-
2
-
-
33644873452
-
The database of macromolecular motions: new features added at the decade mark
-
Flores S, Echols N, Milburn D, et al. The database of macromolecular motions: new features added at the decade mark. Nucleic Acids Res. 2006;34(Database issue):D296-D301.
-
(2006)
Nucleic Acids Res
, vol.34
, Issue.DATABASE ISSUE
, pp. D296-D301
-
-
Flores, S.1
Echols, N.2
Milburn, D.3
-
3
-
-
84923085640
-
Keep on moving: discovering and perturbing the conformational dynamics of enzymes
-
Bhabha G, Biel JT, Fraser JS. Keep on moving: discovering and perturbing the conformational dynamics of enzymes. Acc Chem Res. 2015; 48(2):423-430.
-
(2015)
Acc Chem Res
, vol.48
, Issue.2
, pp. 423-430
-
-
Bhabha, G.1
Biel, J.T.2
Fraser, J.S.3
-
4
-
-
84872678299
-
ViewMotions rainbow: a new method to illustrate molecular motions in proteins
-
Cockrell GM, Kantrowitz ER. ViewMotions rainbow: a new method to illustrate molecular motions in proteins. J Mol Graph Model. 2013;40: 48-53.
-
(2013)
J Mol Graph Model
, vol.40
, pp. 48-53
-
-
Cockrell, G.M.1
Kantrowitz, E.R.2
-
5
-
-
0032530836
-
A database of macromolecular motions
-
Gerstein M, Krebs W. A database of macromolecular motions. Nucleic Acids Res. 1998;26(18):4280-4290.
-
(1998)
Nucleic Acids Res
, vol.26
, Issue.18
, pp. 4280-4290
-
-
Gerstein, M.1
Krebs, W.2
-
6
-
-
1342302339
-
Conformational changes associated with protein-protein interactions
-
Goh CS, Milburn D, Gerstein M. Conformational changes associated with protein-protein interactions. Curr Opin Struct Biol. 2004; 14(1):104-109.
-
(2004)
Curr Opin Struct Biol
, vol.14
, Issue.1
, pp. 104-109
-
-
Goh, C.S.1
Milburn, D.2
Gerstein, M.3
-
8
-
-
0025106487
-
Allosteric control of quaternary states in E. coli aspartate transcarbamylase
-
Stevens RC, Lipscomb WN. Allosteric control of quaternary states in E. coli aspartate transcarbamylase. Biochem Biophys Res Commun. 1990;171(3):1312-1318.
-
(1990)
Biochem Biophys Res Commun
, vol.171
, Issue.3
, pp. 1312-1318
-
-
Stevens, R.C.1
Lipscomb, W.N.2
-
9
-
-
20444474123
-
Distinct conformation-mediated functions of an active site loop in the catalytic reactions of NAD-dependent D-lactate dehydrogenase and formate dehydrogenase
-
Shinoda T, Arai K, Shigematsu-Iida M, et al. Distinct conformation-mediated functions of an active site loop in the catalytic reactions of NAD-dependent D-lactate dehydrogenase and formate dehydrogenase. J Biol Chem. 2005;280(17):17068-17075.
-
(2005)
J Biol Chem
, vol.280
, Issue.17
, pp. 17068-17075
-
-
Shinoda, T.1
Arai, K.2
Shigematsu-Iida, M.3
-
10
-
-
77952355806
-
Role of conformation transitions in adenylate kinase
-
author reply E72
-
Karplus M. Role of conformation transitions in adenylate kinase. Proc Natl Acad Sci U S A. 2010;107(17):E71; author reply E72.
-
(2010)
Proc Natl Acad Sci U S A
, vol.107
, Issue.17
, pp. E71
-
-
Karplus, M.1
-
11
-
-
0035802360
-
Theoretical study of the mechanisms of substrate recognition by catalase
-
Kalko SG, Gelpi JL, Fita I, Orozco M. Theoretical study of the mechanisms of substrate recognition by catalase. J Am Chem Soc. 2001;123(39):9665-9672.
-
(2001)
J Am Chem Soc
, vol.123
, Issue.39
, pp. 9665-9672
-
-
Kalko, S.G.1
Gelpi, J.L.2
Fita, I.3
Orozco, M.4
-
12
-
-
29644440030
-
Role of the main access channel of catalase-peroxidase in catalysis
-
Jakopitsch C, Droghetti E, Schmuckenschlager F, Furtmuller PG, Smulevich G, Obinger C. Role of the main access channel of catalase-peroxidase in catalysis. J Biol Chem. 2005;280(51):42411-42422.
-
(2005)
J Biol Chem
, vol.280
, Issue.51
, pp. 42411-42422
-
-
Jakopitsch, C.1
Droghetti, E.2
Schmuckenschlager, F.3
Furtmuller, P.G.4
Smulevich, G.5
Obinger, C.6
-
13
-
-
33745593982
-
Ligand-induced dynamical regulation of NO conversion in Mycobacterium tuberculosis truncated hemoglobin-N
-
Bidon-Chanal A, Marti MA, Crespo A, et al. Ligand-induced dynamical regulation of NO conversion in Mycobacterium tuberculosis truncated hemoglobin-N. Proteins. 2006;64(2):457-464.
-
(2006)
Proteins
, vol.64
, Issue.2
, pp. 457-464
-
-
Bidon-Chanal, A.1
Marti, M.A.2
Crespo, A.3
-
14
-
-
33846110459
-
Relationship between the size of the bottleneck 15 A from iron in the main channel and the reactivity of catalase corresponding to the molecular size of substrates
-
Hara I, Ichise N, Kojima K, et al. Relationship between the size of the bottleneck 15 A from iron in the main channel and the reactivity of catalase corresponding to the molecular size of substrates. Biochemistry. 2007;46(1):11-22.
-
(2007)
Biochemistry
, vol.46
, Issue.1
, pp. 11-22
-
-
Hara, I.1
Ichise, N.2
Kojima, K.3
-
15
-
-
34249819653
-
Dynamical regulation of ligand migration by a gate-opening molecular switch in truncated hemoglobin-N from Mycobacterium tuberculosis
-
Bidon-Chanal A, Marti MA, Estrin DA, Luque FJ. Dynamical regulation of ligand migration by a gate-opening molecular switch in truncated hemoglobin-N from Mycobacterium tuberculosis. J Am Chem Soc. 2007;129(21):6782-6788.
-
(2007)
J Am Chem Soc
, vol.129
, Issue.21
, pp. 6782-6788
-
-
Bidon-Chanal, A.1
Marti, M.A.2
Estrin, D.A.3
Luque, F.J.4
-
16
-
-
59149085214
-
Ligand migration in the truncated hemoglobin-II from Mycobacterium tuberculosis: the role of G8 tryptophan
-
Guallar V, Lu C, Borrelli K, Egawa T, Yeh SR. Ligand migration in the truncated hemoglobin-II from Mycobacterium tuberculosis: the role of G8 tryptophan. J Biol Chem. 2009;284(5):3106-3116.
-
(2009)
J Biol Chem
, vol.284
, Issue.5
, pp. 3106-3116
-
-
Guallar, V.1
Lu, C.2
Borrelli, K.3
Egawa, T.4
Yeh, S.R.5
-
17
-
-
66149112165
-
Structural characterization of the tunnels of Mycobacterium tuberculosis truncated hemoglobin N from molecular dynamics simulations
-
Daigle R, Guertin M, Lague P. Structural characterization of the tunnels of Mycobacterium tuberculosis truncated hemoglobin N from molecular dynamics simulations. Proteins. 2009;75(3):735-747.
-
(2009)
Proteins
, vol.75
, Issue.3
, pp. 735-747
-
-
Daigle, R.1
Guertin, M.2
Lague, P.3
-
18
-
-
84938980436
-
Conformational changes and allosteric communications in human serum albumin due to ligand binding
-
Ahalawat N, Murarka RK. Conformational changes and allosteric communications in human serum albumin due to ligand binding. J Biomol Struct Dyn. 2015:1-13.
-
(2015)
J Biomol Struct Dyn
, pp. 1-13
-
-
Ahalawat, N.1
Murarka, R.K.2
-
19
-
-
84928910472
-
Molecular dynamics study of naturally existing cavity couplings in proteins
-
Barbany M, Meyer T, Hospital A, et al. Molecular dynamics study of naturally existing cavity couplings in proteins. PLoS One. 2015;10(3): e0119978.
