-
1
-
-
33646943202
-
Molecular dynamics: Survey of methods for simulating the activity of proteins
-
Adcock SA, Mccammon JA (2006) Molecular dynamics: survey of methods for simulating the activity of proteins. Chem Rev 106:1589–1615.
-
(2006)
Chem Rev
, vol.106
, pp. 1589-1615
-
-
Adcock, S.A.1
McCammon, J.A.2
-
2
-
-
0036725277
-
Molecular dynamics simulations of biomolecules
-
Karplus M, McCammon JA (2002) Molecular dynamics simulations of biomolecules. Nat Struct Biol 9:646–652.
-
(2002)
Nat Struct Biol
, vol.9
, pp. 646-652
-
-
Karplus, M.1
McCammon, J.A.2
-
3
-
-
84979892908
-
Molecular dynamics techniques for modeling G protein-coupled receptors
-
McRobb FM, Negri A, Beuming T, Sherman W (2016) Molecular dynamics techniques for modeling G protein-coupled receptors. Curr Opin Pharm 30:69–75. https://doi.org/10.1016/j.coph.2016.07.001.
-
(2016)
Curr Opin Pharm
, vol.30
, pp. 69-75
-
-
McRobb, F.M.1
Negri, A.2
Beuming, T.3
Sherman, W.4
-
4
-
-
33845890639
-
It’s a GPCR world
-
Filmore D (2004) It’s a GPCR world. J Modern D Discov 7:24–27.
-
(2004)
J Modern D Discov
, vol.7
, pp. 24-27
-
-
Filmore, D.1
-
5
-
-
80053615320
-
The significance of G protein-coupled receptor crystallography for drug discovery
-
Salon JA, Lodowski DT, Palczewski K (2011) The significance of G protein-coupled receptor crystallography for drug discovery. Pharm Rev 63:901–937. https://doi.org/10.1124/pr.110.003350.901.
-
(2011)
Pharm Rev
, vol.63
, pp. 901-937
-
-
Salon, J.A.1
Lodowski, D.T.2
Palczewski, K.3
-
7
-
-
84949520925
-
Advances in computational techniques to study GPCR–ligand recognition
-
Ciancetta A, Sabbadin D, Federico S, Spalluto G, Moro S (2015) Advances in computational techniques to study GPCR–ligand recognition. Trends Pharm Sci 36(12):878–890. https://doi.org/10.1016/j.tips.2015.08.006.
-
(2015)
Trends Pharm Sci
, vol.36
, Issue.12
, pp. 878-890
-
-
Ciancetta, A.1
Sabbadin, D.2
Federico, S.3
Spalluto, G.4
Moro, S.5
-
8
-
-
80052077522
-
Showcasing modern molecular dynamics simulations of membrane proteins through G protein-coupled receptors
-
Johnston JM, Filizola M (2011) Showcasing modern molecular dynamics simulations of membrane proteins through G protein-coupled receptors. Curr Opin Struc Biol 21:552–558. https://doi.org/10.1016/j.sbi.2011.06.008.
-
(2011)
Curr Opin Struc Biol
, vol.21
, pp. 552-558
-
-
Johnston, J.M.1
Filizola, M.2
-
9
-
-
0038024615
-
The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints
-
Fredriksson R, Lagerström MC, Lundin L-G, Schiöth HB (2003) The G-protein-coupled receptors in the human genome form five main families. Phylogenetic analysis, paralogon groups, and fingerprints. Mol Endocrinol 63:1256–1272. https://doi.org/10.1124/mol.63.6.1256.
-
(2003)
Mol Endocrinol
, vol.63
, pp. 1256-1272
-
-
Fredriksson, R.1
Lagerström, M.C.2
Lundin, L.-G.3
Schiöth, H.B.4
-
10
-
-
30444454024
-
G-protein-coupled receptors: Past, present and future
-
Hill SJ (2006) G-protein-coupled receptors: past, present and future. Brit J Pharm 147:S27–S37. https://doi.org/10.1038/sj.bjp.0706455.
-
(2006)
Brit J Pharm
, vol.147
, pp. S27-S37
-
-
Hill, S.J.1
-
11
-
-
84992170625
-
Successful strategies to determine high-resolution structures of GPCRs
-
Xiang J, Chun E, Liu C, Jing L, Al-Sahouri Z, Zhu L, Liu W (2016) Successful strategies to determine high-resolution structures of GPCRs. Trends Pharm Sci (in press). https://doi.org/10.1016/j.tips.2016.09.009.
-
(2016)
Trends Pharm Sci
-
-
Xiang, J.1
Chun, E.2
Liu, C.3
Jing, L.4
Al-Sahouri, Z.5
Zhu, L.6
Liu, W.7
-
12
-
-
0031436823
-
Comparative modeling and molecular dynamics studies of the delta, kappa and mu opioid receptors
-
Strahs D, Weinstein H (1997) Comparative modeling and molecular dynamics studies of the delta, kappa and mu opioid receptors. Protein Eng 10(9):1019–1038.
-
(1997)
Protein Eng
, vol.10
, Issue.9
, pp. 1019-1038
-
-
Strahs, D.1
Weinstein, H.2
-
13
-
-
0029897495
-
Constitutively active mutants of the a1B-adrenergic receptor: Role of highly conserved polar amino acids in receptor activation
-
Scheer A, Fanelli F, Costa T, Benedetti PGD, Cotecchia S (1996) Constitutively active mutants of the a1B-adrenergic receptor: role of highly conserved polar amino acids in receptor activation. EMBO J 15:3566–3578.
-
(1996)
EMBO J
, vol.15
, pp. 3566-3578
-
-
Scheer, A.1
Fanelli, F.2
Costa, T.3
Benedetti, P.4
Cotecchia, S.5
-
15
-
-
0034327611
-
Hinges, swivels and switches: The role of prolines in signalling via transmembrane alpha helices
-
Sansom MSP, Weinstein H (2000) Hinges, swivels and switches: the role of prolines in signalling via transmembrane alpha helices. TIPS 21:445–451.
-
(2000)
TIPS
, vol.21
, pp. 445-451
-
-
Sansom, M.1
Weinstein, H.2
-
16
-
-
0034604451
-
Crystal structure of rhodopsin: A G protein-coupled receptor
-
Palczewski K, Kumasaka T, Hori T, Behnke CA, Motoshima H, Fox BA, Le Trong I, Teller DC, Okada T, Stenkamp RE, Yamamoto M, Miyano M (2000) Crystal structure of rhodopsin: a G protein-coupled receptor. Science 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.A.6
Le Trong, I.7
Teller, D.C.8
Okada, T.9
Stenkamp, R.E.10
Yamamoto, M.11
Miyano, M.12
-
17
-
-
0037015153
-
Early steps of the intramolecular signal transduction in rhodopsin explored by molecular dynamics simulations
-
Rohrig UF, Guidoni L, Rothlisberger U (2002) Early steps of the intramolecular signal transduction in rhodopsin explored by molecular dynamics simulations. Biochemistry 41:10799–10809.
-
(2002)
Biochemistry
, vol.41
, pp. 10799-10809
-
-
Rohrig, U.F.1
Guidoni, L.2
Rothlisberger, U.3
-
18
-
-
0141927102
-
Molecular dynamics simulation of dark-adapted rhodopsin in an explicit membrane bilayer: Coupling between local retinal and larger scale conformational change
-
Crozier PS, Stevens MJ, Forrest LR, Woolf TB (2003) Molecular dynamics simulation of dark-adapted rhodopsin in an explicit membrane bilayer: coupling between local retinal and larger scale conformational change. J Mol Biol 333:493–514. https://doi.org/10.1016/j.jmb.2003.08.045.
-
(2003)
J Mol Biol
, vol.333
, pp. 493-514
-
-
Crozier, P.S.1
Stevens, M.J.2
Forrest, L.R.3
Woolf, T.B.4
-
19
-
-
1942519744
-
Membrane model for the G-protein-coupled receptor rhodopsin: Hydrophobic interface and dynamical structure
-
Huber T, Botelho AV, Beyer K, Brown MF (2004) Membrane model for the G-protein-coupled receptor rhodopsin: hydrophobic interface and dynamical structure. Biophys J 86:2078–2100. https://doi.org/10.1016/S0006-3495(04)74268-X.
-
(2004)
Biophys J
, vol.86
, pp. 2078-2100
-
-
Huber, T.1
Botelho, A.V.2
Beyer, K.3
Brown, M.F.4
-
20
-
-
16844365398
-
Role of cholesterol and polyunsaturated chains in lipid - protein interactions: Molecular dynamics simulation of rhodopsin in a realistic membrane environment
-
Pitman MC, Grossfield A, Suits F, Feller SE (2005) Role of cholesterol and polyunsaturated chains in lipid - protein interactions: molecular dynamics simulation of rhodopsin in a realistic membrane environment. J Am Chem Soc 127:4576–4577.
