-
1
-
-
77954257799
-
ConSurf 2010: Calculating evolutionary conservation in sequence and structure of proteins and nucleic acids
-
Ashkenazy H., Erez E., Martz E., Pupko T., Ben-Tal N. ConSurf 2010: Calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Research 2010, 38(Web Server):W529-W533. 10.1093/nar/gkq399.
-
(2010)
Nucleic Acids Research
, vol.38
, Issue.WEB SERVER
-
-
Ashkenazy, H.1
Erez, E.2
Martz, E.3
Pupko, T.4
Ben-Tal, N.5
-
2
-
-
84871286519
-
Restructuring G-protein-coupled receptor activation
-
Audet M., Bouvier M. Restructuring G-protein-coupled receptor activation. Cell 2012, 151(1):14-23. 10.1016/j.cell.2012.09.003.
-
(2012)
Cell
, vol.151
, Issue.1
, pp. 14-23
-
-
Audet, M.1
Bouvier, M.2
-
3
-
-
0035964342
-
Electrostatics of nanosystems: Application to microtubules and the ribosome
-
Baker N.A., Sept D., Joseph S., Holst M.J., McCammon J.A. Electrostatics of nanosystems: Application to microtubules and the ribosome. Proceedings of the National Academy of Sciences of the United States of America 2001, 98(18):10037-10041. 10.1073/pnas.181342398.
-
(2001)
Proceedings of the National Academy of Sciences of the United States of America
, vol.98
, Issue.18
, pp. 10037-10041
-
-
Baker, N.A.1
Sept, D.2
Joseph, S.3
Holst, M.J.4
McCammon, J.A.5
-
4
-
-
0033954256
-
The Protein Data Bank
-
Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., et al. The Protein Data Bank. Nucleic Acids Research 2000, 28(1):235-242.
-
(2000)
Nucleic Acids Research
, vol.28
, Issue.1
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
-
5
-
-
84864751433
-
Membrane-sensitive conformational states of helix 8 in the metabotropic Glu2 receptor, a class C GPCR
-
Bruno A., Costantino G., de Fabritiis G., Pastor M., Selent J. Membrane-sensitive conformational states of helix 8 in the metabotropic Glu2 receptor, a class C GPCR. PLoS One 2012, 7(8):e42023. 10.1371/journal.pone.0042023.
-
(2012)
PLoS One
, vol.7
, Issue.8
-
-
Bruno, A.1
Costantino, G.2
de Fabritiis, G.3
Pastor, M.4
Selent, J.5
-
6
-
-
77958551193
-
APBSmem: A graphical interface for electrostatic calculations at the membrane
-
Callenberg K.M., Choudhary O.P., de Forest G.L., Gohara D.W., Baker N.A., Grabe M. APBSmem: A graphical interface for electrostatic calculations at the membrane. PloS One 2010, 5(9). 10.1371/journal.pone.0012722.
-
(2010)
PloS One
, vol.5
, Issue.9
-
-
Callenberg, K.M.1
Choudhary, O.P.2
de Forest, G.L.3
Gohara, D.W.4
Baker, N.A.5
Grabe, M.6
-
7
-
-
77955391393
-
The HADDOCK web server for data-driven biomolecular docking
-
De Vries S.J., van Dijk M., Bonvin A.M.J.J. The HADDOCK web server for data-driven biomolecular docking. Nature Protocols 2010, 5(5):883-897. 10.1038/nprot.2010.32.
-
(2010)
Nature Protocols
, vol.5
, Issue.5
, pp. 883-897
-
-
De Vries, S.J.1
van Dijk, M.2
Bonvin, A.M.J.J.3
-
8
-
-
84874637986
-
G-protein-coupled receptor structure, ligand binding and activation as studied by solid-state NMR spectroscopy
-
Ding X., Zhao X., Watts A. G-protein-coupled receptor structure, ligand binding and activation as studied by solid-state NMR spectroscopy. The Biochemical Journal 2013, 450(3):443-457. 10.1042/BJ20121644.
-
(2013)
The Biochemical Journal
, vol.450
, Issue.3
, pp. 443-457
-
-
Ding, X.1
Zhao, X.2
Watts, A.3
-
9
-
-
81755163613
-
2-adrenergic receptor
-
2-adrenergic receptor. Proceedings of the National Academy of Sciences of the United States of America 2011, 108(46):18684-18689. 10.1073/pnas.1110499108.