-
(2015)
PLoS One
, vol.10
, Issue.3
-
-
Barbany, M.1
Meyer, T.2
Hospital, A.3
-
20
-
-
84924386814
-
Discovery of multiple hidden allosteric sites by combining Markov state models and experiments
-
Bowman GR, Bolin ER, Hart KM, Maguire BC, Marqusee S. Discovery of multiple hidden allosteric sites by combining Markov state models and experiments. Proc Natl Acad Sci U S A. 2015;112(9): 2734-2739.
-
(2015)
Proc Natl Acad Sci U S A
, vol.112
, Issue.9
, pp. 2734-2739
-
-
Bowman, G.R.1
Bolin, E.R.2
Hart, K.M.3
Maguire, B.C.4
Marqusee, S.5
-
21
-
-
79960017777
-
Protein-DNA recognition triggered by a DNA conformational switch
-
Bouvier B, Zakrzewska K, Lavery R. Protein-DNA recognition triggered by a DNA conformational switch. Angew Chem Int Ed Engl. 2011;50(29):6516-6518.
-
(2011)
Angew Chem Int Ed Engl
, vol.50
, Issue.29
, pp. 6516-6518
-
-
Bouvier, B.1
Zakrzewska, K.2
Lavery, R.3
-
22
-
-
84861775142
-
Towards a molecular view of transcriptional control
-
Zakrzewska K, Lavery R. Towards a molecular view of transcriptional control. Curr Opin Struct Biol. 2012;22(2):160-167.
-
(2012)
Curr Opin Struct Biol
, vol.22
, Issue.2
, pp. 160-167
-
-
Zakrzewska, K.1
Lavery, R.2
-
23
-
-
11444267252
-
The relative flexibility of B-DNA and A-RNA duplexes: database analysis
-
Perez A, Noy A, Lankas F, Luque FJ, Orozco M. The relative flexibility of B-DNA and A-RNA duplexes: database analysis. Nucleic Acids Res. 2004;32(20):6144-6151.
-
(2004)
Nucleic Acids Res
, vol.32
, Issue.20
, pp. 6144-6151
-
-
Perez, A.1
Noy, A.2
Lankas, F.3
Luque, F.J.4
Orozco, M.5
-
24
-
-
14844314722
-
An analysis of core deformations in protein superfamilies
-
Leo-Macias A, Lopez-Romero P, Lupyan D, Zerbino D, Ortiz AR. An analysis of core deformations in protein superfamilies. Biophys J. 2005;88(2):1291-1299.
-
(2005)
Biophys J
, vol.88
, Issue.2
, pp. 1291-1299
-
-
Leo-Macias, A.1
Lopez-Romero, P.2
Lupyan, D.3
Zerbino, D.4
Ortiz, A.R.5
-
25
-
-
64249141496
-
Comparison of molecular dynamics and superfamily spaces of protein domain deformation
-
Velazquez-Muriel JA, Rueda M, Cuesta I, Pascual-Montano A, Orozco M, Carazo JM. Comparison of molecular dynamics and superfamily spaces of protein domain deformation. BMC Struct Biol. 2009;9:6.
-
(2009)
BMC Struct Biol
, vol.9
, pp. 6
-
-
Velazquez-Muriel, J.A.1
Rueda, M.2
Cuesta, I.3
Pascual-Montano, A.4
Orozco, M.5
Carazo, J.M.6
-
26
-
-
84876346374
-
Comparing proteins by their internal dynamics: exploring structure-function relationships beyond static structural alignments
-
Micheletti C. Comparing proteins by their internal dynamics: exploring structure-function relationships beyond static structural alignments. Phys Life Rev. 2013;10(1):1-26.
-
(2013)
Phys Life Rev
, vol.10
, Issue.1
, pp. 1-26
-
-
Micheletti, C.1
-
27
-
-
84908288276
-
Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations
-
Baxa MC, Haddadian EJ, Jumper JM, Freed KF, Sosnick TR. Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations. Proc Natl Acad Sci U S A. 2014;111(43):15396-15401.
-
(2014)
Proc Natl Acad Sci U S A
, vol.111
, Issue.43
, pp. 15396-15401
-
-
Baxa, M.C.1
Haddadian, E.J.2
Jumper, J.M.3
Freed, K.F.4
Sosnick, T.R.5
-
28
-
-
70450255797
-
Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations
-
Noe F, Schuette C, Vanden-Eijnden E, Reich L, Weikl TR. Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations. Proc Natl Acad Sci U S A. 2009;106(45):19011-19016.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, Issue.45
, pp. 19011-19016
-
-
Noe, F.1
Schuette, C.2
Vanden-Eijnden, E.3
Reich, L.4
Weikl, T.R.5
-
29
-
-
79961148664
-
The native ensemble and folding of a protein molten-globule: functional consequence of downhill folding
-
Naganathan AN, Orozco M. The native ensemble and folding of a protein molten-globule: functional consequence of downhill folding. J Am Chem Soc. 2011;133(31):12154-12161.
-
(2011)
J Am Chem Soc
, vol.133
, Issue.31
, pp. 12154-12161
-
-
Naganathan, A.N.1
Orozco, M.2
-
30
-
-
84954268575
-
Atomistic insights on protein-urea structural organization from MD simulations of a chemically denatured protein ensemble determined by NMR
-
Candotti M, Esteban-Martin S, Orozco M. Atomistic insights on protein-urea structural organization from MD simulations of a chemically denatured protein ensemble determined by NMR. FEBS J. 2012;279:531-531.
-
(2012)
FEBS J
, vol.279
, pp. 531-531
-
-
Candotti, M.1
Esteban-Martin, S.2
Orozco, M.3
-
31
-
-
82455179494
-
Understanding biomolecular motion, recognition, and allostery by use of conformational ensembles
-
Bryn Fenwick R, Esteban-Martin S, Salvatella X. Understanding biomolecular motion, recognition, and allostery by use of conformational ensembles. Eur Biophys J. 2011;40(12):1339-1355.
-
(2011)
Eur Biophys J
, vol.40
, Issue.12
, pp. 1339-1355
-
-
Bryn Fenwick, R.1
Esteban-Martin, S.2
Salvatella, X.3
-
32
-
-
0017776823
-
Dynamics of folded proteins
-
McCammon JA, Gelin BR, Karplus M. Dynamics of folded proteins. Nature. 1977;267(5612):585-590.
-
(1977)
Nature
, vol.267
, Issue.5612
, pp. 585-590
-
-
McCammon, J.A.1
Gelin, B.R.2
Karplus, M.3
-
33
-
-
0017100947
-
Theoretical studies of enzymic reactions-dielectric, electrostatic and steric stabilization of carbonium-ion in reaction of lysozyme
-
Warshel A, Levitt M. Theoretical studies of enzymic reactions-dielectric, electrostatic and steric stabilization of carbonium-ion in reaction of lysozyme. J Mol Biol. 1976;103(2):227-249.
-
(1976)
J Mol Biol
, vol.103
, Issue.2
, pp. 227-249
-
-
Warshel, A.1
Levitt, M.2
-
34
-
-
34247520870
-
Structural flexibility of the nucleosome core particle at atomic resolution studied by molecular dynamics simulation
-
Roccatano D, Barthel A, Zacharias M. Structural flexibility of the nucleosome core particle at atomic resolution studied by molecular dynamics simulation. Biopolymers. 2007;85(5-6):407-421.
-
(2007)
Biopolymers
, vol.85
, Issue.5-6
, pp. 407-421
-
-
Roccatano, D.1
Barthel, A.2
Zacharias, M.3
-
35
-
-
33847770470
-
Multiscale modeling of nucleosome dynamics
-
Sharma S, Ding F, Dokholyan NV. Multiscale modeling of nucleosome dynamics. Biophys J. 2007;92(5):1457-1470.
-
(2007)
Biophys J
, vol.92
, Issue.5
, pp. 1457-1470
-
-
Sharma, S.1
Ding, F.2
Dokholyan, N.V.3
-
36
-
-
68349152494
-
Simulation and analysis of single-ribosome translation
-
Tinoco I Jr, Wen JD. Simulation and analysis of single-ribosome translation. Phys Biol. 2009;6(2):025006.