-
(2005)
J am Chem Soc
, vol.127
, pp. 4576-4577
-
-
Pitman, M.C.1
Grossfield, A.2
Suits, F.3
Feller, S.E.4
-
22
-
-
0037214576
-
Molecular dynamics simulations on SDF-1α: Binding with CXCR4 receptor
-
Huang X, Shen J, Cui M, Shen L, Luo X, Ling K, Pei G, Jiang H, Chen K (2003) Molecular dynamics simulations on SDF-1α: binding with CXCR4 receptor. Biophys J 84:171–184. https://doi.org/10.1016/S0006-3495(03)74840-1.
-
(2003)
Biophys J
, vol.84
, pp. 171-184
-
-
Huang, X.1
Shen, J.2
Cui, M.3
Shen, L.4
Luo, X.5
Ling, K.6
Pei, G.7
Jiang, H.8
Chen, K.9
-
23
-
-
21044437346
-
Homology modeling and molecular dynamics simulations of the mu opioid receptor in a membrane – aqueous system
-
Zhang Y, Sham YY, Rajamani R, Gao J, Portoguese PS (2005) Homology modeling and molecular dynamics simulations of the mu opioid receptor in a membrane – aqueous system. Chem Bio Chem 6:853–859. https://doi.org/10.1002/cbic.200400207.
-
(2005)
Chem Bio Chem
, vol.6
, pp. 853-859
-
-
Zhang, Y.1
Sham, Y.Y.2
Rajamani, R.3
Gao, J.4
Portoguese, P.S.5
-
24
-
-
0037168078
-
K-Opioid receptor model in a phospholipid bilayer: Molecular dynamics simulation
-
Iadanza M, Holtje M, Ronsisvalle G, Holtje H-D (2002) k-Opioid receptor model in a phospholipid bilayer: molecular dynamics simulation. J Med Chem 45:4838–4846.
-
(2002)
J Med Chem
, vol.45
, pp. 4838-4846
-
-
Iadanza, M.1
Holtje, M.2
Ronsisvalle, G.3
Holtje, H.-D.4
-
25
-
-
84893954062
-
Molecular control of [dgr]-opioid receptor signalling
-
Fenalti G, Giguere PM, Katritch V, Huang X-P, Thompson AA, Cherezov V, Roth BL, Stevens RC (2014) Molecular control of [dgr]-opioid receptor signalling. Nature 506(7487):191–196. https://doi.org/10.1038/nature12944.
-
(2014)
Nature
, vol.506
, Issue.7487
, pp. 191-196
-
-
Fenalti, G.1
Giguere, P.M.2
Katritch, V.3
Huang, X.-P.4
Thompson, A.A.5
Cherezov, V.6
Roth, B.L.7
Stevens, R.C.8
-
26
-
-
84938359988
-
Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser
-
Kang Y, Zhou XE, Gao X, He Y, Liu W, Ishchenko A, Barty A, White TA, Yefanov O, Han GW, Xu Q, Waal PWD, Ke J, Tan MHE, Zhang C, Moeller A, West GM, Pascal BD, Eps NV, Caro LN, Vishnivetskiy SA, Lee RJ (2015) Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser. Nature 523:561–567. https://doi.org/10.1038/nature14656.
-
(2015)
Nature
, vol.523
, pp. 561-567
-
-
Kang, Y.1
Zhou, X.E.2
Gao, X.3
He, Y.4
Liu, W.5
Ishchenko, A.6
Barty, A.7
White, T.A.8
Yefanov, O.9
Han, G.W.10
Xu, Q.11
Waal, P.12
Ke, J.13
Tan, M.14
Zhang, C.15
Moeller, A.16
West, G.M.17
Pascal, B.D.18
Eps, N.V.19
Caro, L.N.20
Vishnivetskiy, S.A.21
Lee, R.J.22
more..
-
27
-
-
84939795137
-
Structural insights into μ-opioid receptor activation
-
Huang W, Manglik A, Venkatakrishnan AJ, Laeremans T, Feinberg EN, Sanborn AL, Kato HE, Livingston KE, Thorsen TS, Kling RC, Granier S, Gmeiner P, Husbands SM, Traynor JR, Weis WI, Steyaert J, Dror RO, Kobilka BK (2015) Structural insights into μ-opioid receptor activation. Nature 524(7565):315–321. https://doi.org/10.1038/nature14886.
-
(2015)
Nature
, vol.524
, Issue.7565
, pp. 315-321
-
-
Huang, W.1
Manglik, A.2
Venkatakrishnan, A.J.3
Laeremans, T.4
Feinberg, E.N.5
Sanborn, A.L.6
Kato, H.E.7
Livingston, K.E.8
Thorsen, T.S.9
Kling, R.C.10
Granier, S.11
Gmeiner, P.12
Husbands, S.M.13
Traynor, J.R.14
Weis, W.I.15
Steyaert, J.16
Dror, R.O.17
Kobilka, B.K.18
-
28
-
-
80051658642
-
Crystal structure of the β2 adrenergic receptor-Gs protein complex
-
Rasmussen SGF, DeVree BT, Zou Y, Kruse AC, Chung KY, Kobilka TS, Thian FS, Chae PS, Pardon E, Calinski D, Mathiesen JM, Shah STA, Lyons JA, Caffrey M, Gellman SH, Steyaert J, Skiniotis G, Weis WI, Sunahara RK, Kobilka BK (2011) Crystal structure of the β2 adrenergic receptor-Gs protein complex. Nature 477(7366):549–555.
-
(2011)
Nature
, vol.477
, Issue.7366
, pp. 549-555
-
-
Rasmussen, S.1
Devree, B.T.2
Zou, Y.3
Kruse, A.C.4
Chung, K.Y.5
Kobilka, T.S.6
Thian, F.S.7
Chae, P.S.8
Pardon, E.9
Calinski, D.10
Mathiesen, J.M.11
Shah, S.12
Lyons, J.A.13
Caffrey, M.14
Gellman, S.H.15
Steyaert, J.16
Skiniotis, G.17
Weis, W.I.18
Sunahara, R.K.19
Kobilka, B.K.20
more..
-
29
-
-
84890917722
-
Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways
-
Kohlhoff KJ, Shukla D, Lawrenz M, Bowman GR, Konerding DE, Belov D, Altman RB, Pande VS (2014) Cloud-based simulations on Google Exacycle reveal ligand modulation of GPCR activation pathways. Nat Chem 6(1):15–21. https://doi.org/10.1038/nchem.1821.
-
(2014)
Nat Chem
, vol.6
, Issue.1
, pp. 15-21
-
-
Kohlhoff, K.J.1
Shukla, D.2
Lawrenz, M.3
Bowman, G.R.4
Konerding, D.E.5
Belov, D.6
Altman, R.B.7
Pande, V.S.8
-
30
-
-
0037184031
-
Conserved helix 7 tyrosine acts as a multistate conformational switch in the 5HT2C receptor. Identification of a novel “locked-on” phenotype and double revertant mutations
-
Prioleau C, Visiers I, Ebersole BJ, Weinstein H, Sealfon SC (2002) Conserved helix 7 tyrosine acts as a multistate conformational switch in the 5HT2C receptor. Identification of a novel “locked-on” phenotype and double revertant mutations. J Biol Chem 277:36577–36584. https://doi.org/10.1074/jbc.M206223200.
-
(2002)
J Biol Chem
, vol.277
, pp. 36577-36584
-
-
Prioleau, C.1
Visiers, I.2
Ebersole, B.J.3
Weinstein, H.4
Sealfon, S.C.5
-
32
-
-
65249115932
-
Solid-state NMR and molecular dynamics characterization of cannabinoid receptor-1 (CB1) helix 7 conformational plasticity in model membranes
-
Tiburu EK, Bowman AL, Struppe JO, Janero DR, Avraham HK, Makriyannis A (2009) Solid-state NMR and molecular dynamics characterization of cannabinoid receptor-1 (CB1) helix 7 conformational plasticity in model membranes. Biochim Biophys Acta 1788:1159–1167. https://doi.org/10.1016/j.bbamem.2009.02.002.
-
(2009)
Biochim Biophys Acta
, vol.1788
, pp. 1159-1167
-
-
Tiburu, E.K.1
Bowman, A.L.2
Struppe, J.O.3
Janero, D.R.4
Avraham, H.K.5
Makriyannis, A.6
-
33
-
-
84873685831
-
Molecular signatures of G-protein-coupled receptors
-
Venkatakrishnan AJ, Deupi X, Lebon G, Tate CG, Schertler GF, Babu MM (2013) Molecular signatures of G-protein-coupled receptors. Nature 494(7436):185–194.