-
(2011)
Proceedings of the National Academy of Sciences of the United States of America
, 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
-
10
-
-
80052001378
-
Pathway and mechanism of drug binding to G-protein-coupled receptors
-
Dror R., Pan A., Arlow D.H., Borhani D.W., Maragakis P., Shan Y., et al. Pathway and mechanism of drug binding to G-protein-coupled receptors. Proceedings of the National Academy of Sciences of the United States of America 2011, 108(32):13118-13123. 10.1073/pnas.1104614108/-/DCSupplemental.www.pnas.org/cgi/doi/10.1073/pnas.1104614108.
-
(2011)
Proceedings of the National Academy of Sciences of the United States of America
, vol.108
, Issue.32
, pp. 13118-13123
-
-
Dror, R.1
Pan, A.2
Arlow, D.H.3
Borhani, D.W.4
Maragakis, P.5
Shan, Y.6
-
11
-
-
73649109875
-
Activation of the ghrelin receptor is described by a privileged collective motion: A model for constitutive and agonist-induced activation of a sub-class A G-protein coupled receptor (GPCR)
-
Floquet N., M'Kadmi C., Perahia D., Gagne D., Bergé G., Marie J., et al. Activation of the ghrelin receptor is described by a privileged collective motion: A model for constitutive and agonist-induced activation of a sub-class A G-protein coupled receptor (GPCR). Journal of Molecular Biology 2010, 395(4):769-784. 10.1016/j.jmb.2009.09.051.
-
(2010)
Journal of Molecular Biology
, vol.395
, Issue.4
, pp. 769-784
-
-
Floquet, N.1
M'Kadmi, C.2
Perahia, D.3
Gagne, D.4
Bergé, G.5
Marie, J.6
-
12
-
-
0035816704
-
Functionally different agonists induce distinct conformations in the G protein coupling domain of the beta 2 adrenergic receptor
-
Ghanouni P., Gryczynski Z., Steenhuis J.J., Lee T.W., Farrens D.L., Lakowicz J.R., et al. Functionally different agonists induce distinct conformations in the G protein coupling domain of the beta 2 adrenergic receptor. Journal of Biological Chemistry 2001, 276(27):24433-24436. 10.1074/jbc.C100162200.
-
(2001)
Journal of Biological Chemistry
, vol.276
, Issue.27
, pp. 24433-24436
-
-
Ghanouni, P.1
Gryczynski, Z.2
Steenhuis, J.J.3
Lee, T.W.4
Farrens, D.L.5
Lakowicz, J.R.6
-
13
-
-
84858226578
-
Crosstalk within GPCR heteromers in schizophrenia and Parkinson's disease: Physical or just functional?
-
Guixa-Gonzalez R., Bruno A., Marti-Solano M., Selent J. Crosstalk within GPCR heteromers in schizophrenia and Parkinson's disease: Physical or just functional?. Current Medicinal Chemistry 2012, 19(8):1119-1134.
-
(2012)
Current Medicinal Chemistry
, vol.19
, Issue.8
, pp. 1119-1134
-
-
Guixa-Gonzalez, R.1
Bruno, A.2
Marti-Solano, M.3
Selent, J.4
-
15
-
-
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. Journal of Chemical Theory and Computation 2008, 4(3):435-447. 10.1021/ct700301q.
-
(2008)
Journal of Chemical Theory and Computation
, vol.4
, Issue.3
, pp. 435-447
-
-
Hess, B.1
Kutzner, C.2
van der Spoel, D.3
Lindahl, E.4
-
16
-
-
25444528449
-
WEBnm@: A web application for normal mode analyses of proteins
-
Hollup S.M., Salensminde G., Reuter N. WEBnm@: A web application for normal mode analyses of proteins. BMC Bioinformatics 2005, 6:52. 10.1186/1471-2105-6-52.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 52
-
-
Hollup, S.M.1
Salensminde, G.2
Reuter, N.3
-
17
-
-
33751094833
-
Predisposition of the dark state of rhodopsin to functional changes in structure
-
Isin B., Rader A.J., Dhiman H.K., Klein-Seetharaman J., Bahar I. Predisposition of the dark state of rhodopsin to functional changes in structure. Proteins 2006, 65(4):970-983. 10.1002/prot.21158.
-
(2006)
Proteins
, vol.65
, Issue.4
, pp. 970-983
-
-
Isin, B.1
Rader, A.J.2
Dhiman, H.K.3
Klein-Seetharaman, J.4
Bahar, I.5
-
18
-
-
78149422216
-
Protein-protein docking tested in blind predictions: The CAPRI experiment
-
Janin J. Protein-protein docking tested in blind predictions: The CAPRI experiment. Molecular BioSystems 2010, 6(12):2351-2362. 10.1039/c005060c.