-
(2009)
Phys Biol
, vol.6
, Issue.2
-
-
Tinoco, I.1
Wen, J.D.2
-
37
-
-
84855301491
-
A-site residues move independently from P-site residues in all-atom molecular dynamics simulations of the 70S bacterial ribosome
-
Brandman R, Brandman Y, Pande VS. A-site residues move independently from P-site residues in all-atom molecular dynamics simulations of the 70S bacterial ribosome. PLoS One. 2012; 7(1):e29377.
-
(2012)
PLoS One
, vol.7
, Issue.1
-
-
Brandman, R.1
Brandman, Y.2
Pande, V.S.3
-
38
-
-
80052787895
-
Coarse-grained representation of protein flexibility. Foundations, successes, and shortcomings
-
Christov C, editor Computational Chemistry Methods in Structural Biology. Waltham, MA: Academic Press
-
Orozco M, Orellana L, Hospital A, et al. Coarse-grained representation of protein flexibility. Foundations, successes, and shortcomings. In: Christov C, editor. Advances in Proteins Chemistry and Structural Biology, Vol 85: Computational Chemistry Methods in Structural Biology. Waltham, MA: Academic Press; 2011:183-215.
-
(2011)
Advances in Proteins Chemistry and Structural Biology
, vol.85
, pp. 183-215
-
-
Orozco, M.1
Orellana, L.2
Hospital, A.3
-
39
-
-
0033135638
-
Effective energy function for proteins in solution
-
Lazaridis T, Karplus M. Effective energy function for proteins in solution. Proteins. 1999;35(2):133-152.
-
(1999)
Proteins
, vol.35
, Issue.2
, pp. 133-152
-
-
Lazaridis, T.1
Karplus, M.2
-
40
-
-
0032968133
-
Implicit solvent models
-
Roux B, Simonson T. Implicit solvent models. Biophys Chem. 1999;78(1-2):1-20.
-
(1999)
Biophys Chem
, vol.78
, Issue.1-2
, pp. 1-20
-
-
Roux, B.1
Simonson, T.2
-
41
-
-
0034314630
-
Theoretical methods for the description of the solvent effect in biomolecular systems
-
Orozco M, Luque FJ. Theoretical methods for the description of the solvent effect in biomolecular systems. Chem Rev. 2000; 100(11):4187-4226.
-
(2000)
Chem Rev
, vol.100
, Issue.11
, pp. 4187-4226
-
-
Orozco, M.1
Luque, F.J.2
-
42
-
-
0033654297
-
Generalized born models of macromolecular solvation effects
-
Bashford D, Case DA. Generalized born models of macromolecular solvation effects. Ann Rev Phys Chem. 2000;51:129-152.
-
(2000)
Ann Rev Phys Chem
, vol.51
, pp. 129-152
-
-
Bashford, D.1
Case, D.A.2
-
43
-
-
40549111613
-
FACTS: fast analytical continuum treatment of solvation
-
Haberthuer U, Caflisch A. FACTS: fast analytical continuum treatment of solvation. J Comput Chem. 2008;29(5):701-715.
-
(2008)
J Comput Chem
, vol.29
, Issue.5
, pp. 701-715
-
-
Haberthuer, U.1
Caflisch, A.2
-
44
-
-
77950130534
-
Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber
-
Luchko T, Gusarov S, Roe DR, et al. Three-dimensional molecular theory of solvation coupled with molecular dynamics in Amber. J Chem Theory Comput. 2010;6(3):607-624.
-
(2010)
J Chem Theory Comput
, vol.6
, Issue.3
, pp. 607-624
-
-
Luchko, T.1
Gusarov, S.2
Roe, D.R.3
-
45
-
-
80052811746
-
Advances in implicit models of water solvent to compute conformational free energy and molecular dynamics of proteins at constant pH
-
Vorobjev YN. Advances in implicit models of water solvent to compute conformational free energy and molecular dynamics of proteins at constant pH. Adv Protein Chem Struct Biol. 2011;85:281-322.
-
(2011)
Adv Protein Chem Struct Biol
, vol.85
, pp. 281-322
-
-
Vorobjev, Y.N.1
-
46
-
-
84900836393
-
Design and application of implicit solvent models in biomolecular simulations
-
Kleinjung J, Fraternali F. Design and application of implicit solvent models in biomolecular simulations. Curr Opin Struct Biol. 2014;25: 126-134.
-
(2014)
Curr Opin Struct Biol
, vol.25
, pp. 126-134
-
-
Kleinjung, J.1
Fraternali, F.2
-
47
-
-
84924763044
-
Speed of conformational change: comparing explicit and implicit solvent molecular dynamics simulations
-
Anandakrishnan R, Drozdetski A, Walker RC, Onufriev AV. Speed of conformational change: comparing explicit and implicit solvent molecular dynamics simulations. Biophys J. 2015;108(5):1153-1164.
-
(2015)
Biophys J
, vol.108
, Issue.5
, pp. 1153-1164
-
-
Anandakrishnan, R.1
Drozdetski, A.2
Walker, R.C.3
Onufriev, A.V.4
-
48
-
-
84990424072
-
A consistent empirical potential for water-protein interactions
-
Hermans J, Berendsen HJC, Vangunsteren WF, Postma JPM. A consistent empirical potential for water-protein interactions. Biopolymers. 1984;23(8):1513-1518.
-
(1984)
Biopolymers
, vol.23
, Issue.8
, pp. 1513-1518
-
-
Hermans, J.1
Berendsen, H.J.C.2
Vangunsteren, W.F.3
Postma, J.P.M.4
-
49
-
-
6344260593
-
An all-atom empirical energy function for the simulation of nucleic-acids
-
Mackerell AD, Wiorkiewiczkuczera J, Karplus M. An all-atom empirical energy function for the simulation of nucleic-acids. J Am Chem Soc. 1995;117(48):11946-11975.
-
(1995)
J Am Chem Soc
, vol.117
, Issue.48
, pp. 11946-11975
-
-
Mackerell, A.D.1
Wiorkiewiczkuczera, J.2
Karplus, M.3
-
50
-
-
0000438266
-
Parametrization of GROMOS force field for oligosaccharides and assessment of efficiency of molecular dynamics simulations
-
Ott KH, Meyer B. Parametrization of GROMOS force field for oligosaccharides and assessment of efficiency of molecular dynamics simulations. J Comput Chem. 1996;17(8):1068-1084.
-
(1996)
J Comput Chem
, vol.17
, Issue.8
, pp. 1068-1084
-
-
Ott, K.H.1
Meyer, B.2
-
51
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell AD, Bashford D, Bellott M, et al. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B. 1998;102(18):3586-3616.
-
(1998)
J Phys Chem B
, vol.102
, Issue.18
, pp. 3586-3616
-
-
MacKerell, A.D.1
Bashford, D.2
Bellott, M.3
-
52
-
-
0029011701
-
A 2nd generation force-field for the simulation of proteins, nucleic-acids, and organic-molecules
-
Cornell WD, Cieplak P, Bayly CI, et al. A 2nd generation force-field for the simulation of proteins, nucleic-acids, and organic-molecules. J Am Chem Soc. 1995;117(19):5179-5197.
-
(1995)
J Am Chem Soc
, vol.117
, Issue.19
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, C.I.3
-
53
-
-
0035913529
-
Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides
-
Kaminski GA, Friesner RA, Tirado-Rives J, Jorgensen WL. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J Phys Chem B. 2001;105(28):6474-6487.
-
(2001)
J Phys Chem B
, vol.105
, Issue.28
, pp. 6474-6487
-
-
Kaminski, G.A.1
Friesner, R.A.2
Tirado-Rives, J.3
Jorgensen, W.L.4
-
55
-
-
42449095007
-
Towards a molecular dynamics consensus view of B-DNA flexibility
-
Perez A, Lankas F, Luque FJ, Orozco M. Towards a molecular dynamics consensus view of B-DNA flexibility. Nucleic Acids Res. 2008; 36(7):2379-2394.
