xdeupi's theory [43 articles] Export

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	Low barrier kinetics: Dependence on observables and free energy surface [My Copy] Journal of Computational Chemistry, Vol. 27, No. 2. (2006), pp. 125-134. by Hairong Ma, Martin Gruebele posted to theory energy_landscape activation by xdeupi on 2009-11-10 14:46:07 as
	Modern Homology Modeling of G-Protein Coupled Receptors: Which Structural Template to Use? [My Copy] Journal of Medicinal Chemistry, Vol. 52, No. 16. (27 August 2009), pp. 5207-5216. by Juan C. Mobarec, Roberto Sanchez, Marta Filizola posted to theory modeling gpcr docking by xdeupi on 2009-10-08 16:39:12 as along with 2 people dimka reyez
	Identification of two distinct inactive conformations of the beta2-adrenergic receptor reconciles structural and biochemical observations. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 106, No. 12. (24 March 2009), pp. 4689-4694. by Ron O. Dror, Daniel H. Arlow, David W. Borhani, Morten Ø. Jensen, Stefano Piana, David E. Shaw posted to theory structure modeling md flexibility dynamics b2ar activation by xdeupi on 2009-10-08 11:13:04 as along with 2 people dimka agrossfield
	Modeling G protein-coupled receptors for structure-based drug discovery using low-frequency normal modes for refinement of homology models: Application to H3 antagonists. [My Copy] Proteins (12 August 2009) by Brajesh K. Rai, Gregory J. Tawa, Alan H. Katz, Christine Humblet posted to theory modeling md gpcr by xdeupi on 2009-10-06 19:31:07 as
	Computational analysis of membrane proteins: the largest class of drug targets. [My Copy] Drug discovery today (3 September 2009) by Yalini Arinaminpathy, Ekta Khurana, Donald M. Engelman, Mark B. Gerstein posted to theory membrane_proteins drug by xdeupi on 2009-10-06 19:23:18 as
	Homology modeling of GPCRs. [My Copy] Methods in molecular biology (Clifton, N.J.), Vol. 552 (2009), pp. 97-113. by John Simms, Nathan E. Hall, Polo H. Lam, et al.Laurence J. Miller, Arthur Christopoulos, Ruben Abagyan, Patrick M. Sexton posted to theory review modeling gpcr by xdeupi on 2009-10-06 18:14:40 as
	Using sequence similarity networks for visualization of relationships across diverse protein superfamilies. [My Copy] PloS one, Vol. 4, No. 2. (3 February 2009), e4345. by Holly J. Atkinson, John H. Morris, Thomas E. Ferrin, Patricia C. Babbitt posted to theory sequence phylogeny networks by xdeupi on 2009-10-06 18:08:37 as along with 4 people robert85 Keywan druvus oteri
	Structural and dynamic effects of cholesterol at preferred sites of interaction with rhodopsin identified from microsecond length molecular dynamics simulations. [My Copy] Proteins, Vol. 76, No. 2. (1 August 2009), pp. 403-417. by George Khelashvili, Alan Grossfield, Scott E. Feller, Michael C. Pitman, Harel Weinstein posted to theory rhodopsin md cholesterol by xdeupi on 2009-10-06 18:06:55 as along with 1 person and 1 group sobolevnrm baker-group
	gpDB: a database of GPCRs, G-proteins, effectors and their interactions. [My Copy] Bioinformatics (Oxford, England), Vol. 24, No. 12. (15 June 2008), pp. 1471-1472. by Margarita C. Theodoropoulou, Pantelis G. Bagos, Ioannis C. Spyropoulos, Stavros J. Hamodrakas posted to webserver theory gproteins gpcr by xdeupi on 2009-10-06 18:02:45 as along with 1 person guhjy
	MemBrain: improving the accuracy of predicting transmembrane helices. [My Copy] PloS one, Vol. 3, No. 6. (2008) by Hongbin Shen, James J. Chou posted to webserver tmhs theory membrane_proteins helix by xdeupi on 2009-10-06 18:00:49 as
