Tag protein_structure [at least 200 articles] Export

Recent papers classified by the tag protein_structure.

	PiSQRD: a web server for decomposing proteins into quasi-rigid dynamical domains [My Copy] Bioinformatics, Vol. 25, No. 20. (15 October 2009), pp. 2743-2744. by T. Aleksiev, R. Potestio, F. Pontiggia, S. Cozzini, C. Micheletti posted to rigidity protein_structure by apaydin on 2009-11-08 07:58:36 as along with 1 person and 1 group oteri Structural Biology Group TorVergata
	PDBe: Protein Data Bank in Europe [My Copy] Nucl. Acids Res. (25 October 2009), gkp916. by S. Velankar, C. Best, B. Beuth, et al.C. H. Boutselakis, N. Cobley, A. W. Sousa Da Silva, D. Dimitropoulos, A. Golovin, M. Hirshberg, M. John, E. B. Krissinel, R. Newman, T. Oldfield, A. Pajon, C. J. Penkett, J. Pineda-Castillo, G. Sahni, S. Sen, R. Slowley, A. Suarez-Uruena, J. Swaminathan, G. van Ginkel, W. F. Vranken, K. Henrick, G. J. Kleywegt posted to wwpdb protein_structure pdbe pdb ebi database by walshtp on 2009-11-04 15:26:46 as
	Structure of IL-33 and Its Interaction with the ST2 and IL-1RAcP ReceptorsInsight into Heterotrimeric IL-1 Signaling Complexes [My Copy] Vol. 17, No. 10. (14 October 2009), pp. 1398-1410. by Andreas Lingel, Thomas M. Weiss, Marc Niebuhr, et al.Borlan Pan, Brent A. Appleton, Christian Wiesmann, J. Fernando Bazan, Wayne J. Fairbrother posted to protein_structure il-1 cytokine by hryk on 2009-10-24 09:31:56 as
	Protein-binding site prediction based on three-dimensional protein modeling [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 77, No. S9. (2009), pp. 152-156. by Mina Oh, Keehyoung Joo, Jooyoung Lee posted to protein_structure prediction model ligand_binding casp by hryk on 2009-10-24 09:07:00 as along with 1 person reyez
	An epistatic ratchet constrains the direction of glucocorticoid receptor evolution [My Copy] Nature, Vol. 461, No. 7263. (24 September 2009), pp. 515-519. by Jamie T. Bridgham, Eric A. Ortlund, Joseph W. Thornton posted to protein_structure evolution by venancio on 2009-10-23 22:59:44 as along with 9 people and 1 group merpublic docv bpcusack cmzmasek jjray zwang stajich Annab stevanspringer Mycology
	FRODOCK: a new approach for fast rotational protein-protein docking [My Copy] Bioinformatics, Vol. 25, No. 19. (1 October 2009), pp. 2544-2551. by Jose I. Garzon, Jose R. Lopez-Blanco, Carles Pons, et al.Julio Kovacs, Ruben Abagyan, Juan Fernandez-Recio, Pablo Chacon posted to standalone_tool protein_structure docking by jforment to the group Bioinformatics Core Service on 2009-10-21 14:10:16 as
	Fast and accurate predictions of protein stability changes upon mutations using statistical potentials and neural networks: PoPMuSiC-2.0 [My Copy] Bioinformatics, Vol. 25, No. 19. (1 October 2009), pp. 2537-2543. by Yves Dehouck, Aline Grosfils, Benjamin Folch, Dimitri Gilis, Philippe Bogaerts, Marianne Rooman posted to web_tool protein_structure protein_stability protein_design aminoacid_substitution by jforment to the group Bioinformatics Core Service on 2009-10-21 14:07:40 as
	MetaTM - a consensus method for transmembrane protein topology prediction. [My Copy] BMC bioinformatics, Vol. 10, No. 1. (2009), 314. by Martin Klammer, David N. Messina, Thomas Schmitt, Erik L. Sonnhammer posted to web_tool transmembrane_protein standalone_tool protein_topology protein_structure pro by jforment to the group Bioinformatics Core Service on 2009-10-21 14:00:22 as along with 1 person and 2 groups sillitoe Orengo Group Journal Picks Journal picks