-
(2008)
Nucleic Acids Res
, vol.36
, Issue.7
, pp. 2379-2394
-
-
Perez, A.1
Lankas, F.2
Luque, F.J.3
Orozco, M.4
-
57
-
-
67650500988
-
CHARMM: the biomolecular simulation program
-
Brooks BR, Brooks CL 3rd, Mackerell AD Jr, et al. CHARMM: the biomolecular simulation program. J Comput Chem. 2009;30(10): 1545-1614.
-
(2009)
J Comput Chem
, vol.30
, Issue.10
, pp. 1545-1614
-
-
Brooks, B.R.1
Brooks, C.L.2
Mackerell, A.D.3
-
58
-
-
46249092554
-
GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation
-
Hess B, Kutzner C, van der Spoel D, Lindahl E. GROMACS 4: algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput. 2008;4(3):435-447.
-
(2008)
J Chem Theory Comput
, vol.4
, Issue.3
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
van der Spoel, D.3
Lindahl, E.4
-
59
-
-
8344276781
-
NAMD: a parallel, object oriented molecular dynamics program
-
Nelson MT, Humphrey W, Gursoy A, et al. NAMD: a parallel, object oriented molecular dynamics program. Int J Supercomput Appl High Perform Comput. 1996;10(4):251-268.
-
(1996)
Int J Supercomput Appl High Perform Comput
, vol.10
, Issue.4
, pp. 251-268
-
-
Nelson, M.T.1
Humphrey, W.2
Gursoy, A.3
-
61
-
-
67650099787
-
ACEMD: accelerating biomolecular dynamics in the microsecond time scale
-
Harvey MJ, Giupponi G, De Fabritiis G. ACEMD: accelerating biomolecular dynamics in the microsecond time scale. J Chem Theory Comput. 2009;5(6):1632-1639.
-
(2009)
J Chem Theory Comput
, vol.5
, Issue.6
, pp. 1632-1639
-
-
Harvey, M.J.1
Giupponi, G.2
De Fabritiis, G.3
-
62
-
-
49849097184
-
Building Markov state models along pathways to determine free energies and rates of transitions
-
Pan AC, Roux B. Building Markov state models along pathways to determine free energies and rates of transitions. J Chem Phys. 2008; 129(6):064107.
-
(2008)
J Chem Phys
, vol.129
, Issue.6
-
-
Pan, A.C.1
Roux, B.2
-
63
-
-
63449118443
-
Using generalized ensemble simulations and Markov state models to identify conformational states
-
Bowman GR, Huang X, Pande VS. Using generalized ensemble simulations and Markov state models to identify conformational states. Methods. 2009;49(2):197-201.
-
(2009)
Methods
, vol.49
, Issue.2
, pp. 197-201
-
-
Bowman, G.R.1
Huang, X.2
Pande, V.S.3
-
64
-
-
84900548447
-
Markov state models of biomolecular conformational dynamics
-
Chodera JD, Noe F. Markov state models of biomolecular conformational dynamics. Curr Opin Struct Biol. 2014;25:135-144.
-
(2014)
Curr Opin Struct Biol
, vol.25
, pp. 135-144
-
-
Chodera, J.D.1
Noe, F.2
-
65
-
-
84896988865
-
Application of Markov state models to simulate long timescale dynamics of biological macromolecules
-
Da LT, Sheong FK, Silva DA, Huang X. Application of Markov state models to simulate long timescale dynamics of biological macromolecules. Adv Exp Med Biol. 2014;805:29-66.
-
(2014)
Adv Exp Med Biol
, vol.805
, pp. 29-66
-
-
Da, L.T.1
Sheong, F.K.2
Silva, D.A.3
Huang, X.4
-
66
-
-
76149136021
-
Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39)
-
Voelz VA, Bowman GR, Beauchamp K, Pande VS. Molecular simulation of ab initio protein folding for a millisecond folder NTL9(1-39). J Am Chem Soc. 2010;132(5):1526-1528.
-
(2010)
J Am Chem Soc
, vol.132
, Issue.5
, pp. 1526-1528
-
-
Voelz, V.A.1
Bowman, G.R.2
Beauchamp, K.3
Pande, V.S.4
-
67
-
-
79960007037
-
Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations
-
Buch I, Giorgino T, De Fabritiis G. Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations. Proc Natl Acad Sci U S A. 2011;108(25):10184-10189.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, Issue.25
, pp. 10184-10189
-
-
Buch, I.1
Giorgino, T.2
De Fabritiis, G.3
-
68
-
-
2942548219
-
Reconstructing the density of states by history-dependent metadynamics
-
Micheletti C, Laio A, Parrinello M. Reconstructing the density of states by history-dependent metadynamics. Phys Rev Lett. 2004; 92(17):170601.
-
(2004)
Phys Rev Lett
, vol.92
, Issue.17
-
-
Micheletti, C.1
Laio, A.2
Parrinello, M.3
-
69
-
-
17444412296
-
Assessing the accuracy of metadynamics
-
Laio A, Rodriguez-Fortea A, Gervasio FL, Ceccarelli M, Parrinello M. Assessing the accuracy of metadynamics. J Phys Chem B. 2005; 109(14):6714-6721.
-
(2005)
J Phys Chem B
, vol.109
, Issue.14
, pp. 6714-6721
-
-
Laio, A.1
Rodriguez-Fortea, A.2
Gervasio, F.L.3
Ceccarelli, M.4
Parrinello, M.5
-
70
-
-
33644769684
-
Efficient reconstruction of complex free energy landscapes by multiple walkers metadynamics
-
Raiteri P, Laio A, Gervasio FL, Micheletti C, Parrinello M. Efficient reconstruction of complex free energy landscapes by multiple walkers metadynamics. J Phys Chem B. 2006;110(8):3533-3539.
-
(2006)
J Phys Chem B
, vol.110
, Issue.8
, pp. 3533-3539
-
-
Raiteri, P.1
Laio, A.2
Gervasio, F.L.3
Micheletti, C.4
Parrinello, M.5
-
72
-
-
84898060883
-
WExplore: hierarchical exploration of high-dimensional spaces using the weighted ensemble algorithm
-
Dickson A, Brooks CL. WExplore: hierarchical exploration of high-dimensional spaces using the weighted ensemble algorithm. J Phys Chem B. 2014;118(13):3532-3542.
-
(2014)
J Phys Chem B
, vol.118
, Issue.13
, pp. 3532-3542
-
-
Dickson, A.1
Brooks, C.L.2
-
73
-
-
84908234198
-
AWE-WQ: fast-forwarding molecular dynamics using the accelerated weighted ensemble
-
Abdul-Wahid B, Feng H, Rajan D, et al. AWE-WQ: fast-forwarding molecular dynamics using the accelerated weighted ensemble. J Chem Inf Model. 2014;54(10):3033-3043.
-
(2014)
J Chem Inf Model
, vol.54
, Issue.10
, pp. 3033-3043
-
-
Abdul-Wahid, B.1
Feng, H.2
Rajan, D.3
-
74
-
-
84923205901
-
Towards fast, rigorous and efficient conformational sampling of biomolecules: advances in accelerated molecular dynamics
-
Doshi U, Hamelberg D. Towards fast, rigorous and efficient conformational sampling of biomolecules: advances in accelerated molecular dynamics. Biochim Biophys Acta. 2015;1850(5):878-888.
-
(2015)
Biochim Biophys Acta
, vol.1850
, Issue.5
, pp. 878-888
-
-
Doshi, U.1
Hamelberg, D.2
-
75
-
-
84933051465
-
Accelerated molecular dynamics simulations of protein folding
-
Miao Y, Feixas F, Eun C, McCammon JA. Accelerated molecular dynamics simulations of protein folding. J Comput Chem. 2015; 36(20):1536-1549.
-
(2015)
J Comput Chem
, vol.36
, Issue.20
, pp. 1536-1549
-
-
Miao, Y.1
Feixas, F.2
Eun, C.3
McCammon, J.A.4
-
76
-
-
1642546396
-
Atomic simulations of protein folding, using the replica exchange algorithm
-
Nymeyer H, Gnanakaran S, Garcia AE. Atomic simulations of protein folding, using the replica exchange algorithm. Methods Enzymol. 2004;383:119-149.
-
(2004)
Methods Enzymol
, vol.383
, pp. 119-149
-
-
Nymeyer, H.1
Gnanakaran, S.2
Garcia, A.E.3
-
77
-
-
34250323902
-
Molecular dynamics simulations using temperature-enhanced essential dynamics replica exchange
-
Kubitzki MB, de Groot BL. Molecular dynamics simulations using temperature-enhanced essential dynamics replica exchange. Biophys J. 2007;92(12):4262-4270.