	Position of helical kinks in membrane protein crystal structures and the accuracy of computational prediction. [My Copy] Journal of molecular graphics & modelling, Vol. 27, No. 8. (June 2009), pp. 944-950. by Spencer E. Hall, Kyle Roberts, Nagarajan Vaidehi posted to theory pro-kink membrane_proteins kinks helix by xdeupi on 2009-10-06 17:52:20 as
	New vistas in GPCR 3D structure prediction [My Copy] Journal of Molecular Modeling by Anwar Rayan posted to theory sequence_alignment sequence modeling gpcr by xdeupi on 2009-10-06 17:47:03 as along with 1 person arnaucordomi
	Definition of the G Protein-Coupled Receptor Transmembrane Bundle Binding Pocket and Calculation of Receptor Similarities for Drug Design [My Copy] Journal of Medicinal Chemistry, Vol. 52, No. 14. (23 July 2009), pp. 4429-4442. by David E. Gloriam, Steven M. Foord, Frank E. Blaney, Stephen L. Garland posted to theory gpcr drug binding_site by xdeupi on 2009-10-06 17:42:06 as
	Web Server To Identify Similarity of Amino Acid Motifs to Compounds (SAAMCO) [My Copy] Journal of Chemical Information and Modeling, Vol. 48, No. 7. (1 July 2008), pp. 1524-1529. by Fergal P. Casey, Norman E. Davey, Ivan Baran, Radka S. Varekova, Denis C. Shields posted to webserver theory pharmacology ligands drug by xdeupi on 2009-10-05 18:46:59 as along with 1 person higueruelo
	Hot-Spots-Guided Receptor-Based Pharmacophores (HS-Pharm): A Knowledge-Based Approach to Identify Ligand-Anchoring Atoms in Protein Cavities and Prioritize Structure-Based Pharmacophores [My Copy] Journal of Chemical Information and Modeling, Vol. 48, No. 7. (1 July 2008), pp. 1396-1410. by Caterina Barillari, Gilles Marcou, Didier Rognan posted to theory pharmacology ligands drug docking binding b2ar agonist by xdeupi on 2009-10-05 18:45:05 as along with 3 people tbinbal superpyrin higueruelo
	Influence of the g- conformation of Ser and Thr on the structure of transmembrane helices. [My Copy] Journal of structural biology (17 September 2009) by Xavier Deupi, Mireia Olivella, Arantxa Sanz, Nicole Dölker, Mercedes Campillo, Leonardo Pardo posted to tm5 theory structure ser plasticity helix hbond flexibility dynamics amber activation by xdeupi on 2009-09-25 14:15:01 as
	Parameterization of aromatic azido groups: application as photoaffinity probes in molecular dynamics studies [My Copy] Journal of Molecular Modeling by Gilles Pieffet, Pavel Petukhov posted to theory spectroscopy modeling md fluorescence amber by xdeupi on 2009-09-15 14:25:43 as
	Exploring allosteric coupling in the alpha-subunit of heterotrimeric G proteins using evolutionary and ensemble-based approaches. [My Copy] BMC structural biology, Vol. 8 (02 May 2008), 23. by Kemal Sayar, Ozlem Uğur, Tong Liu, Vincent J. Hilser, Ongun Onaran posted to theory gproteins activation by xdeupi on 2009-09-08 12:24:17 as
	The energy landscapes and motions of proteins. [My Copy] Science (New York, N.Y.), Vol. 254, No. 5038. (13 December 1991), pp. 1598-1603. by H. Frauenfelder, S. G. Sligar, P. G. Wolynes posted to theory review plasticity kinetics flexibility energy_landscape dynamics active-state activation by xdeupi on 2009-08-31 15:05:33 as along with 3 people FilipeMaia naitsabes kjell