	ANCHOR: web server for predicting protein binding regions in disordered proteins [My Copy] Bioinformatics, Vol. 25, No. 20. (15 October 2009), pp. 2745-2746. by Zsuzsanna Dosztanyi, Balint Meszaros, Istvan Simon posted to web_tool standalone_tool protein_structure binding by jforment to the group Bioinformatics Core Service on 2009-10-21 12:43:09 as
	MISTRAL: a tool for energy-based multiple structural alignment of proteins [My Copy] Bioinformatics, Vol. 25, No. 20. (15 October 2009), pp. 2663-2669. by Cristian Micheletti, Henri Orland posted to web_tool structure_alignment standalone_tool protein_structure by jforment to the group Bioinformatics Core Service on 2009-10-21 12:34:52 as along with 2 people nickolay reyez
	Direct single-molecule observation of a protein living in two opposed native structures. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 106, No. 25. (23 June 2009), pp. 10153-10158. by Yann Gambin, Alexander Schug, Edward A. Lemke, et al.Jason J. Lavinder, Allan Chris C. Ferreon, Thomas J. Magliery, José N. Onuchic, Ashok A. Deniz posted to protein_structure protein by dbikard on 2009-10-19 13:34:14 as along with 6 people and 1 group yyfwuhan quanwang cnegron sobolevnrm paulschlesinger samjlord moernerlab
	Structural Evidence for a Sequential Release Mechanism for Activation of Heterotrimeric G Proteins [My Copy] Journal of Molecular Biology (22 August 2009) by Neeraj Kapoor, Santosh T. Menon, Radha Chauhan, Pallavi Sachdev, Thomas P. Sakmar posted to protein_structure mutants g_proteins by barry on 2009-10-16 17:17:36 as along with 1 person xdeupi
	Computational design of receptor and sensor proteins with novel functions [My Copy] Nature, Vol. 423, No. 6936. (08 May 2003), pp. 185-190. by Loren L. Looger, Mary A. Dwyer, James J. Smith, Homme W. Hellinga posted to synthetic_biology protein_structure ligand_binding computational_design by dbikard on 2009-10-13 10:37:48 as along with 4 people and 1 group whitead antonkratz dfgreen dgront Jiang Research Group
	A New Method for Fast and Accurate Derivation of Molecular Conformations [My Copy] Journal of Chemical Information and Computer Sciences, Vol. 42 (2002), pp. 64-70. by Ming Zhang, Lydia E. Kavraki, I. Lydia, E. Kavraki posted to proteins protein_structure protein_representation conformational_search by rasfonseca on 2009-10-05 12:16:12 as
	Fold space unlimited [My Copy] Current Opinion in Structural Biology, Vol. 19, No. 3. (08 June 2009), pp. 312-320. by Manfred J. Sippl posted to protein_structure fold-space by skywalkerus02 on 2009-10-04 17:59:11 as along with 2 people and 1 group pansapiens davidalee Orengo Group Journal Picks
	Discrete–continuous duality of protein structure space [My Copy] Current Opinion in Structural Biology, Vol. 19, No. 3. (29 June 2009), pp. 321-328. by Ruslan I. Sadreyev, Bong-Hyun Kim, Nick V. Grishin posted to protein_universe protein_structure protein_space by skywalkerus02 on 2009-10-04 17:56:48 as along with 4 people and 1 group martainn philomorph davidalee paulschlesinger Orengo Group Journal Picks
	Fast and Accurate Predictions of Protein NMR Chemical Shifts from Interatomic Distances [My Copy] Journal of the American Chemical Society, Vol. 131, No. 39. (7 October 2009), pp. 13894-13895. by Kai J. Kohlhoff, Paul Robustelli, Andrea Cavalli, Xavier Salvatella, Michele Vendruscolo posted to structure_calculation protein_structure protein_nmr nmr_chemical_shifts interatomic_distances by paridep on 2009-10-02 01:03:44 as