-
(2013)
Nature
, vol.494
, Issue.7436
, pp. 185-194
-
-
Venkatakrishnan, A.J.1
Deupi, X.2
Lebon, G.3
Tate, C.G.4
Schertler, G.F.5
Babu, M.M.6
-
34
-
-
84875475404
-
Discovery of a novel selective kappa-opioid receptor agonist using crystal structure-based virtual screening
-
Negri A et al (2013) Discovery of a novel selective kappa-opioid receptor agonist using crystal structure-based virtual screening. J Chem Inf Model 53(3):521–526. https://doi.org/10.1021/ci400019t.
-
(2013)
J Chem Inf Model
, vol.53
, Issue.3
, pp. 521-526
-
-
Negri, A.1
-
35
-
-
84875807317
-
Conformation guides molecular efficacy in docking screens of activated β-2 adrenergic G protein coupled receptor
-
Weiss DR et al (2013) Conformation guides molecular efficacy in docking screens of activated β-2 adrenergic G protein coupled receptor. ACS Chem Biol 8(5):1018–1026. https://doi.org/10.1021/cb400103f.
-
(2013)
ACS Chem Biol
, vol.8
, Issue.5
, pp. 1018-1026
-
-
Weiss, D.R.1
-
36
-
-
84984612101
-
Structure-based discovery of opioid analgesics with reduced side effects
-
Manglik A et al (2016) Structure-based discovery of opioid analgesics with reduced side effects. Nature 537(7619):185–190. https://doi.org/10.1038/nature19112.
-
(2016)
Nature
, vol.537
, Issue.7619
, pp. 185-190
-
-
Manglik, A.1
-
37
-
-
84865304129
-
Agonist-bound structures of G protein-coupled receptors
-
Lebon G et al (2012) Agonist-bound structures of G protein-coupled receptors. Curr Opin Struct Biol 22(4):482–490. https://doi.org/10.1016/j.sbi.2012.03.007.
-
(2012)
Curr Opin Struct Biol
, vol.22
, Issue.4
, pp. 482-490
-
-
Lebon, G.1
-
38
-
-
0041919542
-
Improved protein-ligand docking using GOLD
-
Verdonk ML et al (2003) Improved protein-ligand docking using GOLD. Proteins 52(4):609–623. https://doi.org/10.1002/prot.10465.
-
(2003)
Proteins
, vol.52
, Issue.4
, pp. 609-623
-
-
Verdonk, M.L.1
-
39
-
-
76149120388
-
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
-
Trott O, Olson AJ (2010) AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J Comput Chem 31(2):455–461. https://doi.org/10.1002/jcc.21334.
-
(2010)
J Comput Chem
, vol.31
, Issue.2
, pp. 455-461
-
-
Trott, O.1
Olson, A.J.2
-
40
-
-
33750124980
-
Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein−ligand complexes
-
Friesner RA et al (2006) Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein−ligand complexes. J Med Chem 49(21):6177–6196. https://doi.org/10.1021/jm051256o.
-
(2006)
J Med Chem
, vol.49
, Issue.21
, pp. 6177-6196
-
-
Friesner, R.A.1
-
41
-
-
84922211861
-
Beware of docking!
-
Chen YC (2015) Beware of docking! Trends Pharmacol Sci 36(2):78–95. https://doi.org/10.1016/j.tips.2014.12.001.
-
(2015)
Trends Pharmacol Sci
, vol.36
, Issue.2
, pp. 78-95
-
-
Chen, Y.C.1
-
42
-
-
50249114683
-
An improved relaxed complex scheme for receptor flexibility in computer-aided drug design
-
Amaro RE et al (2008) An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. J Comput Aided Mol Des 22(9):693–705. https://doi.org/10.1007/s10822-007-9159-2.
-
(2008)
J Comput Aided Mol Des
, vol.22
, Issue.9
, pp. 693-705
-
-
Amaro, R.E.1
-
43
-
-
84912119192
-
Two classes of cholesterol binding sites for the β2AR revealed by thermostability and NMR
-
Gater DL, Saurel O, Iordanov I, Liu W, Cherezov V, Milon A (2014) Two classes of cholesterol binding sites for the β2AR revealed by thermostability and NMR. Biophys J 107:2305–2312. https://doi.org/10.1016/j.bpj.2014.10.011.
-
(2014)
Biophys J
, vol.107
, pp. 2305-2312
-
-
Gater, D.L.1
Saurel, O.2
Iordanov, I.3
Liu, W.4
Cherezov, V.5
Milon, A.6
-
44
-
-
84866735390
-
High-throughput molecular dynamics: The powerful new tool for drug discovery
-
Harvey MJ, De Fabritiis G (2012) High-throughput molecular dynamics: the powerful new tool for drug discovery. Drug Discov Today 17:1059–1062. https://doi.org/10.1016/j.drudis.2012.03.017.
-
(2012)
Drug Discov Today
, vol.17
, pp. 1059-1062
-
-
Harvey, M.J.1
De Fabritiis, G.2
-
45
-
-
84946416234
-
-
SoftwareX
-
Abraham MJ, Murtola T, Schulz R, Páll S, Smith JC, Hess B, Lindahl E (2015) GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1–2:19–25. https://doi.org/10.1016/j.softx.2015.06.001.
-
(2015)
GROMACS: High Performance Molecular Simulations through Multi-Level Parallelism from Laptops to Supercomputers
, vol.1-2
, pp. 19-25
-
-
Abraham, M.J.1
Murtola, T.2
Schulz, R.3
Páll, S.4
Smith, J.C.5
Hess, B.6
Lindahl, E.7
-
46
-
-
85036617851
-
-
AMBER 2016. University of California, San Francisco
-
Case DA, Betz RM, Cerutti DS, Cheatham TE III, Darden TA, Duke RE, Giese TJ, Gohlke H, Goetz AW, Homeyer N, Izadi S, Janowski P, Kaus J, Kovalenko A, Lee TS, LeGrand S, Li P, Lin C, Luchko T, Luo R, Madej BD, Mermelstein D, Merz KM, Monard G, Nguyen H, Nguyen HT, Omelyan I, Onufriev A, Roe DR, Roitberg A, Sagui C, Simmerling CL, Botello-Smith WM, Swails J, Walker RC, Wang J, Wolf RM, Wu X, Xiao L, Kollman PA (2016) AMBER 2016. University of California, San Francisco.
-
(2016)
-
-
Case, D.A.1
Betz, R.M.2
Cerutti, D.S.3
Cheatham, T.4
Darden, T.A.5
Duke, R.E.6
Giese, T.J.7
Gohlke, H.8
Goetz, A.W.9
Homeyer, N.10
Izadi, S.11
Janowski, P.12
Kaus, J.13
Kovalenko, A.14
Lee, T.S.15
Legrand, S.16
Li, P.17
Lin, C.18
Luchko, T.19
Luo, R.20
Madej, B.D.21
Mermelstein, D.22
Merz, K.M.23
Monard, G.24
Nguyen, H.25
Nguyen, H.T.26
Omelyan, I.27
Onufriev, A.28
Roe, D.R.29
Roitberg, A.30
Sagui, C.31
Simmerling, C.L.32
Botello-Smith, W.M.33
Swails, J.34
Walker, R.C.35
Wang, J.36
Wolf, R.M.37
Wu, X.38
Xiao, L.39
Kollman, P.A.40
more..
-
47
-
-
52949096873
-
Accelerating molecular dynamics simulations using graphics processing units with CUDA
-
Liu W, Schmidt B, Voss G, Müller-Wittig W (2008) Accelerating molecular dynamics simulations using graphics processing units with CUDA. Compu Phys Comm 179:634–641. https://doi.org/10.1016/j.cpc.2008.05.008.
-
(2008)
Compu Phys Comm
, vol.179
, pp. 634-641
-
-
Liu, W.1
Schmidt, B.2
Voss, G.3
Müller-Wittig, W.4
-
48
-
-
34548283148
-
Scalable algorithms for molecular dynamics simulations on commodity clusters
-
ACM Press, New york
-
Bowers KJ, Chow E, Xu H, Dror RO, Eastwood MP, Gregersen BA, Klepeis JL, Kolossvary I, Moraes MA, Sacerdoti FD, Salmon JK, Shan Y, Shaw DE (2006) Scalable algorithms for molecular dynamics simulations on commodity clusters. In: Proceedings of the 2006 ACMI/IEEE conference on supercomputing. ACM Press, New york.
-
(2006)
Proceedings of the 2006 ACMI/IEEE Conference on Supercomputing
-
-
Bowers, K.J.1
Chow, E.2
Xu, H.3
Dror, R.O.4
Eastwood, M.P.5
Gregersen, B.A.6
Klepeis, J.L.7
Kolossvary, I.8
Moraes, M.A.9
Sacerdoti, F.D.10
Salmon, J.K.11
Shan, Y.12
Shaw, D.E.13
-
49
-
-
64649101249
-
Long-timescale molecular dynamics simulations of protein structure and function
-
Klepeis JL, Lindorff-Larsen K, Dror RO, Shaw DE (2009) Long-timescale molecular dynamics simulations of protein structure and function. Curr Opin Struct Biol 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
-
50
-
-
46249090563
-
Anton, a special-purpose machine for molecular dynamics simulation
-
Shaw DE et al (2008) Anton, a special-purpose machine for molecular dynamics simulation. Comm ACM 51(7):91–97. https://doi.org/10.1145/1364782.1364802.