	Dynamic energy landscape view of coupled binding and protein conformational change: Induced-fit versus population-shift mechanisms [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 32. (12 August 2008), pp. 11182-11187. by Kei-ichi Okazaki, Shoji Takada posted to activation active-state dynamics energy_landscape flexibility kinetics modeling nmr plasticity theory by xdeupi on 2009-07-11 11:26:37 as along with 8 people and 2 groups oteri bmduggan okapi aqeel raik ruvido barry zwang structural_bioinformatics McCammon
	The Thermodynamic Landscape of Testosterone Binding to Cytochrome P450 3A4: Ligand Binding and Spin State Equilibria† [My Copy] Biochemistry, Vol. 44, No. 4. (1 February 2005), pp. 1353-1366. by Arthur G. Roberts, Patricia A. Campbell, William M. Atkins posted to binding energy_landscape theory by xdeupi on 2009-06-27 12:33:29 as
	Predicting structurally conserved contacts for homologous proteins using sequence conservation filters [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 77, No. 2. (20 April 2009), pp. 448-453. by Mayako Michino, Charles L. Brooks posted to gpcr structure theory by xdeupi on 2009-06-09 15:46:32 as along with 1 person and 1 group AliC Orengo Group Journal Picks
	Computing Highly Correlated Positions Using Mutual Information and Graph Theory for G Protein-Coupled Receptors [My Copy] PLoS ONE, Vol. 4, No. 3. (5 March 2009), e4681. by Sarosh N. Fatakia, Stefano Costanzi, Carson C. Chow posted to gpcrs sequence theory by xdeupi on 2009-06-08 13:52:17 as along with 1 person and 1 group sobolevnrm baker-group
	Chaos in Biomolecular Dynamics [My Copy] J. Phys. Chem., Vol. 100, No. 20. (16 May 1996), pp. 8101-8105. by H. Zhou, L. Wang posted to dynamics folding md modeling theory by xdeupi on 2009-06-08 12:28:13 as along with 1 person allmensch
	Inter-helical Interactions in Membrane Proteins: Analysis Based on the Local Backbone Geometry and the Side Chain Interactions. [My Copy] Journal of biomolecular structure & dynamics, Vol. 26, No. 6. (June 2009), pp. 719-730. by A. N. Jha, S. Vishveshwara posted to dimer helix membrane_proteins structure theory transmembrane by xdeupi on 2009-05-06 09:54:37 as
	Wide turn diversity in protein transmembrane helices implications for G-protein-coupled receptor and other polytopic membrane protein structure and function. [My Copy] Molecular pharmacology, Vol. 73, No. 4. (April 2008), pp. 1092-1104. by R. Peter Riek, Angela A. Finch, Gillian E. Begg, Robert M. Graham posted to flexibility helix membrane_proteins modeling pro-kink ser structure theory thr transmembrane by xdeupi on 2009-04-17 11:47:42 as
	Virtual photons, dipole fields and energy transfer: a quantum electrodynamical approach [My Copy] European Journal of Physics, Vol. 25, No. 6. (2004), pp. 845-858. by David L. Andrews, David S. Bradshaw posted to fret theory by xdeupi on 2009-03-18 11:15:27 as
	Investigation of transmembrane proteins using a computational approach. [My Copy] BMC genomics, Vol. 9 Suppl 1 (2008) by J. Y. Yang, M. Q. Yang, A. K. Dunker, Y. Deng, X. Huang posted to disorder gpcr loops membrane_proteins structure theory transmembrane by xdeupi on 2008-10-20 22:23:57 as
	Proline-induced distortions of transmembrane helices. [My Copy] J Mol Biol, Vol. 323, No. 5. (8 November 2002), pp. 951-960. by F. S. Cordes, J. N. Bright, M. S. Sansom posted to activation helix membrane_proteins pro-kink structure theory transmembrane by xdeupi on 2008-05-27 11:58:27 as along with 1 person thaliana
