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Group: Bioinformatics - with tag protein_protein [49 articles]

Neue Artikel von Mitliedern der Gruppe Bioinformatics Gruppe with tag protein_protein
  • A Microtubule Interactome: Complexes with Roles in Cell Cycle and Mitosis
    PLoS Biology, Vol. 6, No. 4. (1 April 2008), e98.
    by Julian R Hughes, Ana M Meireles, Katherine H Fisher, Angel Garcia, Philip R Antrobus, Alan Wainman, Nicole Zitzmann, Charlotte Deane, Hiroyuki Ohkura, James G Wakefield
    posted to tubulin protein_protein mts by barry to the group Bioinformatics on 2008-04-29 19:37:04 as ** along with 1 person cdeane
  • Coarse-grained models for simulations of multi-protein complexes: Application to ubiquitin binding
    Journal of Molecular Biology, Vol. In Press, Accepted Manuscript
    by Young C Kim, Gerhard Hummer
    posted to coarse-grained protein_protein ubiqutin by barry to the group Bioinformatics on 2008-01-10 19:41:25 as ** along with 3 people and 2 groups sobolevnrm iantunbridge mikaellund structural_bioinformatics baker-group
  • Complementarity of Structure Ensembles in Protein-Protein Binding
    Structure, Vol. 12, No. 12. (December 2004), pp. 2125-2136.
    by Raik Gruenberg, Johan Leckner, Michael Nilges
    posted to md_simulation protein_dynamics protein_protein by barry to the group Bioinformatics on 2007-10-02 03:05:14 as read along with 3 people and 2 groups lna allmensch cursonivel1 structural_bioinformatics cursonivel1
  • Protein-Protein Docking with Backbone Flexibility
    Journal of Molecular Biology, Vol. 373, No. 2. (19 October 2007), pp. 503-519.
    by Chu Wang, Philip Bradley, David Baker
    posted to docking protein_protein by barry to the group Bioinformatics on 2007-09-27 17:40:34 as *** along with 3 people and 1 group jwm xdeupi Ema structural_bioinformatics
  • Localization of protein-binding sites within families of proteins.
    Protein Sci, Vol. 14, No. 9. (September 2005), pp. 2350-2360.
    by D Korkin, FP Davis, A Sali
    posted to protein_structure protein_sequence protein_protein by barry to the group Bioinformatics on 2007-09-14 01:51:37 as ** along with 5 people and 3 groups wilbur tjimenez bicko chad_davis marcius structural_bioinformatics BioinfoCIPF SGU-CIPF
  • How similar are protein folding and protein binding nuclei? Examination of vibrational motions of energy hot spots and conserved residues.
    Biophys J, Vol. 88, No. 3. (March 2005), pp. 1552-1559.
    by T Haliloglu, O Keskin, B Ma, R Nussinov
    posted to protein_structure protein_protein nma by barry to the group Bioinformatics on 2007-09-13 18:55:42 as ** along with 4 people and 1 group baaden aqeel eweaver choonpeng structural_bioinformatics
  • Dehydron: a structurally encoded signal for protein interaction.
    Biophys J, Vol. 85, No. 3. (September 2003), pp. 1914-1928.
    by A Fernández, R Scott
    posted to protein_structure protein_protein protein_packing hbond dehydron by barry to the group Bioinformatics on 2007-09-13 18:45:52 as ** along with 2 people and 1 group BragilMassoud Evangelia structural_bioinformatics
  • Insufficiently dehydrated hydrogen bonds as determinants of protein interactions.
    Proc Natl Acad Sci U S A, Vol. 100, No. 1. (7 January 2003), pp. 113-118.
    by A Fernández, HA Scheraga
    posted to protein_structure protein_protein protein_packing hbond dehydron by barry to the group Bioinformatics on 2007-09-13 18:45:36 as **** along with 1 person and 1 group BragilMassoud structural_bioinformatics
  • Amino acid preferences at protein binding sites
    FEBS Letters, Vol. 349, No. 1. (25 July 1994), pp. 125-130.
    by Hugo O Villar, Lawrence M Kauvar
    posted to protein_sequence protein_protein by barry to the group Bioinformatics on 2007-09-04 20:17:20 as * along with 1 group structural_bioinformatics
  • Association of putative concave protein-binding sites with the fluctuation behavior of residues.
    Protein Sci, Vol. 15, No. 10. (October 2006), pp. 2265-2277.
    by A Ertekin, R Nussinov, T Haliloglu
    posted to protein_protein protein_dynamics nma by barry to the group Bioinformatics on 2007-09-04 20:13:14 as ***** along with 1 person and 1 group aqeel structural_bioinformatics
  • Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces.