-
(2010)
Molecular BioSystems
, vol.6
, Issue.12
, pp. 2351-2362
-
-
Janin, J.1
-
19
-
-
84867576743
-
Fractal dimension as a measure of surface roughness of G protein-coupled receptors: Implications for structure and function
-
Kaczor A.A., Guixà-González R., Carrió P., Obiol-Pardo C., Pastor M., Selent J. Fractal dimension as a measure of surface roughness of G protein-coupled receptors: Implications for structure and function. Journal of Molecular Modeling 2012, 18(9):4465-4475. 10.1007/s00894-012-1431-2.
-
(2012)
Journal of Molecular Modeling
, vol.18
, Issue.9
, pp. 4465-4475
-
-
Kaczor, A.A.1
Guixà-González, R.2
Carrió, P.3
Obiol-Pardo, C.4
Pastor, M.5
Selent, J.6
-
20
-
-
84978052316
-
Exploring G-protein coupled receptors oligomerization interface with adaptive Poisson-Boltzmann solver (APBS)
-
Kaczor A.A., Lopez L., Pastor M., Selent J. Exploring G-protein coupled receptors oligomerization interface with adaptive Poisson-Boltzmann solver (APBS). Drugs Future 2010, 35(Suppl. A):122-123.
-
(2010)
Drugs Future
, vol.35
, Issue.SUPPL. A
, pp. 122-123
-
-
Kaczor, A.A.1
Lopez, L.2
Pastor, M.3
Selent, J.4
-
21
-
-
80053511695
-
Oligomerization of G protein-coupled receptors: Biochemical and biophysical methods
-
Kaczor A.A., Selent J. Oligomerization of G protein-coupled receptors: Biochemical and biophysical methods. Current Medicinal Chemistry 2011, 18(30):4606-4634.
-
(2011)
Current Medicinal Chemistry
, vol.18
, Issue.30
, pp. 4606-4634
-
-
Kaczor, A.A.1
Selent, J.2
-
22
-
-
84882454897
-
Modeling complexes of transmembrane proteins: Systematic analysis of protein-protein docking tools
-
Kaczor A.A., Selent J., Sanz F., Pastor M. Modeling complexes of transmembrane proteins: Systematic analysis of protein-protein docking tools. Molecular Informatics 2013, 32:717-733.
-
(2013)
Molecular Informatics
, vol.32
, pp. 717-733
-
-
Kaczor, A.A.1
Selent, J.2
Sanz, F.3
Pastor, M.4
-
23
-
-
80051521545
-
Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment
-
Kufareva I., Rueda M., Katritch V., Stevens R.C., Abagyan R. Status of GPCR modeling and docking as reflected by community-wide GPCR Dock 2010 assessment. Structure (London, England: 1993) 2011, 19(8):1108-1126. 10.1016/j.str.2011.05.012.
-
(2011)
Structure (London, England: 1993)
, vol.19
, Issue.8
, pp. 1108-1126
-
-
Kufareva, I.1
Rueda, M.2
Katritch, V.3
Stevens, R.C.4
Abagyan, R.5
-
24
-
-
0020491251
-
A geometric approach to macromolecule-ligand interactions
-
Kuntz I.D., Blaney J.M., Oatley S.J., Langridge R., Ferrin T.E. A geometric approach to macromolecule-ligand interactions. Journal of Molecular Biology 1982, 161(2):269-288.
-
(1982)
Journal of Molecular Biology
, vol.161
, Issue.2
, pp. 269-288
-
-
Kuntz, I.D.1
Blaney, J.M.2
Oatley, S.J.3
Langridge, R.4
Ferrin, T.E.5
-
25
-
-
78650905964
-
ROSETTA3: An object-oriented software suite for the simulation and design of macromolecules
-
Leaver-Fay A., Tyka M., Lewis S.M., Lange O.F., Thompson J., Jacak R., et al. ROSETTA3: An object-oriented software suite for the simulation and design of macromolecules. Methods in Enzymology 2011, 487:545-574. 10.1016/B978-0-12-381270-4.00019-6.
-
(2011)
Methods in Enzymology
, vol.487
, pp. 545-574
-
-
Leaver-Fay, A.1
Tyka, M.2
Lewis, S.M.3
Lange, O.F.4
Thompson, J.5
Jacak, R.6
-
26
-
-
33747858757
-
NOMAD-Ref: Visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis
-
Lindahl E., Azuara C., Koehl P., Delarue M. NOMAD-Ref: Visualization, deformation and refinement of macromolecular structures based on all-atom normal mode analysis. Nucleic Acids Research 2006, 34(Web Server):W52-W56. 10.1093/nar/gkl082.