	Computational analysis of membrane proteins: genomic occurrence, structure prediction and helix interactions. [My Copy] Q Rev Biophys, Vol. 37, No. 2. (May 2004), pp. 121-146. by U. Lehnert, Y. Xia, T. E. Royce, et al.C. S. Goh, Y. Liu, A. Senes, H. Yu, Z. L. Zhang, D. M. Engelman, M. Gerstein posted to membrane_proteins review structure theory transmembrane by xdeupi on 2008-05-01 19:11:17 as along with 1 person thaliana
	Protein-Protein Docking with Backbone Flexibility [My Copy] Journal of Molecular Biology, Vol. 373, No. 2. (19 October 2007), pp. 503-519. by Chu Wang, Philip Bradley, David Baker posted to docking flexibility modeling theory by xdeupi on 2008-04-07 14:23:45 as along with 6 people and 2 groups mijam kgutwin csrocha barry jwm Ema structural_bioinformatics Bioinformatics
	Protein-Protein Docking with Simultaneous Optimization of Rigid-body Displacement and Side-chain Conformations [My Copy] Journal of Molecular Biology, Vol. 331, No. 1. (1 August 2003), pp. 281-299. by Jeffrey J. Gray, Stewart Moughon, Chu Wang, et al.Ora Schueler-Furman, Brian Kuhlman, Carol A. Rohl, David Baker posted to dimer docking modeling theory by xdeupi on 2008-04-07 14:18:56 as along with 4 people ima bluvsh1 selrac timg
	The relation between the divergence of sequence and structure in proteins. [My Copy] The EMBO journal, Vol. 5, No. 4. (April 1986), pp. 823-826. by C. Chothia, A. M. Lesk posted to sequence structure theory by xdeupi on 2008-04-02 15:48:23 as along with 14 people and 6 groups dfdong martainn ucbcjbm bertelsen semin sgoetz cen4ik ana pansapiens jwm Einat marcius ffranca insectopalo structural_bioinformatics Radiation_Damage Stressosome Bioinformatics BioinfoCIPF SGU-CIPF
	FRET Study of Membrane Proteins: Simulation-Based Fitting for Analysis of Membrane Protein Embedment and Association [My Copy] Biophys. J., Vol. 91, No. 2. (15 July 2006), pp. 454-466. by Petr V. Nazarov, Rob B. Koehorst, Werner L. Vos, Vladimir V. Apanasovich, Marcus A. Hemminga posted to dimer fluorescence fret theory by xdeupi on 2008-04-02 13:50:03 as along with 1 person dimka
	Primary photoprocess in vision: minimal motion to reach the photo- and bathorhodopsin intermediates. [My Copy] J Phys Chem B, Vol. 109, No. 18. (12 May 2005), pp. 9104-9110. by F. Blomgren, S. Larsson posted to activation retinal rhodopsin theory by xdeupi on 2007-07-30 16:59:24 as along with 1 group LabCompMed
	Refinement of a homology model of the mu-opioid receptor using distance constraints from intrinsic and engineered zinc-binding sites. [My Copy] Biochemistry, Vol. 43, No. 27. (13 July 2004), pp. 8700-8710. by C. B. Fowler, I. D. Pogozheva, H. LeVine, H. I. Mosberg posted to active-state modeling opioid structure theory by xdeupi on 2007-07-11 16:51:53 as along with 1 person and 1 group merj LabCompMed
	Development and testing of a general amber force field. [My Copy] J Comput Chem, Vol. 25, No. 9. (15 July 2004), pp. 1157-1174. by J. Wang, R. M. Wolf, J. W. Caldwell, P. A. Kollman, D. A. Case posted to amber dynamics md theory by xdeupi on 2007-06-26 13:51:26 as along with 10 people and 1 group rdf paddydu nigham lillekatt gane5h kazemi megs easybakemuffin AndreaColetta pavanghatty LabCompMed
	Performance of the general amber force field in modeling aqueous POPC membrane bilayers [My Copy] Journal of Computational Chemistry, Vol. 28, No. 12. (12 April 2007), pp. 2051-2058. by Balázs Jójárt, Tamás A. Martinek posted to amber dynamics md membrane modeling theory by xdeupi on 2007-06-26 13:32:45 as along with 3 people and 1 group dimka easybakemuffin viktor21614 LabCompMed