-
(2008)
Comm ACM
, vol.51
, Issue.7
, pp. 91-97
-
-
Shaw, D.E.1
-
51
-
-
78651399683
-
Structure and function of an irreversible agonist-β2 adrenoceptor complex
-
Rosenbaum DM, Zhang C, Lyons JA, Holl R, Aragao D, Arlow DH, Rasmussen SGF, Choi H-j, Devree BT, Sunahara RK, Chae PS, Gellman SH, Dror RO, Shaw DE, Weis WI, Caffrey M, Gmeiner P, Kobilka BK (2011) Structure and function of an irreversible agonist-β2 adrenoceptor complex. Nature 469:236–240. https://doi.org/10.1038/nature09665.
-
(2011)
Nature
, vol.469
, pp. 236-240
-
-
Rosenbaum, D.M.1
Zhang, C.2
Lyons, J.A.3
Holl, R.4
Aragao, D.5
Arlow, D.H.6
Rasmussen, S.7
Choi, H.-J.8
Devree, B.T.9
Sunahara, R.K.10
Chae, P.S.11
Gellman, S.H.12
Dror, R.O.13
Shaw, D.E.14
Weis, W.I.15
Caffrey, M.16
Gmeiner, P.17
Kobilka, B.K.18
-
52
-
-
81755163613
-
Activation mechanism of the β2-adrenergic receptor
-
Dror RO, Arlow DH, Maragakis P, Mildorf TJ, Pan AC, Xu H, Borhani DW, Shaw DE (2011) Activation mechanism of the β2-adrenergic receptor. Proc Natl Acad Sci U S A 108(46):18684–18689.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, Issue.46
, pp. 18684-18689
-
-
Dror, R.O.1
Arlow, D.H.2
Maragakis, P.3
Mildorf, T.J.4
Pan, A.C.5
Xu, H.6
Borhani, D.W.7
Shaw, D.E.8
-
53
-
-
78651411166
-
Structure of a nanobody-stabilized active state of the β(2) adrenoceptor
-
Rasmussen SGF, Choi H-J, Fung JJ, Pardon E, Casarosa P, Chae PS, Devree BT, Rosenbaum DM, Thian FS, Kobilka TS, Schnapp A, Konetzki I, Sunahara RK, Gellman SH, Pautsch A, Steyaert J, Weis WI, Kobilka BK (2011) Structure of a nanobody-stabilized active state of the β(2) adrenoceptor. Nature 469:175–180. https://doi.org/10.1038/nature09648.
-
(2011)
Nature
, vol.469
, pp. 175-180
-
-
Rasmussen, S.1
Choi, H.-J.2
Fung, J.J.3
Pardon, E.4
Casarosa, P.5
Chae, P.S.6
Devree, B.T.7
Rosenbaum, D.M.8
Thian, F.S.9
Kobilka, T.S.10
Schnapp, A.11
Konetzki, I.12
Sunahara, R.K.13
Gellman, S.H.14
Pautsch, A.15
Steyaert, J.16
Weis, W.I.17
Kobilka, B.K.18
-
54
-
-
36448995359
-
High-resolution crystal structure of an engineered human β2-adrenergic G protein–coupled receptor
-
Cherezov V, Rosenbaum DM, Hanson MA, Rasmussen SGF, Thian FS, Kobilka TS, Choi H-J, Kuhn P, Weis WI, Kobilka BK, Stevens RC (2007) High-resolution crystal structure of an engineered human β2-adrenergic G protein–coupled receptor. Science 318(5854):1258–1265.
-
(2007)
Science
, vol.318
, Issue.5854
, pp. 1258-1265
-
-
Cherezov, V.1
Rosenbaum, D.M.2
Hanson, M.A.3
Rasmussen, S.4
Thian, F.S.5
Kobilka, T.S.6
Choi, H.-J.7
Kuhn, P.8
Weis, W.I.9
Kobilka, B.K.10
Stevens, R.C.11
-
55
-
-
84908031988
-
A dynamic view of molecular switch behavior at serotonin receptors: Implications for functional selectivity
-
Marti-Solano M, Sanz F, Pastor M, Selent J (2014) A dynamic view of molecular switch behavior at serotonin receptors: implications for functional selectivity. PLoS One 9:e109312. https://doi.org/10.1371/journal.pone.0109312.
-
(2014)
Plos One
, vol.9
-
-
Marti-Solano, M.1
Sanz, F.2
Pastor, M.3
Selent, J.4
-
56
-
-
84864944680
-
Science in the cloud: Accelerating discovery in the 21st century
-
Hellerstein JL, Kohlhoff KJ, Konerding DE (2012) Science in the cloud: accelerating discovery in the 21st century. IEEE Internet Comput 16(4):64–68. https://doi.org/10.1109/MIC.2012.87.
-
(2012)
IEEE Internet Comput
, vol.16
, Issue.4
, pp. 64-68
-
-
Hellerstein, J.L.1
Kohlhoff, K.J.2
Konerding, D.E.3
-
57
-
-
65449161390
-
Ligand binding and micro-switches in 7TM receptor structures
-
Nygaard R, Frimurer TM, Holst B, Rosenkilde MM, Schwartz TW (2009) Ligand binding and micro-switches in 7TM receptor structures. Trends Pharm Sci 30:249–259. https://doi.org/10.1016/j.tips.2009.02.006.
-
(2009)
Trends Pharm Sci
, vol.30
, pp. 249-259
-
-
Nygaard, R.1
Frimurer, T.M.2
Holst, B.3
Rosenkilde, M.M.4
Schwartz, T.W.5
-
58
-
-
84997830677
-
How Oliceridine (TRV-130) binds and stabilizes a μ-opioid receptor conformational state that selectively triggers G protein-signaling pathways
-
Schneider S, Provasi D, Filizola M (2016) How Oliceridine (TRV-130) binds and stabilizes a μ-opioid receptor conformational state that selectively triggers G protein-signaling pathways. Biochemistry 55:6456–6466. https://doi.org/10.1021/acs.biochem.6b00948.
-
(2016)
Biochemistry
, vol.55
, pp. 6456-6466
-
-
Schneider, S.1
Provasi, D.2
Filizola, M.3
-
59
-
-
84978923182
-
In silico exploration of the conformational universe of GPCRs
-
Rodríguez-Espigares I, Kaczor AA, Selent J (2016) In silico exploration of the conformational universe of GPCRs. Mol Inform 35:227–237. https://doi.org/10.1002/minf.201600012.
-
(2016)
Mol Inform
, vol.35
, pp. 227-237
-
-
Rodríguez-Espigares, I.1
Kaczor, A.A.2
Selent, J.3
-
60
-
-
84866146945
-
Routine access to millisecond time scale events with accelerated molecular dynamics
-
Pierce LCT, Salomon-Ferrer R, De Oliveira C AF, JA MC, Walker RC (2012) Routine access to millisecond time scale events with accelerated molecular dynamics. J Chem Theory Comput 8:2997–3002.
-
(2012)
J Chem Theory Comput
, vol.8
, pp. 2997-3002
-
-
Pierce, L.1
Salomon-Ferrer, R.2
De Oliveira, C.3
Ja, M.C.4
Walker, R.C.5
-
61
-
-
33644772083
-
Equilibrium free energies from nonequilibrium metadynamics
-
Bussi G, Laio A, Parrinello M (2006) Equilibrium free energies from nonequilibrium metadynamics. Phys Rev Lett 96(9):090601.
-
(2006)
Phys Rev Lett
, vol.96
, Issue.9
-
-
Bussi, G.1
Laio, A.2
Parrinello, M.3
-
63
-
-
0027794972
-
Targeted molecular dynamics simulation of conformational change-application to the T ↔ R transition in insulin
-
Schlitter J, Engels M, Krüger P, Jacoby E, Wollmer A (1993) Targeted molecular dynamics simulation of conformational change-application to the T ↔ R transition in insulin. Mol Sim 10:291–308. https://doi.org/10.1080/08927029308022170.
-
(1993)
Mol Sim
, vol.10
, pp. 291-308
-
-
Schlitter, J.1
Engels, M.2
Krüger, P.3
Jacoby, E.4
Wollmer, A.5
-
64
-
-
0028455053
-
Targeted molecular dynamics: A new approach for searching pathways of conformational transitions
-
Schlitter J, Engels M, Krueger P (1994) Targeted molecular dynamics: a new approach for searching pathways of conformational transitions. J Mol Graph 1994:84–89.