    Proc Natl Acad Sci U S A, Vol. 100, No. 10. (13 May 2003), pp. 5772-5777.
    by B Ma, T Elkayam, H Wolfson, R Nussinov
    posted to protein_structure protein_sequence protein_protein hot_spots by barry to the group Bioinformatics on 2007-09-04 19:49:40 as ** along with 8 people and 1 group mdimmic bicko lyongu nickolay choonpeng cjeans carlescorbi ladab structural_bioinformatics
  • Optimization of specificity in a cellular protein interaction network by negative selection.
    Nature, Vol. 426, No. 6967. (11 December 2003), pp. 676-680.
    by A Zarrinpar, SH Park, WA Lim
    posted to protein_structure protein_sequence protein_protein protein_evolution protein_design by barry to the group Bioinformatics on 2007-09-04 19:25:04 as ** along with 3 people and 1 group paolomarcatili grahamc cjeans structural_bioinformatics
  • Conformational entropy in molecular recognition by proteins
    Nature, Vol. 448, No. 7151. (2007), pp. 325-9.
    by KK Frederick, MS Marlow, KG Valentine, AJ Wand
    posted to protein_protein protein_ligand nmr by barry to the group Bioinformatics on 2007-08-28 02:08:20 as read along with 1 person and 2 groups sobolevnrm structural_bioinformatics baker-group
  • Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking.
    J Mol Biol, Vol. 344, No. 3. (26 November 2004), pp. 781-795.
    by X Li, O Keskin, B Ma, R Nussinov, J Liang
    posted to protein_protein by barry to the group Bioinformatics on 2007-08-14 22:53:26 as * along with 10 people and 1 group paolomarcatili baaden bicko nickolay j3xucite bluvsh1 xz grahamc Evangelia ladab structural_bioinformatics
  • Intrinsic disorder as a mechanism to optimize allosteric coupling in proteins.
    Proc Natl Acad Sci U S A (9 May 2007)
    by Vincent J J Hilser, E Brad B Thompson
    posted to protein_structure protein_protein protein_dynamics disorder allosteric by barry to the group Bioinformatics on 2007-05-25 01:36:39 as **** along with 4 people and 2 groups apaydin choonpeng cursonivel1 cactus structural_bioinformatics cursonivel1
  • Electrostatically optimized Ras-binding Ral guanine dissociation stimulator mutants increase the rate of association by stabilizing the encounter complex.
    Proc Natl Acad Sci U S A, Vol. 101, No. 25. (22 June 2004), pp. 9223-9228.
    by C Kiel, T Selzer, Y Shaul, G Schreiber, C Herrmann
    posted to ras protein_protein electrostatics bd_simulation by barry to the group Bioinformatics on 2007-01-16 23:20:45 as ** along with 1 group structural_bioinformatics
  • Insights into Protein-Protein Interfaces using a Bayesian Network Prediction Method
    Journal of Molecular Biology, Vol. In Press, Corrected Proof
    by James R Bradford, Chris J Needham, Andrew J Bulpitt, David R Westhead
    posted to bayesian_classifiers bioinf_methods protein_protein by barry to the group Bioinformatics on 2006-08-28 18:00:47 as ** along with 7 people and 1 group paolomarcatili marti conkymacro ameetsoni grahamc massivemayhem phoenixzxl structural_bioinformatics
  • Structural Diversity of Domain Superfamilies in the CATH Database.
    J Mol Biol (2 June 2006)
    by Gabrielle A A Reeves, Timothy J J Dallman, Oliver C C Redfern, Adrian Akpor, Christine A A Orengo
    posted to cath protein_design protein_evolution protein_protein protein_structure by barry to the group Bioinformatics on 2006-07-07 19:57:04 as **** along with 2 people and 4 groups marcius sobolevnrm structural_bioinformatics BioinfoCIPF SGU-CIPF baker-group
  • Flexibility and conformational entropy in protein-protein binding.
    Structure, Vol. 14, No. 4. (April 2006), pp. 683-693.
    by R Grünberg, M Nilges, J Leckner
    posted to md_simulation protein_dynamics protein_protein by barry to the group Bioinformatics on 2006-05-22 19:20:49 as ** along with 4 people and 1 group pansapiens lna aqeel allmensch structural_bioinformatics
  • Flexibility and conformational entropy in protein-protein binding
    Structure (London, England: 1993), Vol. 14, No. 4. (April 2006), pp. 683-693.
    by Raik Grunberg, Michael Nilges, Johan Leckner
    posted to md_simulation protein_dynamics protein_protein protein_structure by barry to the group Bioinformatics on 2006-05-08 20:05:12 as *** along with 1 person and 4 groups joergkurtwegner structural_bioinformatics Molecular-Modelling Drug-Design Cheminformatics
  • Prediction of protein-protein interactions using distant conservation of sequence patterns and structure relationships.
