding, unfolding and fluctuations by computer simulation. II. A. Threedimensionallattice model of lysozyme. Biopolymers, 1978, 17, 1531-1548.
-
(1978)
Biopolymers
, vol.17
, pp. 1531-1548
-
-
Ueda, Y.1
Taketomi, H.2
Nobuhiro, G.3
-
30
-
-
2342471328
-
Simulation of an ensemble of conformationaltransitions in a united-residue model of calmodulin
-
Zuckerman, D. M. Simulation of an ensemble of conformationaltransitions in a united-residue model of calmodulin. J. Phys. Chem.B, 2004, 108, 5127-5137.
-
(2004)
J. Phys. Chem.B
, vol.108
, pp. 5127-5137
-
-
Zuckerman, D.M.1
-
31
-
-
36749060078
-
Efficient and verifiedsimulation of a path ensemble for conformational change in aunited-residue model of calmodulin
-
Zhang, B. W.; Jasnow, D.; Zuckerman, D. M. Efficient and verifiedsimulation of a path ensemble for conformational change in aunited-residue model of calmodulin. Proc. Natl. Acad. Sci. USA, 2007, 104, 18043-18048.
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 18043-18048
-
-
Zhang, B.W.1
Jasnow, D.2
Zuckerman, D.M.3
-
32
-
-
0004016501
-
Comparison of simple potential functions for simulatingliquid water
-
Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of simple potential functions for simulatingliquid 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
-
33
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell, A. D.; Bashford, D.; Bellott, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Profhom, B.; Reiher, W. E.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J. Phys. Chem. B, 1998, 102, 3586-3616.
-
(1998)
J. Phys. Chem. B
, vol.102
, pp. 3586-3616
-
-
McKerell, A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack, R.L.4
Evanseck, J.D.5
Field, M.J.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.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Profhom, B.19
Reiher, W.E.20
Roux, B.21
Schlenkrich, M.22
Smith, J.C.23
Stote, R.24
Straub, J.25
Watanabe, M.26
Wiorkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
|