-
(1994)
J Mol Graph
, vol.1994
, pp. 84-89
-
-
Schlitter, J.1
Engels, M.2
Krueger, P.3
-
65
-
-
66749085629
-
Comparison of three perturbation molecular dynamics methods for modeling conformational transitions
-
Huang H, Ozkirimli E, Post CB (2009) Comparison of three perturbation molecular dynamics methods for modeling conformational transitions. J Chem Theor Comput 5:1304–1314. https://doi.org/10.1021/ct9000153.
-
(2009)
J Chem Theor Comput
, vol.5
, pp. 1304-1314
-
-
Huang, H.1
Ozkirimli, E.2
Post, C.B.3
-
66
-
-
0030059225
-
Ligand binding: Molecular mechanics calculation of the streptavidin-biotin rupture force
-
Grubmuller H, Heymann B, Tavan P (1996) Ligand binding: molecular mechanics calculation of the streptavidin-biotin rupture force. Science 271:997–999.
-
(1996)
Science
, vol.271
, pp. 997-999
-
-
Grubmuller, H.1
Heymann, B.2
Tavan, P.3
-
67
-
-
0001160648
-
Adiabatic bias molecular dynamics: A method to navigate the conformational space of complex molecular systems
-
Marchi M, Ballone P (1999) Adiabatic bias molecular dynamics: a method to navigate the conformational space of complex molecular systems. J Chem Phys 110:3697–3702. https://doi.org/10.1063/1.478259.
-
(1999)
J Chem Phys
, vol.110
, pp. 3697-3702
-
-
Marchi, M.1
Ballone, P.2
-
68
-
-
0033531973
-
Forced unfolding of fibronectin type 3 modules: An analysis by biased molecular dynamics simulations
-
Paci E, Karplus M (1999) Forced unfolding of fibronectin type 3 modules: an analysis by biased molecular dynamics simulations. J Mol Bio 288:441–459.
-
(1999)
J Mol Bio
, vol.288
, pp. 441-459
-
-
Paci, E.1
Karplus, M.2
-
69
-
-
38449096891
-
Sampling of slow diffusive conformational transitions with accelerated molecular dynamics
-
Hamelberg D, De Oliveira CAF, McCammon JA (2007) Sampling of slow diffusive conformational transitions with accelerated molecular dynamics. J Chem Phys 127:155102. https://doi.org/10.1063/1.2789432.
-
(2007)
J Chem Phys
, vol.127
-
-
Hamelberg, D.1
De Oliveira, C.2
McCammon, J.A.3
-
70
-
-
81255138340
-
Studying functional dynamics in bio-molecules using accelerated molecular dynamics
-
Markwick PRL, McCammon JA (2011) Studying functional dynamics in bio-molecules using accelerated molecular dynamics. Phys Chem Chem Phys 13:20053–20065. https://doi.org/10.1039/c1cp22100k.
-
(2011)
Phys Chem Chem Phys
, vol.13
, pp. 20053-20065
-
-
Markwick, P.1
McCammon, J.A.2
-
71
-
-
84879707465
-
Activation and dynamic network of the M2 muscarinic receptor
-
Miao Y, Nichols SE, Gasper PM, Metzger VT, McCammon JA (2013) Activation and dynamic network of the M2 muscarinic receptor. Proc Natl Acad Sci U S A 110(27):10982–10987. https://doi.org/10.1073/pnas.1309755110.
-
(2013)
Proc Natl Acad Sci U S A
, vol.110
, Issue.27
, pp. 10982-10987
-
-
Miao, Y.1
Nichols, S.E.2
Gasper, P.M.3
Metzger, V.T.4
McCammon, J.A.5
-
72
-
-
69349100797
-
PLUMED: A portable plugin for free-energy calculations with molecular dynamics
-
Bonomi M, Branduardi D, Bussi G, Camilloni C, Provasi D, Raiteri P, Donadio D, Marinelli F, Pietrucci F, Broglia RA, Parrinello M (2009) PLUMED: a portable plugin for free-energy calculations with molecular dynamics. Comput Phys Comm 180(10):1961–1972. https://doi.org/10.1016/j.cpc.2009.05.011.
-
(2009)
Comput Phys Comm
, vol.180
, Issue.10
, pp. 1961-1972
-
-
Bonomi, M.1
Branduardi, D.2
Bussi, G.3
Camilloni, C.4
Provasi, D.5
Raiteri, P.6
Donadio, D.7
Marinelli, F.8
Pietrucci, F.9
Broglia, R.A.10
Parrinello, M.11
-
73
-
-
80055099699
-
Ligand-induced modulation of the free-energy landscape of G protein-coupled receptors explored by adaptive biasing techniques
-
Provasi D, Artacho MC, Negri A, Mobarec JC, Filizola M (2011) Ligand-induced modulation of the free-energy landscape of G protein-coupled receptors explored by adaptive biasing techniques. PLoS Comput Biol 7:e1002193. https://doi.org/10.1371/journal.pcbi.1002193.
-
(2011)
Plos Comput Biol
, vol.7
-
-
Provasi, D.1
Artacho, M.C.2
Negri, A.3
Mobarec, J.C.4
Filizola, M.5
-
74
-
-
67650477115
-
Reconstructing the equilibrium boltzmann distribution from well-tempered metadynamics
-
Bonomi M, Barducci A, Parrinello M (2009) Reconstructing the equilibrium boltzmann distribution from well-tempered metadynamics. J Comput Chem 30:1615–1621. https://doi.org/10.1002/jcc.
-
(2009)
J Comput Chem
, vol.30
, pp. 1615-1621
-
-
Bonomi, M.1
Barducci, A.2
Parrinello, M.3
-
75
-
-
77956638608
-
Putative active states of a prototypic g-protein-coupled receptor from biased molecular dynamics
-
Provasi D, Filizola M (2010) Putative active states of a prototypic g-protein-coupled receptor from biased molecular dynamics. Biophys J 98:2347–2355. https://doi.org/10.1016/j.bpj.2010.01.047.
-
(2010)
Biophys J
, vol.98
, pp. 2347-2355
-
-
Provasi, D.1
Filizola, M.2
-
76
-
-
38349091489
-
Well-tempered metadynamics: A smoothly converging and tunable free-energy method
-
Barducci A, Bussi G, Parrinello M (2008) Well-tempered metadynamics: a smoothly converging and tunable free-energy method. Phys Rev Lett 100(2):020603.
-
(2008)
Phys Rev Lett
, vol.100
, Issue.2
-
-
Barducci, A.1
Bussi, G.2
Parrinello, M.3
-
77
-
-
0035800850
-
Activation of the β2 -adrenergic receptor involves disruption of an ionic lock between the cytoplasmic ends of transmembrane segments 3 and 6
-
Ballesteros JA, Jensen AD, Liapakis G, Rasmussen SGF, Shi L, Gether U, Javitch JA (2001) Activation of the β2 -adrenergic receptor involves disruption of an ionic lock between the cytoplasmic ends of transmembrane segments 3 and 6. J Biol Chem 276:29171–29177. https://doi.org/10.1074/jbc.M103747200.
-
(2001)
J Biol Chem
, vol.276
, pp. 29171-29177
-
-
Ballesteros, J.A.1
Jensen, A.D.2
Liapakis, G.3
Rasmussen, S.4
Shi, L.5
Gether, U.6
Javitch, J.A.7
-
78
-
-
0037174606
-
Javitch JA (2002) β2 adrenergic receptor activation: Modulation of the proline kink in transmembrane 6 by a rotamer toggle switch
-
Shi L, Liapakis G, Xu R, Guarnieri F, Ballesteros JA, Javitch JA (2002) β2 adrenergic receptor activation: modulation of the proline kink in transmembrane 6 by a rotamer toggle switch. J Biol Chem 277:40989–40996. https://doi.org/10.1074/jbc.M206801200.
-
J Biol Chem
, vol.277
, pp. 40989-40996
-
-
Shi, L.1
Liapakis, G.2
Xu, R.3
Guarnieri, F.4
Ballesteros, J.A.5
-
81
-
-
84861961427
-
Structural basis for allosteric regulation of GPCRs by sodium ions
-
Liu W, Chun E, Thompson AA, Chubukov P, Xu F, Katritch V, Han GW, Roth CB, Heitman LH, Ijzerman AP, Cherezov V, Stevens RC (2012) Structural basis for allosteric regulation of GPCRs by sodium ions. Science 337(6091):232–236.