-
(2007)
Biophys J
, vol.92
, Issue.12
, pp. 4262-4270
-
-
Kubitzki, M.B.1
de Groot, B.L.2
-
78
-
-
80052803759
-
Computing alchemical free energy differences with Hamiltonian replica exchange molecular dynamics (H-REMD) simulations
-
Meng Y, Dashti DS, Roitberg AE. Computing alchemical free energy differences with Hamiltonian replica exchange molecular dynamics (H-REMD) simulations. J Chem Theory Comput. 2011; 7(9):2721-2727.
-
(2011)
J Chem Theory Comput
, vol.7
, Issue.9
, pp. 2721-2727
-
-
Meng, Y.1
Dashti, D.S.2
Roitberg, A.E.3
-
79
-
-
0036606101
-
Simulating proteins at constant pH: an approach combining molecular dynamics and Monte Carlo simulation
-
Burgi R, Kollman PA, Van Gunsteren WF. Simulating proteins at constant pH: an approach combining molecular dynamics and Monte Carlo simulation. Proteins. 2002;47(4):469-480.
-
(2002)
Proteins
, vol.47
, Issue.4
, pp. 469-480
-
-
Burgi, R.1
Kollman, P.A.2
Van Gunsteren, W.F.3
-
80
-
-
34247591986
-
Molecular simulation with variable protonation states at constant pH
-
Stern HA. Molecular simulation with variable protonation states at constant pH. J Chem Phys. 2007;126(16):164112.
-
(2007)
J Chem Phys
, vol.126
, Issue.16
-
-
Stern, H.A.1
-
81
-
-
0030970305
-
Simulation of protein conformational freedom as a function of pH: constant-pH molecular dynamics using implicit titration
-
Baptista AM, Martel PJ, Petersen SB. Simulation of protein conformational freedom as a function of pH: constant-pH molecular dynamics using implicit titration. Proteins. 1997;27(4):523-544.
-
(1997)
Proteins
, vol.27
, Issue.4
, pp. 523-544
-
-
Baptista, A.M.1
Martel, P.J.2
Petersen, S.B.3
-
82
-
-
84902127084
-
Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism
-
Goh GB, Hulbert BS, Zhou H, Brooks CL. Constant pH molecular dynamics of proteins in explicit solvent with proton tautomerism. Proteins. 2014;82(7):1319-1331.
-
(2014)
Proteins
, vol.82
, Issue.7
, pp. 1319-1331
-
-
Goh, G.B.1
Hulbert, B.S.2
Zhou, H.3
Brooks, C.L.4
-
83
-
-
81055155931
-
pH replica-exchange method based on discrete protonation states
-
Itoh SG, Damjanovic A, Brooks BR. pH replica-exchange method based on discrete protonation states. Proteins. 2011;79(12):3420-3436.
-
(2011)
Proteins
, vol.79
, Issue.12
, pp. 3420-3436
-
-
Itoh, S.G.1
Damjanovic, A.2
Brooks, B.R.3
-
84
-
-
78149459697
-
MoDEL (molecular dynamics extended library): a database of atomistic molecular dynamics trajectories
-
Meyer T, D'Abramo M, Hospital A, et al. MoDEL (molecular dynamics extended library): a database of atomistic molecular dynamics trajectories. Structure. 2010;18(11):1399-1409.
-
(2010)
Structure
, vol.18
, Issue.11
, pp. 1399-1409
-
-
Meyer, T.1
D'Abramo, M.2
Hospital, A.3
-
85
-
-
47149096704
-
CHARMM-GUI: a web-based graphical user interface for CHARMM
-
Jo S, Kim T, Iyer VG, Im W. CHARMM-GUI: a web-based graphical user interface for CHARMM. J Comput Chem. 2008;29(11):1859-1865.
-
(2008)
J Comput Chem
, vol.29
, Issue.11
, pp. 1859-1865
-
-
Jo, S.1
Kim, T.2
Iyer, V.G.3
Im, W.4
-
86
-
-
54249092923
-
CHARMMing: a new, flexible web portal for CHARMM
-
Miller BT, Singh RP, Klauda JB, Hodoscek M, Brooks BR, Woodcock HL 3rd. CHARMMing: a new, flexible web portal for CHARMM. J Chem Inf Model. 2008;48(9):1920-1929.
-
(2008)
J Chem Inf Model
, vol.48
, Issue.9
, pp. 1920-1929
-
-
Miller, B.T.1
Singh, R.P.2
Klauda, J.B.3
Hodoscek, M.4
Brooks, B.R.5
Woodcock, H.L.6
-
87
-
-
34249704620
-
GUIMACS-a Java based front end for GROMACS
-
Kota P. GUIMACS-a Java based front end for GROMACS. In Silico Biol. 2007;7(1):95-99.
-
(2007)
In Silico Biol
, vol.7
, Issue.1
, pp. 95-99
-
-
Kota, P.1
-
88
-
-
82755197570
-
Gromita: a fully integrated graphical user interface to gromacs 4
-
Sellis D, Vlachakis D, Vlassi M. Gromita: a fully integrated graphical user interface to gromacs 4. Bioinform Biol Insights. 2009;3:99-102.
-
(2009)
Bioinform Biol Insights
, vol.3
, pp. 99-102
-
-
Sellis, D.1
Vlachakis, D.2
Vlassi, M.3
-
89
-
-
70350508192
-
jSimMacs for GROMACS: a Java application for advanced molecular dynamics simulations with remote access capability
-
Roopra S, Knapp B, Omasits U, Schreiner W. jSimMacs for GROMACS: a Java application for advanced molecular dynamics simulations with remote access capability. J Chem Inf Model. 2009; 49(10):2412-2417.
-
(2009)
J Chem Inf Model
, vol.49
, Issue.10
, pp. 2412-2417
-
-
Roopra, S.1
Knapp, B.2
Omasits, U.3
Schreiner, W.4
-
91
-
-
84860456767
-
MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations
-
Hospital A, Andrio P, Fenollosa C, Cicin-Sain D, Orozco M, Gelpi JL. MDWeb and MDMoby: an integrated web-based platform for molecular dynamics simulations. Bioinformatics. 2012;28(9):1278-1279.
-
(2012)
Bioinformatics
, vol.28
, Issue.9
, pp. 1278-1279
-
-
Hospital, A.1
Andrio, P.2
Fenollosa, C.3
Cicin-Sain, D.4
Orozco, M.5
Gelpi, J.L.6
-
92
-
-
73649152457
-
Allosteric proteins and cellular control systems
-
Monod J, Changeux JP, Jacob F. Allosteric proteins and cellular control systems. J Mol Biol. 1963;6(4):306-329.
-
(1963)
J Mol Biol
, vol.6
, Issue.4
, pp. 306-329
-
-
Monod, J.1
Changeux, J.P.2
Jacob, F.3
-
93
-
-
78651189765
-
On nature of allosteric transitions-a plausible model
-
Monod J, Wyman J, Changeux JP. On nature of allosteric transitions-a plausible model. J Mol Biol. 1965;12(1):88-118.
-
(1965)
J Mol Biol
, vol.12
, Issue.1
, pp. 88-118
-
-
Monod, J.1
Wyman, J.2
Changeux, J.P.3
-
94
-
-
0013863816
-
Comparison of experimental binding data and theoretical models in proteins containing subunits
-
Koshland DE, Nemethy G, Filmer D. Comparison of experimental binding data and theoretical models in proteins containing subunits. Biochemistry. 1966;5(1):365-385.
-
(1966)
Biochemistry
, vol.5
, Issue.1
, pp. 365-385
-
-
Koshland, D.E.1
Nemethy, G.2
Filmer, D.3
-
95
-
-
36849048228
-
Intrinsic motions along an enzymatic reaction trajectory
-
Henzler-Wildman KA, Thai V, Lei M, et al. Intrinsic motions along an enzymatic reaction trajectory. Nature. 2007;450(7171):838-844.