	Prediction of protein coarse contact maps. [My Copy] Journal of bioinformatics and computational biology, Vol. 1, No. 2. (July 2003), pp. 411-431. by Alessandro Vullo, Paolo Frasconi posted to proteins protein_structure predictions by rasfonseca on 2009-09-28 14:58:11 as
	Kappa-alpha plot derived structural alphabet and BLOSUM-like substitution matrix for rapid search of protein structure database [My Copy] Genome Biology, Vol. 8, No. 3. (03 March 2007), R31. by Chi H. Tung, Jhang W. Huang, Jinn M. Yang posted to proteins protein_structure protein_representation by rasfonseca on 2009-09-28 08:57:49 as
	Protein Decoy Generation Using Branch and Bound with Efficient Bounding [My Copy] Algorithms in Bioinformatics (2008), pp. 382-393. by Martin Paluszewski, Pawel Winter posted to protein_structure protein_representation decoys by rasfonseca on 2009-09-28 08:56:29 as
	Biophysical techniques for ligand screening and drug design. [My Copy] Current opinion in pharmacology (4 July 2009) by Jean-Paul P. Renaud, Marc-André A. Delsuc posted to protein_structure protein_sequence protein_regions protein-design peptides peptide-binding peptide modelling biophysics by niallhaslam on 2009-09-22 09:50:29 as along with 1 person ubcg08l
	Probing the “Dark Matter” of Protein Fold Space [My Copy] Structure, Vol. 17, No. 9. (09 September 2009), pp. 1244-1252. by William R. Taylor, Vijayalakshmi Chelliah, Siv M. Hollup, James T. MacDonald, Inge Jonassen posted to protein_structure protein_fold_space by walshtp on 2009-09-17 07:55:09 as
	Epitopia: a web-server for predicting B-cell epitopes [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (14 September 2009), 287. by Nimrod Rubinstein, Itay Mayrose, Eric Martz, Tal Pupko posted to web_server structure-prediction structure protein_structure protein_sequence prediction_tools immunoinformatics immunogenicity epitope_prediction epitope computational_tool cell_epitopes b_cell by niallhaslam on 2009-09-16 12:08:27 as
	Protein sectors: evolutionary units of three-dimensional structure. [My Copy] Cell, Vol. 138, No. 4. (21 August 2009), pp. 774-786. by Najeeb Halabi, Olivier Rivoire, Stanislas Leibler, Rama Ranganathan posted to selection protein_structure evolutionary_constraint correlated_evolution by biomcgary on 2009-09-10 21:52:53 as along with 10 people and 1 group yyfwuhan cmzmasek dgront robfsouza pansapiens pablocarb vvoorr dayjm jwm jbhiatt Marcotte_Lab
	Molecular mechanisms for protein-encoded inheritance [My Copy] Nat Struct Mol Biol, Vol. 16, No. 9. (September 2009), pp. 973-978. by Jed J. W. Wiltzius, Meytal Landau, Rebecca Nelson, et al.Michael R. Sawaya, Marcin I. Apostol, Lukasz Goldschmidt, Angela B. Soriaga, Duilio Cascio, Kanagalaghatta Rajashankar, David Eisenberg posted to protein_structure folding by melo_mcr on 2009-09-04 22:45:52 as
	Structural basis for inhibitor specificity in human poly(ADP-ribose) polymerase-3. [My Copy] Journal of medicinal chemistry, Vol. 52, No. 9. (14 May 2009), pp. 3108-3111. by Lari Lehtiö, Ann-Sofie S. Jemth, Ruairi Collins, et al.Olga Loseva, Andreas Johansson, Natalia Markova, Martin Hammarström, Alex Flores, Lovisa Holmberg-Schiavone, Johan Weigelt, Thomas Helleday, Herwig Schüler, Tobias Karlberg posted to sgc protein_structure human_proteins crystal_structure by pekrau to the group SGC Stockholm on 2009-09-03 16:18:43 as