-
(2006)
Nucleic Acids Research
, vol.34
, Issue.WEB SERVER
-
-
Lindahl, E.1
Azuara, C.2
Koehl, P.3
Delarue, M.4
-
27
-
-
84861961427
-
Structural basis for allosteric regulation of GPCRs by sodium ions
-
Liu W., Chun E., Thompson A.A., Chubukov P., Xu F., Katritch V., et al. Structural basis for allosteric regulation of GPCRs by sodium ions. Science 2012, 337(6091):232-236. 10.1126/science.1219218.
-
(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
-
28
-
-
84870702282
-
Structure-function studies with G protein-coupled receptors as a paradigm for improving drug discovery and development of therapeutics
-
McNeely P.M., Naranjo A.N., Robinson A.S. Structure-function studies with G protein-coupled receptors as a paradigm for improving drug discovery and development of therapeutics. Biotechnology Journal 2012, 7(12):1451-1461. 10.1002/biot.201200076.
-
(2012)
Biotechnology Journal
, vol.7
, Issue.12
, pp. 1451-1461
-
-
McNeely, P.M.1
Naranjo, A.N.2
Robinson, A.S.3
-
29
-
-
80455164853
-
Quantitative modeling of membrane deformations by multihelical membrane proteins: Application to G-protein coupled receptors
-
Mondal S., Khelashvili G., Shan J., Andersen O.S., Weinstein H. Quantitative modeling of membrane deformations by multihelical membrane proteins: Application to G-protein coupled receptors. Biophysical Journal 2011, 101(9):2092-2101. 10.1016/j.bpj.2011.09.037.
-
(2011)
Biophysical Journal
, vol.101
, Issue.9
, pp. 2092-2101
-
-
Mondal, S.1
Khelashvili, G.2
Shan, J.3
Andersen, O.S.4
Weinstein, H.5
-
30
-
-
41149141017
-
Influence of oligomerization on the dynamics of G-protein coupled receptors as assessed by normal mode analysis
-
Niv M.Y., Filizola M. Influence of oligomerization on the dynamics of G-protein coupled receptors as assessed by normal mode analysis. Proteins 2008, 71(2):575-586. 10.1002/prot.21787.
-
(2008)
Proteins
, vol.71
, Issue.2
, pp. 575-586
-
-
Niv, M.Y.1
Filizola, M.2
-
31
-
-
34548671028
-
Modeling activated states of GPCRs: The rhodopsin template
-
Niv M.Y., Skrabanek L., Filizola M., Weinstein H. Modeling activated states of GPCRs: The rhodopsin template. Journal of Computer-Aided Molecular Design 2006, 20(7-8):437-448. 10.1007/s10822-006-9061-3.
-
(2006)
Journal of Computer-Aided Molecular Design
, vol.20
, Issue.7-8
, pp. 437-448
-
-
Niv, M.Y.1
Skrabanek, L.2
Filizola, M.3
Weinstein, H.4
-
32
-
-
84858236079
-
Ensemble of G protein-coupled receptor active states
-
Park P.S. Ensemble of G protein-coupled receptor active states. Current Medicinal Chemistry 2012, 19(8):1146-1154.
-
(2012)
Current Medicinal Chemistry
, vol.19
, Issue.8
, pp. 1146-1154
-
-
Park, P.S.1
-
33
-
-
34548146523
-
G protein-coupled receptors self-assemble in dynamics simulations of model bilayers
-
Periole X., Huber T., Marrink S.-J., Sakmar T.P. G protein-coupled receptors self-assemble in dynamics simulations of model bilayers. Journal of the American Chemical Society 2007, 129(33):10126-10132. 10.1021/ja0706246.
-
(2007)
Journal of the American Chemical Society
, vol.129
, Issue.33
, pp. 10126-10132
-
-
Periole, X.1
Huber, T.2
Marrink, S.-J.3
Sakmar, T.P.4
-
34
-
-
84863535732
-
Structural determinants of the supramolecular organization of G protein-coupled receptors in bilayers
-
Periole X., Knepp A.M., Sakmar T.P., Marrink S.J., Huber T. Structural determinants of the supramolecular organization of G protein-coupled receptors in bilayers. Journal of the American Chemical Society 2012, 134(26):10959-10965. 10.1021/ja303286e.