-
(2007)
Nature
, vol.450
, Issue.7171
, pp. 838-844
-
-
Henzler-Wildman, K.A.1
Thai, V.2
Lei, M.3
-
96
-
-
84869073773
-
Finding conformational transition pathways from discrete molecular dynamics simulations
-
Sfriso P, Emperador A, Orellana L, Hospital A, Lluis Gelpi J, Orozco M. Finding conformational transition pathways from discrete molecular dynamics simulations. J Chem Theory Comput. 2012; 8(11):4707-4718.
-
(2012)
J Chem Theory Comput
, vol.8
, Issue.11
, pp. 4707-4718
-
-
Sfriso, P.1
Emperador, A.2
Orellana, L.3
Hospital, A.4
Lluis Gelpi, J.5
Orozco, M.6
-
97
-
-
84880986455
-
Exploration of conformational transition pathways from coarse-grained simulations
-
Sfriso P, Hospital A, Emperador A, Orozco M. Exploration of conformational transition pathways from coarse-grained simulations. Bioinformatics. 2013;29(16):1980-1986.
-
(2013)
Bioinformatics
, vol.29
, Issue.16
, pp. 1980-1986
-
-
Sfriso, P.1
Hospital, A.2
Emperador, A.3
Orozco, M.4
-
98
-
-
0036708474
-
Efficient generation of feasible pathways for protein conformational transitions
-
Kim MK, Jernigan RL, Chirikjian GS. Efficient generation of feasible pathways for protein conformational transitions. Biophys J. 2002;83(3):1620-1630.
-
(2002)
Biophys J
, vol.83
, Issue.3
, pp. 1620-1630
-
-
Kim, M.K.1
Jernigan, R.L.2
Chirikjian, G.S.3
-
99
-
-
25844431698
-
Coarse-grained normal mode analysis in structural biology
-
Bahar I, Rader AJ. Coarse-grained normal mode analysis in structural biology. Curr Opin Struct Biol. 2005;15(5):586-592.
-
(2005)
Curr Opin Struct Biol
, vol.15
, Issue.5
, pp. 586-592
-
-
Bahar, I.1
Rader, A.J.2
-
100
-
-
77956593836
-
Approaching elastic network models to molecular dynamics flexibility
-
Orellana L, Rueda M, Ferrer-Costa C, Lopez-Blanco JR, Chacon P, Orozco M. Approaching elastic network models to molecular dynamics flexibility. J Chem Theory Comput. 2010;6(9):2910-2923.
-
(2010)
J Chem Theory Comput
, vol.6
, Issue.9
, pp. 2910-2923
-
-
Orellana, L.1
Rueda, M.2
Ferrer-Costa, C.3
Lopez-Blanco, J.R.4
Chacon, P.5
Orozco, M.6
-
101
-
-
84954268576
-
Understanding protein dynamics with coarse-grained models: from structures to disease
-
Orellana L, Orozco M. Understanding protein dynamics with coarse-grained models: from structures to disease. FEBS J. 2012;279: 528-528.
-
(2012)
FEBS J
, vol.279
, pp. 528-528
-
-
Orellana, L.1
Orozco, M.2
-
102
-
-
0027794972
-
Targeted molecular-dynamics simulation of conformational change-application to the T-R transition in insulin
-
Schlitter J, Engels M, Kruger P, Jacoby E, Wollmer A. Targeted molecular-dynamics simulation of conformational change-application to the T-R transition in insulin. Mol Simul. 1993;10(2-6):291-308.
-
(1993)
Mol Simul
, vol.10
, Issue.2-6
, pp. 291-308
-
-
Schlitter, J.1
Engels, M.2
Kruger, P.3
Jacoby, E.4
Wollmer, A.5
-
103
-
-
0035085863
-
Extending the capabilities of targeted molecular dynamics: simulation of a large conformational transition in plasminogen activator inhibitor 1
-
Kruger P, Verheyden S, Declerck PJ, Engelborghs Y. Extending the capabilities of targeted molecular dynamics: simulation of a large conformational transition in plasminogen activator inhibitor 1. Protein Sci. 2001;10(4):798-808.
-
(2001)
Protein Sci
, vol.10
, Issue.4
, pp. 798-808
-
-
Kruger, P.1
Verheyden, S.2
Declerck, P.J.3
Engelborghs, Y.4
-
104
-
-
34249904963
-
Targeted molecular dynamics simulation studies of binding and conformational changes in E. coli MurD
-
Perdih A, Kotnik M, Hodoscek M, Solmajer T. Targeted molecular dynamics simulation studies of binding and conformational changes in E. coli MurD. Proteins. 2007;68(1):243-254.
-
(2007)
Proteins
, vol.68
, Issue.1
, pp. 243-254
-
-
Perdih, A.1
Kotnik, M.2
Hodoscek, M.3
Solmajer, T.4
-
105
-
-
84930867419
-
Understanding allosteric interactions in G protein-coupled receptors using supervised molecular dynamics: a prototype study analysing the human A3 adenosine receptor positive allosteric modulator LUF6000
-
Deganutti G, Cuzzolin A, Ciancetta A, Moro S. Understanding allosteric interactions in G protein-coupled receptors using supervised molecular dynamics: a prototype study analysing the human A3 adenosine receptor positive allosteric modulator LUF6000. Bioorg Med Chem. 2015;23(14):4065-4071.
-
(2015)
Bioorg Med Chem
, vol.23
, Issue.14
, pp. 4065-4071
-
-
Deganutti, G.1
Cuzzolin, A.2
Ciancetta, A.3
Moro, S.4
-
106
-
-
84873292211
-
Architecture and membrane interactions of the EGF receptor
-
Arkhipov A, Shan Y, Das R, et al. Architecture and membrane interactions of the EGF receptor. Cell. 2013;152(3):557-569.
-
(2013)
Cell
, vol.152
, Issue.3
, pp. 557-569
-
-
Arkhipov, A.1
Shan, Y.2
Das, R.3
-
107
-
-
64649101249
-
Long-timescale molecular dynamics simulations of protein structure and function
-
Klepeis JL, Lindorff-Larsen K, Dror RO, Shaw DE. Long-timescale molecular dynamics simulations of protein structure and function. Curr Opin Struct Biol. 2009;19(2):120-127.
-
(2009)
Curr Opin Struct Biol
, vol.19
, Issue.2
, pp. 120-127
-
-
Klepeis, J.L.1
Lindorff-Larsen, K.2
Dror, R.O.3
Shaw, D.E.4
-
108
-
-
84903863906
-
Statistical allosteric coupling to the active site indole ring flip equilibria in the FK506-binding domain
-
Anderson JS, Mustafi SM, Hernández G, LeMaster DM. Statistical allosteric coupling to the active site indole ring flip equilibria in the FK506-binding domain. Biophys Chem. 2014;192:41-48.
-
(2014)
Biophys Chem
, vol.192
, pp. 41-48
-
-
Anderson, J.S.1
Mustafi, S.M.2
Hernández, G.3
LeMaster, D.M.4
-
109
-
-
84935009324
-
Conformational processing of oncogenic v-Src kinase by the molecular chaperone Hsp90
-
Boczek EE, Reefschläger LG, Dehling M, et al. Conformational processing of oncogenic v-Src kinase by the molecular chaperone Hsp90. Proc Natl Acad Sci U S A. 2015;112(25):E3189-E3198.
-
(2015)
Proc Natl Acad Sci U S A
, vol.112
, Issue.25
, pp. E3189-E3198
-
-
Boczek, E.E.1
Reefschläger, L.G.2
Dehling, M.3
-
110
-
-
0024293473
-
Crystallization of a ternary complex of lactate-dehydrogenase from Bacillus stearothermophilus
-
Wigley DB, Muirhead H, Gamblin SJ, Holbrook JJ. Crystallization of a ternary complex of lactate-dehydrogenase from Bacillus stearothermophilus. J Mol Biol. 1988;204(4):1041-1043.
-
(1988)
J Mol Biol
, vol.204
, Issue.4
, pp. 1041-1043
-
-
Wigley, D.B.1
Muirhead, H.2
Gamblin, S.J.3
Holbrook, J.J.4
-
111
-
-
0026512524
-
Structure of a ternary complex of an allosteric lactate-dehydrogenase from Bacillus stearothermophilus at 2.5 A resolution
-
Wigley DB, Gamblin SJ, Turkenburg JP, et al. Structure of a ternary complex of an allosteric lactate-dehydrogenase from Bacillus stearothermophilus at 2.5 A resolution. J Mol Biol. 1992;223(1):317-335.