	The DEXD/H-box RNA Helicase DDX19 Is Regulated by an alpha-Helical Switch [My Copy] J. Biol. Chem., Vol. 284, No. 16. (17 April 2009), pp. 10296-10300. by Ruairi Collins, Tobias Karlberg, Lari Lehtio, et al.Patrick Schutz, Susanne van den Berg, Lars-Goran Dahlgren, Martin Hammarstrom, Johan Weigelt, Herwig Schuler posted to sgc protein_structure human_proteins crystal_structure by pekrau to the group SGC Stockholm on 2009-09-03 16:17:13 as
	Structural Basis for the inhibition mechanism of human cystathionine-gamma -Lyase: An enzyme responsible for the production of H2S [My Copy] J. Biol. Chem. (19 November 2008), M805459200. by Qingxiang Sun, Ruairi Collins, Shufen Huang, et al.Lovisa Holmberg-Schiavone, Ganesh S. Anand, Choon-Hong Tan, Susanne Van-Den-Berg, Lih-Wen Deng, Philip K. Moore, Tobias Karlberg, J. Sivaraman posted to sgc protein_structure human_proteins enzyme crystal_structure by pekrau to the group SGC Stockholm on 2009-09-03 16:16:12 as
	Zinc Binding Catalytic Domain of Human Tankyrase 1 [My Copy] Journal of Molecular Biology, Vol. 379, No. 1. (23 May 2008), pp. 136-145. by L. Lehtio, R. Collins, S. Vandenberg, et al.A. Johansson, L. Dahlgren, M. Hammarstrom, T. Helleday, L. Holmbergschiavone, T. Karlberg, J. Weigelt posted to sgc proteins protein_structure human_proteins crystal_structure by pekrau to the group SGC Stockholm on 2009-09-03 16:07:55 as
	Structural genomics and drug discovery: all in the family [My Copy] Current Opinion in Chemical Biology, Vol. 12, No. 1. (February 2008), pp. 32-39. by Johan Weigelt, Linda D. B. Mcbroom-Cerajewski, Matthieu Schapira, Yong Zhao, Cheryl H. Arrowmsmith posted to sgc structural_genomics protein_structure drug_target crystal_structure by pekrau to the group SGC Stockholm on 2009-09-03 16:01:38 as along with 1 person richardbickerton
	Controlling the secondary-structure-forming tendencies of proteins by a backbone torsion-energy term [My Copy] Molecular Simulation (2009) by Yoshitake Sakae, Yuko Okamoto posted to protein_structure prediction by flbarroso on 2009-08-28 12:38:47 as
	Assessment of the protein-structure refinement category in CASP8. [My Copy] Proteins, Vol. 9999, No. 9999. (20 July 2009), NA. by Justin L. Maccallum, Lan Hua, Michael J. Schnieders, Vijay S. Pande, Matthew P. Jacobson, Ken A. Dill posted to protein_structure casp8 by ppgardne to the group Journal picks on 2009-08-28 09:22:21 as along with 1 person timhubbard
	Evaluation of CASP8 model quality predictions [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2009), NA. by Domenico Cozzetto, Andriy Kryshtafovych, Anna Tramontano posted to protein_structure casp8 by ppgardne to the group Journal picks on 2009-08-28 09:22:07 as
	Determination method of the balance of the secondary-structure-forming tendencies of force fields [My Copy] Molecular Simulation (2009) by Yoshitake Sakae, Yuko Okamoto posted to protein_structure prediction force-fields by flbarroso on 2009-08-25 18:21:24 as
	p3d--Python module for structural bioinformatics. [My Copy] BMC bioinformatics, Vol. 10, No. 1. (2009), 258. by Christian Fufezan, Michael Specht posted to python protein_structure by AlexBateman to the group Journal picks on 2009-08-21 13:52:07 as along with 4 people operon nuin nickolay walshtp
	Positively charged residues at the N-terminal arm of the homeodomain are required for efficient DNA binding by homeodomain-leucine zipper proteins. [My Copy] Journal of molecular biology, Vol. 308, No. 1. (20 April 2001), pp. 39-47. by C. M. Palena, A. E. Tron, C. W. Bertoncini, D. H. Gonzalez, R. L. Chan posted to transcription_factor protein_structure plantipoii hd-zip by agustinarce on 2009-08-17 23:25:21 as