-
(2012)
Science
, vol.337
, Issue.6091
, pp. 232-236
-
-
Liu, W.1
Chun, E.2
Thompson, A.A.3
Chubukov, P.4
Xu, F.5
Katritch, V.6
Han, G.W.7
Roth, C.B.8
Heitman, L.H.9
Ijzerman, A.P.10
Cherezov, V.11
Stevens, R.C.12
-
82
-
-
66649096395
-
Conserved waters mediate structural and functional activation of family a (Rhodopsin-like) G protein-coupled receptors
-
Angel TE, Chance MR, Palczewski K (2009) Conserved waters mediate structural and functional activation of family a (rhodopsin-like) G protein-coupled receptors. Proc Natl Acad Sci U S A 106:8555–8560.
-
(2009)
Proc Natl Acad Sci U S A
, vol.106
, pp. 8555-8560
-
-
Angel, T.E.1
Chance, M.R.2
Palczewski, K.3
-
83
-
-
77953967138
-
Molecular dynamics simulations reveal fundamental role of water as factor determining affinity of binding of β-blocker nebivolol to β-adrenergic receptor
-
Kaszuba K, Róg T, Bryl K, Vattulainen I, Karttunen M (2010) Molecular dynamics simulations reveal fundamental role of water as factor determining affinity of binding of β-blocker nebivolol to β-adrenergic receptor. J Phys Chem B 114:8374–8386. https://doi.org/10.1021/jp909971f.
-
(2010)
J Phys Chem B
, vol.114
, pp. 8374-8386
-
-
Kaszuba, K.1
Róg, T.2
Bryl, K.3
Vattulainen, I.4
Karttunen, M.5
-
84
-
-
84857748866
-
Rapid and accurate prediction and scoring of water molecules in protein binding sites
-
Ross GA, Morris GM, Biggin PC (2012) Rapid and accurate prediction and scoring of water molecules in protein binding sites. PLoS One 7(3):e32036.
-
(2012)
Plos One
, vol.7
, Issue.3
-
-
Ross, G.A.1
Morris, G.M.2
Biggin, P.C.3
-
85
-
-
84948694462
-
Water sites, networks, and free energies with grand canonical Monte Carlo
-
Ross GA, Bodnarchuk MS, Essex JW (2015) Water sites, networks, and free energies with grand canonical Monte Carlo. J Am Chem Soc 137(47):14930–14943. https://doi.org/10.1021/jacs.5b07940.
-
(2015)
J am Chem Soc
, vol.137
, Issue.47
, pp. 14930-14943
-
-
Ross, G.A.1
Bodnarchuk, M.S.2
Essex, J.W.3
-
86
-
-
84925796676
-
Evaluation of water displacement energetics in protein binding sites with grid cell theory
-
Gerogiokas G, Southey MWY, Mazanetz MP, Hefeitz A, Bodkin M, Law RJ, Michel J (2015) Evaluation of water displacement energetics in protein binding sites with grid cell theory. Phys Chem Chem Phys 17:8416–8426. https://doi.org/10.1039/C4CP05572A.
-
(2015)
Phys Chem Chem Phys
, vol.17
, pp. 8416-8426
-
-
Gerogiokas, G.1
Southey, M.2
Mazanetz, M.P.3
Hefeitz, A.4
Bodkin, M.5
Law, R.J.6
Michel, J.7
-
87
-
-
84991573850
-
Assessment of hydration thermodynamics at protein interfaces with grid cell theory
-
Gerogiokas G, Southey MWY, Mazanetz MP, Heifetz A, Bodkin M, Law RJ, Henchman RH, Michel J (2016) Assessment of hydration thermodynamics at protein interfaces with grid cell theory. J Phys Chem B 120:10442–10452. https://doi.org/10.1021/acs.jpcb.6b07993.
-
(2016)
J Phys Chem B
, vol.120
, pp. 10442-10452
-
-
Gerogiokas, G.1
Southey, M.2
Mazanetz, M.P.3
Heifetz, A.4
Bodkin, M.5
Law, R.J.6
Henchman, R.H.7
Michel, J.8
-
88
-
-
70349683018
-
Prediction of the water content in protein binding sites
-
Michel J, Tirado-Rives J, Jorgensen WL (2009) Prediction of the water content in protein binding sites. J Phys Chem 113:13337–13346. https://doi.org/10.1021/jp9047456.
-
(2009)
J Phys Chem
, vol.113
, pp. 13337-13346
-
-
Michel, J.1
Tirado-Rives, J.2
Jorgensen, W.L.3
-
89
-
-
75749123456
-
High-throughput virtual screening of proteins using GRID molecular interaction fields
-
Sciabola S, Stanton RV, Mills JE, Flocco MM, Baroni M, Cruciani G, Perruccio F, Mason JS (2010) High-throughput virtual screening of proteins using GRID molecular interaction fields. J Chem Inf Model 50:155–169.
-
(2010)
J Chem Inf Model
, vol.50
, pp. 155-169
-
-
Sciabola, S.1
Stanton, R.V.2
Mills, J.E.3
Flocco, M.M.4
Baroni, M.5
Cruciani, G.6
Perruccio, F.7
Mason, J.S.8
-
90
-
-
84997817419
-
AutoDock-GIST: Incorporating thermodynamics of active-site water into scoring function for accurate protein-ligand docking
-
Uehara S, Tanaka S (2016) AutoDock-GIST: incorporating thermodynamics of active-site water into scoring function for accurate protein-ligand docking. Molecules 21:E1604. https://doi.org/10.3390/molecules21111604.
-
(2016)
Molecules
, vol.21
-
-
Uehara, S.1
Tanaka, S.2
-
91
-
-
80052001378
-
Pathway and mechanism of drug binding to G-protein-coupled receptors
-
Dror RO, Pan AC, Arlow DH, Borhani DW, Maragakis P, Shan Y, Xu H, Shaw DE (2011) Pathway and mechanism of drug binding to G-protein-coupled receptors. Proc Natl Acad Sci U S A 108(32):13118–13123.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, Issue.32
, pp. 13118-13123
-
-
Dror, R.O.1
Pan, A.C.2
Arlow, D.H.3
Borhani, D.W.4
Maragakis, P.5
Shan, Y.6
Xu, H.7
Shaw, D.E.8
-
92
-
-
84901827515
-
Drug-target residence time—a case for G protein-coupled receptors
-
Guo D, Hillger JM, Ijzerman AP, Heitman LH (2014) Drug-target residence time—a case for G protein-coupled receptors. Med Res Rev 34(4):856–892. https://doi.org/10.1002/med.21307.
-
(2014)
Med Res Rev
, vol.34
, Issue.4
, pp. 856-892
-
-
Guo, D.1
Hillger, J.M.2
Ijzerman, A.P.3
Heitman, L.H.4
-
93
-
-
77955329488
-
Drug-target residence time: Critical information for lead optimization
-
Lu H, Tonge PJ (2010) Drug-target residence time: critical information for lead optimization. Curr Opin Chem Biol 14:467–474. https://doi.org/10.1016/j.cbpa.2010.06.176.
-
(2010)
Curr Opin Chem Biol
, vol.14
, pp. 467-474
-
-
Lu, H.1
Tonge, P.J.2
-
94
-
-
40449118501
-
Applications of binding kinetics to drug discovery: Translation of binding mechanisms to clinically differentiated therapeutic responses
-
Swinney DC (2008) Applications of binding kinetics to drug discovery: translation of binding mechanisms to clinically differentiated therapeutic responses. Pharmaceut Med 22:23–34. https://doi.org/10.1007/BF03256679.
-
(2008)
Pharmaceut Med
, vol.22
, pp. 23-34
-
-
Swinney, D.C.1
-
95
-
-
58449131873
-
The role of binding kinetics in therapeutically useful drug action
-
Swinney DC (2009) The role of binding kinetics in therapeutically useful drug action. Curr Opin Drug Discov Devel 12:31–39.
-
(2009)
Curr Opin Drug Discov Devel
, vol.12
, pp. 31-39
-
-
Swinney, D.C.1
-
97
-
-
47949129742
-
Structure of a β1-adrenergic G-protein-coupled receptor
-
Warne T, Serrano-Vega MJ, Baker JG, Moukhametzianov R, Edwards PC, Henderson R, Leslie AGW, Tate CG, Schertler GFX (2008) Structure of a β1-adrenergic G-protein-coupled receptor. Nature 454:486–491. https://doi.org/10.1038/nature07101.
-
(2008)
Nature
, vol.454
, pp. 486-491
-
-
Warne, T.1
Serrano-Vega, M.J.2
Baker, J.G.3
Moukhametzianov, R.4
Edwards, P.C.5
Henderson, R.6
Leslie, A.7
Tate, C.G.8
Schertler, G.9
-
98
-
-
84894680958
-
Supervised molecular dynamics (SuMD) as a helpful tool to depict GPCR-ligand recognition pathway in a nanosecond time scale
-
Sabbadin D, Moro S (2014) Supervised molecular dynamics (SuMD) as a helpful tool to depict GPCR-ligand recognition pathway in a nanosecond time scale. J Chem Inf Model 54:372–376. https://doi.org/10.1021/ci400766b.