-
(1992)
J Mol Biol
, vol.223
, Issue.1
, pp. 317-335
-
-
Wigley, D.B.1
Gamblin, S.J.2
Turkenburg, J.P.3
-
112
-
-
0028362842
-
Allosteric activation in Bacillus stearothermophilus lactate-dehydrogenase investigated by an x-ray crystallographic analysis of a mutant designed to prevent tetramerization of the enzyme
-
Cameron AD, Roper DI, Moreton KM, Muirhead H, Holbrook JJ, Wigley DB. Allosteric activation in Bacillus stearothermophilus lactate-dehydrogenase investigated by an x-ray crystallographic analysis of a mutant designed to prevent tetramerization of the enzyme. J Mol Biol. 1994;238(4):615-625.
-
(1994)
J Mol Biol
, vol.238
, Issue.4
, pp. 615-625
-
-
Cameron, A.D.1
Roper, D.I.2
Moreton, K.M.3
Muirhead, H.4
Holbrook, J.J.5
Wigley, D.B.6
-
113
-
-
0026669091
-
Construction of a stable dimer of Bacillus stearothermophilus lactate dehydrogenase
-
Jackson RM, Gelpi JL, Cortes A, et al. Construction of a stable dimer of Bacillus stearothermophilus lactate dehydrogenase. Biochemistry. 1992;31(35):8307-8314.
-
(1992)
Biochemistry
, vol.31
, Issue.35
, pp. 8307-8314
-
-
Jackson, R.M.1
Gelpi, J.L.2
Cortes, A.3
-
114
-
-
77950831084
-
Refinement of ensembles describing unstructured proteins using NMR residual dipolar couplings
-
Esteban-Martin S, Bryn Fenwick R, Salvatella X. Refinement of ensembles describing unstructured proteins using NMR residual dipolar couplings. J Am Chem Soc. 2010;132(13):4626-4632.
-
(2010)
J Am Chem Soc
, vol.132
, Issue.13
, pp. 4626-4632
-
-
Esteban-Martin, S.1
Bryn Fenwick, R.2
Salvatella, X.3
-
115
-
-
0001858251
-
Application of a theory of enzyme specificity to protein synthesis
-
Koshland DE. Application of a theory of enzyme specificity to protein synthesis. Proc Natl Acad Sci U S A. 1958;44(2):98-104.
-
(1958)
Proc Natl Acad Sci U S A
, vol.44
, Issue.2
, pp. 98-104
-
-
Koshland, D.E.1
-
116
-
-
84869987609
-
Conformer generation with OMEGA: learning from the data set and the analysis of failures
-
Hawkins PCD, Nicholls A. Conformer generation with OMEGA: learning from the data set and the analysis of failures. J Chem Inf Model. 2012;52(11):2919-2936.
-
(2012)
J Chem Inf Model
, vol.52
, Issue.11
, pp. 2919-2936
-
-
Hawkins, P.C.D.1
Nicholls, A.2
-
117
-
-
84954213355
-
A script for automated 3-dimentional structure generation and conformer search from 2-dimentional chemical drawing
-
Ishikawa Y. A script for automated 3-dimentional structure generation and conformer search from 2-dimentional chemical drawing. Bioinformation. 2013;9(19):988-992.
-
(2013)
Bioinformation
, vol.9
, Issue.19
, pp. 988-992
-
-
Ishikawa, Y.1
-
118
-
-
84893393300
-
ALFA: Automatic ligand flexibility assignment
-
Klett J, Cortes-Cabrera A, Gil-Redondo R, Gago F, Morreale A. ALFA: Automatic ligand flexibility assignment. J Chem Inf Model. 2014;54(1):314-323.
-
(2014)
J Chem Inf Model
, vol.54
, Issue.1
, pp. 314-323
-
-
Klett, J.1
Cortes-Cabrera, A.2
Gil-Redondo, R.3
Gago, F.4
Morreale, A.5
-
119
-
-
12144289984
-
Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy
-
Friesner RA, Banks JL, Murphy RB, et al. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem. 2004;47(7):1739-1749.
-
(2004)
J Med Chem
, vol.47
, Issue.7
, pp. 1739-1749
-
-
Friesner, R.A.1
Banks, J.L.2
Murphy, R.B.3
-
120
-
-
37349085453
-
A flexible approach to induced fit docking
-
Nabuurs SB, Wagener M, De Vlieg J. A flexible approach to induced fit docking. J Med Chem. 2007;50(26):6507-6518.
-
(2007)
J Med Chem
, vol.50
, Issue.26
, pp. 6507-6518
-
-
Nabuurs, S.B.1
Wagener, M.2
De Vlieg, J.3
-
121
-
-
34147107263
-
PELE: protein energy landscape exploration. A novel Monte Carlo based technique
-
Borrelli KW, Vitalis A, Alcantara R, Guallar V. PELE: protein energy landscape exploration. A novel Monte Carlo based technique. J Chem Theory Comput. 2005;1(6):1304-1311.
-
(2005)
J Chem Theory Comput
, vol.1
, Issue.6
, pp. 1304-1311
-
-
Borrelli, K.W.1
Vitalis, A.2
Alcantara, R.3
Guallar, V.4
-
122
-
-
84873694997
-
Efficient relaxation of protein-protein interfaces by discrete molecular dynamics simulations
-
Emperador A, Solernou A, Sfriso P, et al. Efficient relaxation of protein-protein interfaces by discrete molecular dynamics simulations. J Chem Theory Comput. 2013;9(2):1222-1229.
-
(2013)
J Chem Theory Comput
, vol.9
, Issue.2
, pp. 1222-1229
-
-
Emperador, A.1
Solernou, A.2
Sfriso, P.3
-
123
-
-
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(10):539-546.
-
(2010)
Trends Biochem Sci
, vol.35
, Issue.10
, pp. 539-546
-
-
Csermely, P.1
Palotai, R.2
Nussinov, R.3
-
124
-
-
30044434744
-
Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state
-
Tobi D, Bahar I. Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state. Proc Natl Acad Sci U S A. 2005;102(52):18908-18913.
-
(2005)
Proc Natl Acad Sci U S A
, vol.102
, Issue.52
, pp. 18908-18913
-
-
Tobi, D.1
Bahar, I.2
-
125
-
-
77953923520
-
Structural ensemble in computational drug screening
-
Fukunishi Y. Structural ensemble in computational drug screening. Exp Opin Drug Metab Toxicol. 2010;6(7):835-849.
-
(2010)
Exp Opin Drug Metab Toxicol
, vol.6
, Issue.7
, pp. 835-849
-
-
Fukunishi, Y.1
-
126
-
-
84855955506
-
A molecular dynamics ensemble-based approach for the mapping of druggable binding sites
-
Ivetac A, McCammon JA. A molecular dynamics ensemble-based approach for the mapping of druggable binding sites. Methods Mol Biol. 2011;819:3-12.
-
(2011)
Methods Mol Biol
, vol.819
, pp. 3-12
-
-
Ivetac, A.1
McCammon, J.A.2
-
127
-
-
84896689539
-
Ligand docking simulations by generalized-ensemble algorithms
-
KarabenchevaChristova T, editor, Waltham, MA: Academic Press
-
Okamoto Y, Kokubo H, Tanaka T. Ligand docking simulations by generalized-ensemble algorithms. In: KarabenchevaChristova T, editor. Dynamics of Proteins and Nucleic Acids. Vol 92. Waltham, MA: Academic Press; 2013:63-91.
-
(2013)
Dynamics of Proteins and Nucleic Acids
, vol.92
, pp. 63-91
-
-
Okamoto, Y.1
Kokubo, H.2
Tanaka, T.3
-
128
-
-
84929018196
-
SEABED: Small molEcule activity scanner weB servicE baseD
-
Fenollosa C, Oton M, Andrio P, Cortes J, Orozco M, Goni JR. SEABED: Small molEcule activity scanner weB servicE baseD. Bioinformatics. 2015;31(5):773-775.