    Bioinformatics, Vol. 21, No. 16. (15 August 2005), pp. 3360-3368.
    by J Espadaler, O Romero-Isart, RM Jackson, B Oliva
    posted to protein_protein protein_sequence protein_structure sequence_comparison structure_comparison by barry to the group Bioinformatics on 2006-03-06 22:20:06 as ** along with 2 people and 1 group bicko baldo structural_bioinformatics
  • Prediction of protein-protein interactions by combining structure and sequence conservation in protein interfaces.
    Bioinformatics, Vol. 21, No. 12. (15 June 2005), pp. 2850-2855.
    by AS Aytuna, A Gursoy, O Keskin
    posted to bioinf_methods protein_protein protein_sequence protein_structure by barry to the group Bioinformatics on 2006-03-06 22:03:40 as ** along with 4 people and 1 group apaydin bicko j3xucite dyermd structural_bioinformatics
  • Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins.
    J Mol Biol, Vol. 307, No. 5. (13 April 2001), pp. 1487-1502.
    by R Landgraf, I Xenarios, D Eisenberg
    posted to protein_design protein_protein protein_sequence protein_structure residue_annotation by barry to the group Bioinformatics on 2006-03-02 22:37:16 as ** along with 6 people and 1 group pansapiens sriram_s cjeans mingzhi Pao-Yang marti structural_bioinformatics
  • Computational alanine scanning of protein-protein interfaces.
    Sci STKE, Vol. 2004, No. 219. (10 February 2004)
    by T Kortemme, DE Kim, D Baker
    posted to bioinf_methods protein_protein protein_structure by barry to the group Bioinformatics on 2005-12-07 23:56:00 as ***** along with 4 people and 5 groups skoddet sangeetha blackbart joergkurtwegner structural_bioinformatics Molecular-Modelling Drug-Design Cheminformatics insilicodrug
  • Protein-protein interactions: a review of protein dimer structures.
    Prog Biophys Mol Biol, Vol. 63, No. 1. (1995), pp. 31-65.
    by S Jones, JM Thornton
    posted to bioinf_methods protein_protein protein_structure review by barry to the group Bioinformatics on 2005-12-07 23:47:30 as *** along with 2 people and 4 groups chad_davis joergkurtwegner structural_bioinformatics Molecular-Modelling Drug-Design Cheminformatics
  • Structure, function, and evolution of transient and obligate protein-protein interactions.
    Proc Natl Acad Sci U S A (25 July 2005)
    by Julian Mintseris, Zhiping Weng
    posted to protein_protein review by barry to the group Bioinformatics on 2005-10-17 18:55:00 as ** along with 9 people and 2 groups higueruelo bjorns wiehe julianm bicko chad_davis cjeans Evangelia marti structural_bioinformatics ZLAB
  • Improved side-chain modeling for protein-protein docking.
    Protein Sci, Vol. 14, No. 5. (May 2005), pp. 1328-1339.
    by C Wang, O Schueler-Furman, D Baker
    posted to protein_dynamics protein_protein by barry to the group Bioinformatics on 2005-10-17 18:53:58 as ** along with 9 people and 2 groups aqeel jwm bicko yongzhao blackbart bluvsh1 hmk selrac Evangelia structural_bioinformatics TSRI_MGL
  • Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility.
    Proteins, Vol. 60, No. 2. (1 August 2005), pp. 187-194.
    by O Schueler-Furman, C Wang, D Baker
    posted to bioinf_methods protein_dynamics protein_protein by barry to the group Bioinformatics on 2005-10-17 18:52:59 as ** along with 3 people and 1 group jwm bicko bluvsh1 structural_bioinformatics
  • Anchor residues in protein-protein interactions.
    Proc Natl Acad Sci U S A, Vol. 101, No. 31. (3 August 2004), pp. 11287-11292.
    by D Rajamani, S Thiel, S Vajda, CJ Camacho
    posted to protein_protein by barry to the group Bioinformatics on 2005-10-17 18:51:04 as ** along with 3 people and 1 group bicko bluvsh1 boris_aguilar structural_bioinformatics
  • Soft protein-protein docking in internal coordinates.