-
(2012)
Journal of the American Chemical Society
, vol.134
, Issue.26
, pp. 10959-10965
-
-
Periole, X.1
Knepp, A.M.2
Sakmar, T.P.3
Marrink, S.J.4
Huber, T.5
-
35
-
-
84872926726
-
Molecular modeling and simulation of membrane lipid-mediated effects on GPCRs
-
Sadiq S.K., Guixa-Gonzalez R., Dainese E., Pastor M., De Fabritiis G., Selent J. Molecular modeling and simulation of membrane lipid-mediated effects on GPCRs. Current Medicinal Chemistry 2013, 20(1):22-38.
-
(2013)
Current Medicinal Chemistry
, vol.20
, Issue.1
, pp. 22-38
-
-
Sadiq, S.K.1
Guixa-Gonzalez, R.2
Dainese, E.3
Pastor, M.4
De Fabritiis, G.5
Selent, J.6
-
36
-
-
21644459373
-
Progress in protein-protein docking: Atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility
-
Schueler-Furman O., Wang C., Baker D. Progress in protein-protein docking: Atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility. Proteins 2005, 60(2):187-194. 10.1002/prot.20556.
-
(2005)
Proteins
, vol.60
, Issue.2
, pp. 187-194
-
-
Schueler-Furman, O.1
Wang, C.2
Baker, D.3
-
37
-
-
80053487319
-
Oligomerization of G protein-coupled receptors: Computational methods
-
Selent J., Kaczor A.A. Oligomerization of G protein-coupled receptors: Computational methods. Current Medicinal Chemistry 2011, 18(30):4588-4605.
-
(2011)
Current Medicinal Chemistry
, vol.18
, Issue.30
, pp. 4588-4605
-
-
Selent, J.1
Kaczor, A.A.2
-
38
-
-
78049415021
-
Induced effects of sodium ions on dopaminergic G-protein coupled receptors
-
pii: e1000884
-
Selent J., Sanz F., Pastor M., De Fabritiis G. Induced effects of sodium ions on dopaminergic G-protein coupled receptors. PLoS Computational Biology 2010, 6(8). pii: e1000884. 10.1371/journal.pcbi.1000884.
-
(2010)
PLoS Computational Biology
, vol.6
, Issue.8
-
-
Selent, J.1
Sanz, F.2
Pastor, M.3
De Fabritiis, G.4
-
39
-
-
34548135296
-
TMM@: A web application for the analysis of transmembrane helix mobility
-
Skjaerven L., Jonassen I., Reuter N. TMM@: A web application for the analysis of transmembrane helix mobility. BMC Bioinformatics 2007, 8:232. 10.1186/1471-2105-8-232.
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 232
-
-
Skjaerven, L.1
Jonassen, I.2
Reuter, N.3
-
40
-
-
3242875210
-
ElNemo: A normal mode web server for protein movement analysis and the generation of templates for molecular replacement
-
Suhre K., Sanejouand Y.-H. ElNemo: A normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Research 2004, 32(Web Server):W610-W614. 10.1093/nar/gkh368.
-
(2004)
Nucleic Acids Research
, vol.32
, Issue.WEB SERVER
-
-
Suhre, K.1
Sanejouand, Y.-H.2
-
41
-
-
67649550094
-
Low-frequency vibrational modes and infrared absorbance of red, blue and green opsin
-
Thirumuruganandham S.P., Urbassek H.M. Low-frequency vibrational modes and infrared absorbance of red, blue and green opsin. Journal of Molecular Modeling 2009, 15(8):959-969. 10.1007/s00894-008-0446-1.
-
(2009)
Journal of Molecular Modeling
, vol.15
, Issue.8
, pp. 959-969
-
-
Thirumuruganandham, S.P.1
Urbassek, H.M.2
-
42
-
-
33747840389
-
GRAMM-X public web server for protein-protein docking
-
Tovchigrechko A., Vakser I.A. GRAMM-X public web server for protein-protein docking. Nucleic Acids Research 2006, 34(Suppl. 2):W310-W314. 10.1093/nar/gkl206.
-
(2006)
Nucleic Acids Research
, vol.34
, Issue.SUPPL. 2
-
-
Tovchigrechko, A.1
Vakser, I.A.2
-
43
-
-
0018165127
-
Computer analysis of protein-protein interaction
-
Wodak S.J., Janin J. Computer analysis of protein-protein interaction. Journal of Molecular Biology 1978, 124(2):323-342.
-
(1978)
Journal of Molecular Biology
, vol.124
, Issue.2
, pp. 323-342
-
-
Wodak, S.J.1
Janin, J.2
|