-
(2015)
Bioinformatics
, vol.31
, Issue.5
, pp. 773-775
-
-
Fenollosa, C.1
Oton, M.2
Andrio, P.3
Cortes, J.4
Orozco, M.5
Goni, J.R.6
-
129
-
-
77955574450
-
Ensemble docking from homology models
-
Maria Novoa E, Ribas de Pouplana L, Barril X, Orozco M. Ensemble docking from homology models. J Chem Theory Comput. 2010; 6(8):2547-2557.
-
(2010)
J Chem Theory Comput
, vol.6
, Issue.8
, pp. 2547-2557
-
-
Maria Novoa, E.1
Ribas de Pouplana, L.2
Barril, X.3
Orozco, M.4
-
130
-
-
84862282513
-
Exploring protein flexibility: incorporating structural ensembles from crystal structures and simulation into virtual screening protocols
-
Osguthorpe DJ, Sherman W, Hagler AT. Exploring protein flexibility: incorporating structural ensembles from crystal structures and simulation into virtual screening protocols. J Phys Chem B. 2012; 116(23):6952-6959.
-
(2012)
J Phys Chem B
, vol.116
, Issue.23
, pp. 6952-6959
-
-
Osguthorpe, D.J.1
Sherman, W.2
Hagler, A.T.3
-
131
-
-
84863714870
-
Application of drug-perturbed essential dynamics/molecular dynamics (ED/MD) to virtual screening and rational drug design
-
Chaudhuri R, Carrillo O, Laughton CA, Orozco M. Application of drug-perturbed essential dynamics/molecular dynamics (ED/MD) to virtual screening and rational drug design. J Chem Theory Comput. 2012;8(7):2204-2214.
-
(2012)
J Chem Theory Comput
, vol.8
, Issue.7
, pp. 2204-2214
-
-
Chaudhuri, R.1
Carrillo, O.2
Laughton, C.A.3
Orozco, M.4
-
132
-
-
84911206910
-
Three-dimensional protein structure prediction: methods and computational strategies
-
Dorn M, E Silva MB, Buriol LS, Lamb LC. Three-dimensional protein structure prediction: methods and computational strategies. Comput Biol Chem. 2014;53:251-276.
-
(2014)
Comput Biol Chem
, vol.53
, pp. 251-276
-
-
Dorn, M.1
Silva, M.B.E.2
Buriol, L.S.3
Lamb, L.C.4
-
133
-
-
80055081145
-
How fast-folding proteins fold
-
Lindorff-Larsen K, Piana S, Dror RO, Shaw DE. How fast-folding proteins fold. Science. 2011;334(6055):517-520.
-
(2011)
Science
, vol.334
, Issue.6055
, pp. 517-520
-
-
Lindorff-Larsen, K.1
Piana, S.2
Dror, R.O.3
Shaw, D.E.4
-
134
-
-
84868155171
-
Protein folding kinetics and thermodynamics from atomistic simulation
-
Piana S, Lindorff-Larsen K, Shaw DE. Protein folding kinetics and thermodynamics from atomistic simulation. Proc Natl Acad Sci U S A. 2012;109(44):17845-17850.
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
, Issue.44
, pp. 17845-17850
-
-
Piana, S.1
Lindorff-Larsen, K.2
Shaw, D.E.3
-
136
-
-
0034985005
-
Ab initio protein structure prediction: progress and prospects
-
Bonneau R, Baker D. Ab initio protein structure prediction: progress and prospects. Ann Rev Biophys Biomol Struct. 2001;30: 173-189.
-
(2001)
Ann Rev Biophys Biomol Struct
, vol.30
, pp. 173-189
-
-
Bonneau, R.1
Baker, D.2
-
137
-
-
77955016492
-
Exploring the potential of template-based modelling
-
Lance BK, Deane CM, Wood GR. Exploring the potential of template-based modelling. Bioinformatics. 2010;26(15):1849-1856.
-
(2010)
Bioinformatics
, vol.26
, Issue.15
, pp. 1849-1856
-
-
Lance, B.K.1
Deane, C.M.2
Wood, G.R.3
-
138
-
-
36749030503
-
High accuracy template based modeling by global optimization
-
Joo K, Lee J, Lee S, Seo JH, Lee SJ, Lee J. High accuracy template based modeling by global optimization. Proteins. 2007;69:83-89.
-
(2007)
Proteins
, vol.69
, pp. 83-89
-
-
Joo, K.1
Lee, J.2
Lee, S.3
Seo, J.H.4
Lee, S.J.5
Lee, J.6
-
139
-
-
20444484434
-
A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction
-
Moult J. A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. Curr Opin Struct Biol. 2005;15(3): 285-289.
-
(2005)
Curr Opin Struct Biol
, vol.15
, Issue.3
, pp. 285-289
-
-
Moult, J.1
-
140
-
-
77954065271
-
I-TASSER: a unified platform for automated protein structure and function prediction
-
Roy A, Kucukural A, Zhang Y. I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc. 2010; 5(4):725-738.
-
(2010)
Nat Protoc
, vol.5
, Issue.4
, pp. 725-738
-
-
Roy, A.1
Kucukural, A.2
Zhang, Y.3
-
141
-
-
64549115839
-
Protein structure prediction: when is it useful?
-
Zhang Y. Protein structure prediction: when is it useful? Curr Opin Struct Biol. 2009;19(2):145-155.
-
(2009)
Curr Opin Struct Biol
, vol.19
, Issue.2
, pp. 145-155
-
-
Zhang, Y.1
-
142
-
-
0038386050
-
3D-jury: a simple approach to improve protein structure predictions
-
Ginalski K, Elofsson A, Fischer D, Rychlewski L. 3D-jury: a simple approach to improve protein structure predictions. Bioinformatics. 2003;19(8):1015-1018.
-
(2003)
Bioinformatics
, vol.19
, Issue.8
, pp. 1015-1018
-
-
Ginalski, K.1
Elofsson, A.2
Fischer, D.3
Rychlewski, L.4
-
143
-
-
14644438345
-
Progress and challenges in high-resolution refinement of protein structure models
-
Misura KMS, Baker D. Progress and challenges in high-resolution refinement of protein structure models. Proteins. 2005;59(1):15-29.
-
(2005)
Proteins
, vol.59
, Issue.1
, pp. 15-29
-
-
Misura, K.M.S.1
Baker, D.2
-
144
-
-
0027136282
-
Comparative protein modeling by satisfaction of spatial restraints
-
Sali A, Blundell TL. Comparative protein modeling by satisfaction of spatial restraints. J Mol Biol. 1993;234(3):779-815.
-
(1993)
J Mol Biol
, vol.234
, Issue.3
, pp. 779-815
-
-
Sali, A.1
Blundell, T.L.2
-
145
-
-
84863775602
-
Refinement of protein structure homology models via long, all-atom molecular dynamics simulations
-
Raval A, Piana S, Eastwood MP, Dror RO, Shaw DE. Refinement of protein structure homology models via long, all-atom molecular dynamics simulations. Proteins. 2012;80(8):2071-2079.
-
(2012)
Proteins
, vol.80
, Issue.8
, pp. 2071-2079
-
-
Raval, A.1
Piana, S.2
Eastwood, M.P.3
Dror, R.O.4
Shaw, D.E.5
-
146
-
-
84873657174
-
Protein structure refinement through structure selection and averaging from molecular dynamics ensembles
-
Mirjalili V, Feig M. Protein structure refinement through structure selection and averaging from molecular dynamics ensembles. J Chem Theory Comput. 2013;9(2):1294-1303.
-
(2013)
J Chem Theory Comput
, vol.9
, Issue.2
, pp. 1294-1303
-
-
Mirjalili, V.1
Feig, M.2
-
147
-
-
34248549547
-
Can molecular dynamics simulations provide high-resolution refinement of protein structure?
-
Chen J, Brooks CL III. Can molecular dynamics simulations provide high-resolution refinement of protein structure? Proteins. 2007;67(4):922-930.
-
(2007)
Proteins
, vol.67
, Issue.4
, pp. 922-930
-
-
Chen, J.1
Brooks, C.L.2
-
148
-
-
84875592758
-
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit
-
Pronk S, Pall S, Schulz R, et al. GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit. Bioinformatics. 2013;29(7):845-854.
-
(2013)
Bioinformatics
, vol.29
, Issue.7
, pp. 845-854
-
-
Pronk, S.1
Pall, S.2
Schulz, R.3
|