    Protein Sci, Vol. 11, No. 2. (February 2002), pp. 280-291.
    by J Fernández-Recio, M Totrov, R Abagyan
    posted to bioinf_methods protein_protein by barry to the group Bioinformatics on 2005-10-17 18:49:54 as ** along with 5 people and 1 group bicko bluvsh1 cjeans selrac wilbur structural_bioinformatics
  • Statistical analysis and prediction of protein-protein interfaces
    Proteins: Structure, Function, and Bioinformatics, Vol. 60, No. 3. (19 May 2005), pp. 353-366.
    by Andrew J Bordner, Ruben Abagyan
    posted to bioinf_methods protein_protein svm by barry to the group Bioinformatics on 2005-10-17 18:44:16 as ** along with 6 people and 1 group bicko lyongu ameetsoni cjeans Evangelia marti structural_bioinformatics
  • Unveiling the full potential of flexible receptor docking using multiple crystallographic structures.
    J Med Chem, Vol. 48, No. 13. (30 June 2005), pp. 4432-4443.
    by X Barril, SD Morley
    posted to protein_dynamics protein_protein by barry to the group Bioinformatics on 2005-10-08 00:59:52 as ** along with 3 people and 2 groups BragilMassoud apaydin yongzhao structural_bioinformatics TSRI_MGL
  • Processivity of the single-headed kinesin KIF1A through biased binding to tubulin.
    Nature, Vol. 424, No. 6948. (31 July 2003), pp. 574-577.
    by Y Okada, H Higuchi, N Hirokawa
    posted to kif1a kinesin molecular_motors protein_protein tubulin by barry to the group Bioinformatics on 2005-06-24 23:26:22 as ***** along with 1 person and 1 group qwermish structural_bioinformatics
  • KIF1A alternately uses two loops to bind microtubules.
    Science, Vol. 305, No. 5684. (30 July 2004), pp. 678-683.
    by R Nitta, M Kikkawa, Y Okada, N Hirokawa
    posted to kif1a kinesin molecular_motors protein_protein by barry to the group Bioinformatics on 2005-06-24 23:23:02 as ***** along with 2 people and 1 group shuns qwermish structural_bioinformatics
  • Modulation of kinesin binding by the C-termini of tubulin.
    EMBO J, Vol. 23, No. 5. (10 March 2004), pp. 989-999.
    by G Skiniotis, JC Cochran, J Müller, E Mandelkow, SP Gilbert, A Hoenger
    posted to kinesin molecular_motors protein_protein tubulin by barry to the group Bioinformatics on 2005-06-24 23:20:59 as ***** along with 1 group structural_bioinformatics
  • Structure-based systems biology: a zoom lens for the cell.
    FEBS Lett, Vol. 579, No. 8. (21 March 2005), pp. 1854-1858.
    by P Aloy, RB Russell
    posted to bioinformatics gotit protein_protein review structural_bioinformatics systems_biology by barry to the group Bioinformatics on 2005-04-25 22:46:34 as ** along with 4 people and 1 group chad_davis karbak lyongu biosv structural_bioinformatics
  • Anchor residues in protein-protein interactions
    Proceedings Of The National Academy Of Sciences Of The United States Of America, Vol. 101, No. 31. (03 August 2004), pp. 11287-11292.
    by Deepa Rajamani, Spencer Thiel, Sandor Vajda, Carlos J Camacho
    posted to gotit protein_protein structural_bioinformatics by barry to the group Bioinformatics on 2005-04-14 20:14:54 as *** along with 1 group structural_bioinformatics
  • A simple physical model for binding energy hot spots in protein-protein complexes
    Proceedings Of The National Academy Of Sciences Of The United States Of America, Vol. 99, No. 22. (29 October 2002), pp. 14116-14121.
    by Tanja Kortemme, David Baker
    posted to bioinf_methods gotit protein_protein structural_bioinformatics by barry to the group Bioinformatics on 2005-04-14 20:11:47 as ***** along with 1 group structural_bioinformatics
  • Protein-protein interactions: structurally conserved residues distinguish between binding sites and exposed protein surfaces
    Proceedings Of The National Academy Of Sciences Of The United States Of America, Vol. 100, No. 10. (13 May 2003), pp. 5772-5777.
    by Buyong Ma, Tal Elkayam, Haim Wolfson, Ruth Nussinov
    posted to gotit protein_protein sequence_comparison structural_bioinformatics by barry to the group Bioinformatics on 2005-04-14 20:08:28 as ***** along with 1 group structural_bioinformatics
  • Dehydron: a structurally encoded signal for protein interaction
    Biophysical Journal, Vol. 85, No. 3. (September 2003), pp. 1914-1928.