-
(2014)
J Chem Inf Model
, vol.54
, pp. 372-376
-
-
Sabbadin, D.1
Moro, S.2
-
99
-
-
56749103466
-
The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist
-
Jaakola VP, Griffith MT, Hanson MA, Cherezov V, Chien EY, Lane JR, Ijzerman AP, Stevens RC (2008) The 2.6 angstrom crystal structure of a human A2A adenosine receptor bound to an antagonist. Science 322(5905):1211–1217. https://doi.org/10.1126/science.1164772.
-
(2008)
Science
, vol.322
, Issue.5905
, pp. 1211-1217
-
-
Jaakola, V.P.1
Griffith, M.T.2
Hanson, M.A.3
Cherezov, V.4
Chien, E.Y.5
Lane, J.R.6
Ijzerman, A.P.7
Stevens, R.C.8
-
100
-
-
84858034356
-
2A antagonists using structure based drug design
-
2A antagonists using structure based drug design. J Med Chem 55:1898–1903.
-
(2012)
J Med Chem
, vol.55
, pp. 1898-1903
-
-
Congreve, M.1
Rews, S.P.2
Dore, A.S.3
Hollenstein, K.4
Hurrell, E.5
Langmead, C.J.6
Mason, J.S.7
Ng, I.W.8
Tehan, B.9
Zhukov, A.10
Weir, M.11
Marshall, F.H.12
-
101
-
-
79960181417
-
Structure of the adenosine a 2A receptor in complex with ZM241385 and the xanthines XAC and caffeine
-
Doré AS, Robertson N, Errey JC, Ng I, Hollenstein K, Tehan B, Hurrell E, Bennett K, Congreve M, Magnani F, Tate CG, Weir M, Marshall FH (2011) Structure of the adenosine a 2A receptor in complex with ZM241385 and the xanthines XAC and caffeine. Structure 19:1283–1293. https://doi.org/10.1016/j.str.2011.06.014.
-
(2011)
Structure
, vol.19
, pp. 1283-1293
-
-
Doré, A.S.1
Robertson, N.2
Errey, J.C.3
Ng, I.4
Hollenstein, K.5
Tehan, B.6
Hurrell, E.7
Bennett, K.8
Congreve, M.9
Magnani, F.10
Tate, C.G.11
Weir, M.12
Marshall, F.H.13
-
102
-
-
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
-
Deganutti G, Cuzzolin A, Ciancetta A, Moro S (2015) Understanding allosteric interactions in G protein-coupled receptors using supervised molecular dynamics: a prototype study analysing the human A3 adenosine receptor positive allosteric modulator. Bioorg Med Chem 23:4065–4071. https://doi.org/10.1016/j.bmc.2015.03.039.
-
(2015)
Bioorg Med Chem
, vol.23
, pp. 4065-4071
-
-
Deganutti, G.1
Cuzzolin, A.2
Ciancetta, A.3
Moro, S.4
-
103
-
-
70350230389
-
Exploring molecular mechanisms of ligand recognition by opioid receptors with metadynamics
-
Provasi D, Bortolato A, Filizola M (2009) Exploring molecular mechanisms of ligand recognition by opioid receptors with metadynamics. Biochemistry 48:10020–10029. https://doi.org/10.1021/bi901494n.
-
(2009)
Biochemistry
, vol.48
, pp. 10020-10029
-
-
Provasi, D.1
Bortolato, A.2
Filizola, M.3
-
104
-
-
84975801200
-
Uncoupling the structure-activity relationships of β2 adrenergic receptor ligands from membrane binding
-
Dickson CJ, Hornak V, Velez-Vega C, McKay DJJ, Reilly J, Sandham DA, Shaw D, Fairhurst RA, Charlton SJ, Sykes DA, Pearlstein RA, Duca JS (2016) Uncoupling the structure-activity relationships of β2 adrenergic receptor ligands from membrane binding. J Med Chem 59:5780–5789. https://doi.org/10.1021/acs.jmedchem.6b00358.
-
(2016)
J Med Chem
, vol.59
, pp. 5780-5789
-
-
Dickson, C.J.1
Hornak, V.2
Velez-Vega, C.3
McKay, D.4
Reilly, J.5
Sandham, D.A.6
Shaw, D.7
Fairhurst, R.A.8
Charlton, S.J.9
Sykes, D.A.10
Pearlstein, R.A.11
Duca, J.S.12
-
105
-
-
84960157108
-
Lipid interaction sites on channels, transporters and receptors: Recent insights from molecular dynamics simulations
-
Hedger G, Sansom MSP (2016) Lipid interaction sites on channels, transporters and receptors: recent insights from molecular dynamics simulations. Biochim Biophys Acta 1858(10):2390–2400. https://doi.org/10.1016/j.bbamem.2016.02.037.
-
(2016)
Biochim Biophys Acta
, vol.1858
, Issue.10
, pp. 2390-2400
-
-
Hedger, G.1
Sansom, M.2
-
106
-
-
79959564813
-
Agonist-bound adenosine A2A receptor structures reveal common features of GPCR activation
-
Lebon G, Warne T, Edwards PC, Bennett K, Langmead CJ, Leslie AGW, Tate CG (2011) Agonist-bound adenosine A2A receptor structures reveal common features of GPCR activation. Nature 474:521–525. https://doi.org/10.1038/nature10136.
-
(2011)
Nature
, vol.474
, pp. 521-525
-
-
Lebon, G.1
Warne, T.2
Edwards, P.C.3
Bennett, K.4
Langmead, C.J.5
Leslie, A.6
Tate, C.G.7
-
107
-
-
84867366833
-
Predictions for cholesterol interaction sites on the A2A adenosine receptor
-
Lee JY, Lyman E (2012) Predictions for cholesterol interaction sites on the A2A adenosine receptor. J Am Chem Soc 134:16512–16515.
-
(2012)
J am Chem Soc
, vol.134
, pp. 16512-16515
-
-
Lee, J.Y.1
Lyman, E.2
-
108
-
-
84944790041
-
Can specific protein-lipid interactions stabilize an active state of the Beta 2 adrenergic receptor?
-
Neale C, Herce HD, Pomès R, García AE (2015) Can specific protein-lipid interactions stabilize an active state of the Beta 2 adrenergic receptor? Biophys J 109:1652–1662. https://doi.org/10.1016/j.bpj.2015.08.028.
-
(2015)
Biophys J
, vol.109
, pp. 1652-1662
-
-
Neale, C.1
Herce, H.D.2
Pomès, R.3
García, A.E.4
-
109
-
-
84951907601
-
Allosteric regulation of G protein–coupled receptor activity by phospholipids
-
Dawaliby R, Trubbia C, Delporte C, Masureel M, Van Antwerpen P, Kobilka BK, Govaerts C (2016) Allosteric regulation of G protein–coupled receptor activity by phospholipids. Nature Chem Biol 12:35–41. https://doi.org/10.1038/nchembio.1960.
-
(2016)
Nature Chem Biol
, vol.12
, pp. 35-41
-
-
Dawaliby, R.1
Trubbia, C.2
Delporte, C.3
Masureel, M.4
Van Antwerpen, P.5
Kobilka, B.K.6
Govaerts, C.7
-
110
-
-
85007409810
-
Mechanism of allosteric regulation of β2-adrenergic receptor by cholesterol
-
Manna M, Niemelä M, Tynkkynen J, Javanainen M, Kulig W, Müller DJ, Rog T, Vattulainen I (2016) Mechanism of allosteric regulation of β2-adrenergic receptor by cholesterol. eLife 5:e18432. https://doi.org/10.7554/eLife.18432.
-
(2016)
Elife
, vol.5
-
-
Manna, M.1
Niemelä, M.2
Tynkkynen, J.3
Javanainen, M.4
Kulig, W.5
Müller, D.J.6
Rog, T.7
Vattulainen, I.8
-
111
-
-
34548146523
-
G Protein-coupled receptors self-assemble in dynamics simulations of model bilayers
-
Periole X, Huber T, Marrink S-j, Sakmar TP (2007) G Protein-coupled receptors self-assemble in dynamics simulations of model bilayers. J Am Chem Soc 129:10126–10132. https://doi.org/10.1021/ja0706246.
-
(2007)
J am Chem Soc
, vol.129
, pp. 10126-10132
-
-
Periole, X.1
Huber, T.2
Marrink, S.-J.3
Sakmar, T.P.4
-
112
-
-
84882398607
-
Perspective on the Martini model
-
Marrink SJ, Tieleman DP (2013) Perspective on the Martini model. Chem Soc Rev 42(16):6801–6822. https://doi.org/10.1039/C3CS60093A.