	Effect of different treatments of long-range interactions and sampling conditions in molecular dynamic simulations of rhodopsin embedded in a dipalmitoyl phosphatidylcholine bilayer. [My Copy] J Comput Chem (31 January 2007) by Arnau Cordomí, Olle Edholm, Juan J J. Perez posted to dynamics md membrane rhodopsin theory by xdeupi on 2007-06-25 10:30:55 as along with 2 people and 1 group patricia arnaucordomi LabCompMed
	Refinement of Protein Structures by Iterative Comparative Modeling and CryoEM Density Fitting [My Copy] Journal of Molecular Biology, Vol. 357, No. 5. (14 April 2006), pp. 1655-1668. by Maya Topf, Matthew L. Baker, Marc A. Marti-Renom, Wah Chiu, Andrej Sali posted to crystallography em modeling structure theory by xdeupi on 2007-06-12 11:28:16 as along with 1 group LabCompMed
	Structures and spectral signatures of protonated water networks in bacteriorhodopsin. [My Copy] Proc Natl Acad Sci U S A, Vol. 104, No. 17. (24 April 2007), pp. 6980-6985. by G. Mathias, D. Marx posted to activation gpcr protonation rhodopsin theory water by xdeupi on 2007-06-11 10:25:44 as along with 2 people and 1 group vahmurk saravan LabCompMed
	An automated approach for clustering an ensemble of NMR-derived protein structures into conformationally related subfamilies [My Copy] Protein Eng., Vol. 9, No. 11. (1996), pp. 1063-1065. by Lawrence A. Kelley, Stephen P. Gardner, Michael J. Sutcliffe posted to dynamics helix md modeling structure theory by xdeupi on 2007-05-31 10:31:28 as along with 1 group LabCompMed
	Implementation of the SCC-DFTB Method for Hybrid QM/MM Simulations within the Amber Molecular Dynamics Package. [My Copy] J Phys Chem A (24 May 2007) by Gustavo D. Seabra, Ross C. Walker, Marcus Elstner, David A. Case, Adrian E. Roitberg posted to amber dynamics theory by xdeupi on 2007-05-28 08:54:09 as along with 3 people and 1 group krapnik charris5 vahmurk LabCompMed

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activation	173
gpcr	112
structure	89
rhodopsin	79
review	65
modeling	62
b2ar	58
dynamics	56
helix	50
transmembrane	47
agonist	46
binding	44
theory	43
ligands	41
drug	36
md	35
switch	34
membrane_proteins	31
pharmacology	31
crystallography	30
nmr	30
membrane	26
gproteins	24
dimer	20
fluorescence	18
sequence	17
ser	17
active-state	15
pro-kink	15
folding	14
fret	14
genome	14
loops	14
flexibility	13
disease	12
tm6	12
cterm	11
mutation	11
retinal	11
amber	10
energy_landscape	10
evolution	10
toggle	10
docking	9
kinetics	9
lipids	9
neurokinin	9
tm5	9
arrestin	8
chemokine	8
gpcrs	8
hbond	8
helix8	8
imaging	8
bimane	7
cancer	7
channel	7
ecl2	7
gly	7
icl3	7
ionic	7
lmc_101	7
plasticity	7
protonation	7
tm3	7
w648	7
cation-pi	6
ccr5	6
cys_scanning	6
d250	6
internalization	6
npxxy	6
opioid	6
thyrotropin	6
tm2	6
xray	6
amine	5
binding_kinetics	5
conformational_changes	5
dimerization	5
dry	5
expression	5
lock	5
polymorphism	5
spectroscopy	5
thr	5
trp	5
antagonist	4
cam	4
cholesterol	4
disorder	4
hormone	4
n749	4
nterm	4
pathway	4
tm7	4
water	4
angiotensin	3
biased_agonism	3
cxcr1	3
grk	3
histamine	3
n745	3
oligomerization	3
spin_labeling	3
toac	3
webserver	3
5ht1a	2
chimera	2
crosslinking	2
em	2
leukotriene	2
lhr	2
networks	2
pathways	2
phylogeny	2
s542	2
solvation	2
tm1	2
tmhs	2
txp	2
b1ar	1
binding_site	1
class_c	1
efficacy	1
gaba	1
induced_fit	1
inverse_agonist	1
kinase	1
kinks	1
metai	1
oligomers	1
peptide	1
priviledged_structures	1
protein_docking	1
selectivity	1
sequence_alignment	1
tm4	1
transducin	1
vasopressin	1

xdeupi's theory [43 articles] Export

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