    by Ariel Fernandez, Ridgway Scott
    posted to gotit protein_protein structural_bioinformatics by barry to the group Bioinformatics on 2005-04-14 19:52:37 as ***** along with 1 group structural_bioinformatics
  • Protein-Protein Interactions: Coupling of Structurally Conserved Residues and of Hot Spots across Interfaces. Implications for Docking
    Structure, Vol. 12, No. 6. (June 2004), pp. 1027-1038.
    by Inbal Halperin, Haim Wolfson, Ruth Nussinov
    posted to gotit protein_protein structural_bioinformatics by barry to the group Bioinformatics on 2005-04-14 19:51:11 as ** along with 2 people and 1 group bicko Evangelia structural_bioinformatics
  • Anatomy of hot spots in protein interfaces
    Journal of Molecular Biology, Vol. 280, No. 1. (03 July 1998), pp. 1-9.
    by Andrew A Bogan, Kurt S Thorn
    posted to gotit protein_protein structural_bioinformatics by barry to the group Bioinformatics on 2005-04-14 19:49:45 as ***** along with 1 person and 1 group bicko structural_bioinformatics
  • Dissecting protein-protein recognition sites
    Proteins, Vol. 47, No. 3. (15 May 2002), pp. 334-343.
    by Pinak Chakrabarti, Joel Janin
    posted to protein_protein protein_structure structural_bioinformatics by barry to the group Bioinformatics on 2005-04-14 19:47:32 as ***** along with 1 person and 1 group selrac structural_bioinformatics
  • Identifying DNA-binding proteins using structural motifs and the electrostatic potential
    Nucleic Acids Research, Vol. 32, No. 16. (2004), pp. 4732-4741.
    by Hugh P Shanahan, Mario A Garcia, Susan Jones, Janet M Thornton
    posted to bioinf_methods protein_protein protein_structure structural_bioinformatics by barry to the group Bioinformatics on 2005-04-14 19:42:27 as ** along with 1 group structural_bioinformatics
  • Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?
    Protein Science: a Publication Of The Protein Society, Vol. 13, No. 1. (January 2004), pp. 190-202.
    by Daniel R Caffrey, Shyamal Somaroo, Jason D Hughes, Julian Mintseris, Enoch S Huang
    posted to bioinformatics protein_protein protein_sequence protein_structure structural_bioinformatics by barry to the group Bioinformatics on 2005-04-14 19:38:42 as **** along with 1 person and 1 group wilbur structural_bioinformatics
  • An Accurate, Sensitive, and Scalable Method to Identify Functional Sites in Protein Structures
    Journal of Molecular Biology, Vol. 326, No. 1. (07 February 2003), pp. 255-261.
    by Hui Yao, David M Kristensen, Ivana Mihalek, Mathew E Sowa, Chad Shaw, Marek Kimmel, Lydia Kavraki, Olivier Lichtarge
    posted to protein_protein protein_sequence protein_structure structural_bioinformatics by barry to the group Bioinformatics on 2005-04-14 19:37:04 as ***** along with 1 person and 1 group BragilMassoud structural_bioinformatics
  • Change in protein flexibility upon complex formation: analysis of Ras-Raf using molecular dynamics and a molecular framework approach.
    Proteins, Vol. 56, No. 2. (1 August 2004), pp. 322-337.
    by H Gohlke, LA Kuhn, DA Case
    posted to md_simulation protein_protein protein_structure structural_bioinformatics by barry to the group Bioinformatics on 2005-03-16 03:52:20 as ***** along with 3 people and 1 group lna aqeel blackbart structural_bioinformatics
  • iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions
    Bioinformatics, Vol. 21, No. 3. (01 February 2005), 410.
    by Robert D Finn, Mhairi Marshall, Alex Bateman
    posted to protein_protein protein_structure structural_bioinformatics by barry to the group Bioinformatics on 2005-03-16 03:24:16 as *** along with 5 people and 1 group mdimmic chad_davis choonpeng massivemayhem antonkratz structural_bioinformatics
  • Comparative assessment of large-scale data sets of protein-protein interactions.
    Nature, Vol. 417, No. 6887. (23 May 2002), pp. 399-403.
    by C von Mering, R Krause, B Snel, M Cornell, SG Oliver, S Fields, P Bork
    posted to interaction_maps protein_protein by barry to the group Bioinformatics on 2005-03-16 03:21:25 as ** along with 19 people and 5 groups carlk camster dragonrez bicko lfriedl chad_davis alexg j3xucite bundschu yeastyboy ruvido raiyar grahamc iris_2001 cmor shu Evangelia shikin Pao-Yang dbk-lab structural_bioinformatics kdl generif_paper GeneGo
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