-
(2013)
Chem Soc Rev
, vol.42
, Issue.16
, pp. 6801-6822
-
-
Marrink, S.J.1
Tieleman, D.P.2
-
113
-
-
0031740415
-
Hydrophobic mismatch between proteins and lipids in membranes
-
Killian JA (1998) Hydrophobic mismatch between proteins and lipids in membranes. Biochim Biophys Acta 1376:401–415. https://doi.org/10.1016/S0304-4157(98)00017-3.
-
(1998)
Biochim Biophys Acta
, vol.1376
, pp. 401-415
-
-
Killian, J.A.1
-
114
-
-
84864880937
-
Characterization of the motion of membrane proteins using high-speed atomic force microscopy
-
Casuso I, Khao J, Chami M, Paul-Gilloteaux P, Husain M, Duneau J-P, Stahlberg H, Sturgis JN, Scheuring S (2012) Characterization of the motion of membrane proteins using high-speed atomic force microscopy. Nature Nanotech 7:525–529. https://doi.org/10.1038/nnano.2012.109.
-
(2012)
Nature Nanotech
, vol.7
, pp. 525-529
-
-
Casuso, I.1
Khao, J.2
Chami, M.3
Paul-Gilloteaux, P.4
Husain, M.5
Duneau, J.-P.6
Stahlberg, H.7
Sturgis, J.N.8
Scheuring, S.9
-
115
-
-
33845505655
-
Curvature and hydrophobic forces drive oligomerization and modulate activity of rhodopsin in membranes
-
Botelho AV, Huber T, Sakmar TP, Brown MF (2006) Curvature and hydrophobic forces drive oligomerization and modulate activity of rhodopsin in membranes. Biophys J 91:4464–4477. https://doi.org/10.1529/biophysj.106.082776.
-
(2006)
Biophys J
, vol.91
, pp. 4464-4477
-
-
Botelho, A.V.1
Huber, T.2
Sakmar, T.P.3
Brown, M.F.4
-
116
-
-
85016114203
-
Interplay of G protein-coupled receptors with the membrane: Insights from supra-atomic coarse grain molecular dynamics simulations
-
Periole X (2016) Interplay of G protein-coupled receptors with the membrane: insights from supra-atomic coarse grain molecular dynamics simulations. Chem Rev 117:156–185. https://doi.org/10.1021/acs.chemrev.6b00344.
-
(2016)
Chem Rev
, vol.117
, pp. 156-185
-
-
Periole, X.1
-
117
-
-
84896539831
-
2-adrenergic receptor via cholesterol occupancy sites
-
2-adrenergic receptor via cholesterol occupancy sites. Biophys J 106(6):1290–1300. https://doi.org/10.1016/j.bpj.2014.02.002.
-
(2014)
Biophys J
, vol.106
, Issue.6
, pp. 1290-1300
-
-
Prasanna, X.1
-
118
-
-
84926360598
-
Preferred supramolecular organization and dimer interfaces of opioid receptors from simulated self-association
-
Provasi D et al (2015) Preferred supramolecular organization and dimer interfaces of opioid receptors from simulated self-association. PLoS Comp Biol 11(3):1–21. https://doi.org/10.1371/journal.pcbi.1004148.
-
(2015)
Plos Comp Biol
, vol.11
, Issue.3
, pp. 1-21
-
-
Provasi, D.1
-
119
-
-
84948845292
-
Organization and dynamics of receptor proteins in a plasma membrane
-
Koldsø H, Sansom MSP (2015) Organization and dynamics of receptor proteins in a plasma membrane. J Am Chem Soc 137:14694–14704. https://doi.org/10.1021/jacs.5b08048.
-
(2015)
J am Chem Soc
, vol.137
, pp. 14694-14704
-
-
Koldsø, H.1
Sansom, M.2
-
120
-
-
84857254248
-
Crystal structure of a lipid G protein – coupled receptor
-
Reinhart G, Desale H, Clemons B, Cahalan SM, Schuerer SC (2012) Crystal structure of a lipid G protein – coupled receptor. Science 335:851–856.
-
(2012)
Science
, vol.335
, pp. 851-856
-
-
Reinhart, G.1
Desale, H.2
Clemons, B.3
Cahalan, S.M.4
Schuerer, S.C.5
-
121
-
-
0024996249
-
Modulation of the potency and efficacy of μ-mediated antinociception by delta agonists in the mouse
-
Jiang Q, Mosberg HI, Porreca F (1990) Modulation of the potency and efficacy of μ-mediated antinociception by delta agonists in the mouse. J Pharmacol Exp Ther 254:683–689.
-
(1990)
J Pharmacol Exp Ther
, vol.254
, pp. 683-689
-
-
Jiang, Q.1
Mosberg, H.I.2
Porreca, F.3
-
122
-
-
84976904319
-
GPCRdb: An information system for G protein-coupled receptors
-
Isberg V, Mordalski S, Munk C, Rataj K, Harpsøe K, Hauser AS, Vroling B, Bojarski AJ, Vriend G, Gloriam DE (2016) GPCRdb: an information system for G protein-coupled receptors. Nucleic Acids Res 44(D1):D356–D364. https://doi.org/10.1093/nar/gkv1178.
-
(2016)
Nucleic Acids Res
, vol.44
, Issue.D1
, pp. D356-D364
-
-
Isberg, V.1
Mordalski, S.2
Munk, C.3
Rataj, K.4
Harpsøe, K.5
Hauser, A.S.6
Vroling, B.7
Bojarski, A.J.8
Vriend, G.9
Gloriam, D.E.10
-
123
-
-
84947998906
-
Activation and allosteric modulation of human μ opioid receptor in molecular dynamics
-
Bartuzi D, Kaczor AA, Matosiuk D (2015) Activation and allosteric modulation of human μ opioid receptor in molecular dynamics. J Chem Inf Model 55(11):2421–2434. https://doi.org/10.1021/acs.jcim.5b00280.
-
(2015)
J Chem Inf Model
, vol.55
, Issue.11
, pp. 2421-2434
-
-
Bartuzi, D.1
Kaczor, A.A.2
Matosiuk, D.3
-
124
-
-
79954524314
-
From coarse grained to atomistic: A serial multiscale approach to membrane protein simulations
-
Stansfeld PJ, Sansom MSP (2011) From coarse grained to atomistic: a serial multiscale approach to membrane protein simulations. J Chem Theory Comput 7(4):1157–1166. https://doi.org/10.1021/ct100569y.
-
(2011)
J Chem Theory Comput
, vol.7
, Issue.4
, pp. 1157-1166
-
-
Stansfeld, P.J.1
Sansom, M.2
-
125
-
-
84894191338
-
Going backward: A flexible geometric approach to reverse transformation from coarse grained to atomistic models
-
Wassenaar TA, Pluhackova K, Böckmann RA, Marrink SJ, Tieleman DP (2014) Going backward: a flexible geometric approach to reverse transformation from coarse grained to atomistic models. J Chem Theor Comput 10(2):676–690. https://doi.org/10.1021/ct400617g.
-
(2014)
J Chem Theor Comput
, vol.10
, Issue.2
, pp. 676-690
-
-
Wassenaar, T.A.1
Pluhackova, K.2
Böckmann, R.A.3
Marrink, S.J.4
Tieleman, D.P.5
-
126
-
-
84955167919
-
CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field
-
Lee J, Cheng X, Swails JM, Yeom MS, Eastman PK, Lemkul JA, Wei S, Buckner J, Jeong JC, Qi Y, Jo S, Pande VS, Case DA, Brooks CL, MacKerell AD, Klauda JB, Im W (2016) CHARMM-GUI input generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM simulations using the CHARMM36 additive force field. J Chem Theor Comput 12(1):405–413. https://doi.org/10.1021/acs.jctc.5b00935.
-
(2016)
J Chem Theor Comput
, vol.12
, Issue.1
, pp. 405-413
-
-
Lee, J.1
Cheng, X.2
Swails, J.M.3
Yeom, M.S.4
Eastman, P.K.5
Lemkul, J.A.6
Wei, S.7
Buckner, J.8
Jeong, J.C.9
Qi, Y.10
Jo, S.11
Pande, V.S.12
Case, D.A.13
Brooks, C.L.14
Mackerell, A.D.15
Klauda, J.B.16
Im, W.17
-
127
-
-
84925062589
-
Computational lipidomics with insane: A versatile tool for generating custom membranes for molecular simulations
-
Wassenaar TA, Ingólfsson HI, Böckmann RA, Tieleman DP, Marrink SJ (2015) Computational lipidomics with insane: a versatile tool for generating custom membranes for molecular simulations. J Chem Theor Comput 11(5):2144–2155.
-
(2015)
J Chem Theor Comput
, vol.11
, Issue.5
, pp. 2144-2155
-
-
Wassenaar, T.A.1
Ingólfsson, H.I.2
Böckmann, R.A.3
Tieleman, D.P.4
Marrink, S.J.5
|