	Intrinsic Disorder in Protein Interactions: Insights From a Comprehensive Structural Analysis [My Copy] PLoS Comput Biol, Vol. 5, No. 3. (13 March 2009), e1000316. by Jessica H. Fong, Benjamin A. Shoemaker, Sergiy O. Garbuzynskiy, Michail Y. Lobanov, Oxana V. Galzitskaya, Anna R. Panchenko posted to protein_structure plantipoii by agustinarce on 2009-08-17 23:14:07 as along with 7 people kiekyon pablocarb chica phoenixzxl zwang bobychan bpcusack
	GlobPlot: Exploring protein sequences for globularity and disorder. [My Copy] Nucleic acids research, Vol. 31, No. 13. (1 July 2003), pp. 3701-3708. by Rune Linding, Robert B. Russell, Victor Neduva, Toby J. Gibson posted to protein_structure plantipoii bioinformatics by agustinarce on 2009-08-17 23:12:13 as along with 2 people niallhaslam chad_davis
	Role of linkers in communication between protein modules. [My Copy] Current opinion in chemical biology, Vol. 4, No. 1. (February 2000), pp. 22-27. by R. S. Gokhale, C. Khosla posted to protein_structure plantipoii by agustinarce on 2009-08-17 23:07:44 as along with 1 person IrinaMoreira
	Global distribution of conformational states derived from redundant models in the PDB points to non-uniqueness of the protein structure [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 26. (30 June 2009), pp. 10505-10510. by Prasad V. Burra, Ying Zhang, Adam Godzik, Boguslaw Stec posted to protein_structure by apaydin on 2009-08-17 15:26:23 as along with 6 people and 1 group ubcg08l sobolevnrm philcarter aalibes TRHvidsten zwang Orengo Group Journal Picks
	Determination of Protein Structures—A Series of Fortunate Events☆ [My Copy] Biophysical Journal, Vol. 95, No. 1. (25 July 2008), pp. 1-9. by M. Chruszcz posted to protein_structure by flbarroso on 2009-08-16 20:35:26 as along with 3 people paulschlesinger pansapiens wilbur
	Engineered Myosin VI Motors Reveal Minimal Structural Determinants of Directionality and Processivity. [My Copy] Journal of molecular biology (22 July 2009) by Jung-Chi C. Liao, Mary Williard W. Elting, Scott L. Delp, James A. Spudich, Zev Bryant posted to molecular_motors myosin protein_structure by barry on 2009-08-07 00:05:27 as along with 1 person melting
	The structural basis of Arf effector specificity: the crystal structure of ARF6 in a complex with JIP4. [My Copy] The EMBO journal (30 July 2009) by Tatiana Isabet, Guillaume Montagnac, Karine Regazzoni, et al.Bertrand Raynal, Fatima El E. Khadali, Patrick England, Michel Franco, Philippe Chavrier, Anne Houdusse, Julie Ménétrey posted to arf g_proteins protein_structure by barry on 2009-08-06 23:56:27 as
	A novel method for detecting intramolecular coevolution: adding a further dimension to selective constraints analyses. [My Copy] Genetics, Vol. 173, No. 1. (1 May 2006), pp. 9-23. by M. A. Fares, S. A. Travers posted to co-adaptation co-evolution evolutionary_constraint protein protein_structure by biomcgary on 2009-07-24 19:24:25 as along with 9 people and 3 groups chica qluo marti stevanspringer operon caporaso breden cjeans tale FAB-lab biomedical-nlp SFUAntibodyResearch
	Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution [My Copy] Biology Direct, Vol. 3, No. 1. (07 October 2008), 40. by Maxim Wolf, Yuri Wolf, Eugene Koonin posted to evolution_rate evolutionary_constraint gene_expression protein protein_folding protein_structure by biomcgary on 2009-07-21 22:36:52 as along with 1 person gjuggler
	AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling. [My Copy] Journal of computational chemistry, Vol. 25, No. 4. (March 2004), pp. 479-499. by E. Gallicchio, R. M. Levy posted to energy_function folding protein_structure by melo_mcr on 2009-07-16 02:48:18 as along with 6 people flbarroso aphou dfgreen RamuAnandakrishnan jwagoner onufriev
	ABSINTH: a new continuum solvation model for simulations of polypeptides in aqueous solutions. [My Copy] Journal of computational chemistry, Vol. 30, No. 5. (15 April 2009), pp. 673-699. by A. Vitalis, R. V. Pappu posted to energy_function folding protein_structure by melo_mcr on 2009-07-16 02:46:35 as along with 2 people and 1 group sobolevnrm agrossfield baker-group
	Nothing about protein structure classification makes sense except in the light of evolution [My Copy] Current Opinion in Structural Biology, Vol. 19, No. 3. (24 April 2009), pp. 329-334. by Ruben E. Valas, Song Yang, Philip E. Bourne posted to protein_structure by dgront on 2009-07-15 22:00:48 as along with 12 people and 3 groups mkotlyar skywalkerus02 nyyu robfsouza apaydin barry coela Zephyrus sobolevnrm zwang friendpine paulschlesinger structural_bioinformatics R.E.A.D baker-group
	Constant time clash detection in protein folding. [My Copy] Journal of bioinformatics and computational biology, Vol. 7, No. 1. (February 2009), pp. 55-74. by M. M. Bugalho, A. L. Oliveira posted to data_structure docking folding protein_structure by melo_mcr on 2009-07-15 19:46:58 as
	Discrimination of the native from misfolded protein models with an energy function including implicit solvation. [My Copy] Journal of molecular biology, Vol. 288, No. 3. (7 May 1999), pp. 477-487. by T. Lazaridis, M. Karplus posted to energy_function folding protein_structure by melo_mcr on 2009-07-15 19:40:48 as along with 1 person bluvsh1

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structure_comparison	269
protein_dynamics	198
protein_sequence	165
protein_evolution	153
protein_design	139
protein_folding	120
review	105
structure_prediction	101
interaction_hierarchy	86
bioinf_methods	85
bioinformatics	75
molecular_motors	75
protein_protein	64
structural_bioinformatics	61
structure_classification	60
structure_alignment	59
kinesin	58
evolution	57
biophysics	55
nma	54
structure_flexible	54
md_simulation	52
fold_space	48
protein_function	46
comparative_modeling	43
folding	42
computational_biology	36
pca	33
allosteric	31
data	31
myosin	31
web_server	31
contact_maps	30
docking	30
molecular_dynamics	30
clustering	29
free_energy	28
core_structure	27
sequence_comparison	27
structure_superposition	27
cytoskeleton	25
homology_analogy	24
protein_fragments	24
protein_interaction	23
tubulin	23
casp	22
correlated_mutations	22
structural_genomics	22
hbond	21
indels	21
sequence_structure	21
algorithms	20
databases	20
protein_packing	20
comparative_model	19
core_residues	19
protein_universe	19
benchmark	18
model_assessment	18
statistical_coupling_analysis	18
alternatives	17
p-loop	17
classification	16
contacts	16
nmr	16
cafasp	15
contact_order	15
foce_field	15
function	15
hydrogen-bond	15
jcsg	15
multiple_structure_comparison	15
packing_density	15
structure_core	15
computational	14
mine	14
networks	14
protein_stability	14
g_proteins	13
protein_ligand	13
software	13
correlated_motions	12
decoy_detection	12
domain_motions	12
entropy	12
flexible_structure_alignment	12
kinases	12
protein	12
protein-dna_interaction	12
drug_design	11
electrostatics	11
dna_binding	10
enzyme	10
graphical_models	10
molecular_mechanics	10
motifs	10
physics	10
prediction	10
protein_dna	10
score	10

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