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Tag protein_protein [63 articles]

Recent papers classified by the tag protein_protein.
  • Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome.
    Genome Biol, Vol. 6, No. 5. (2005)
    by AK Ramani, RC Bunescu, RJ Mooney, EM Marcotte
    posted to protein_protein textmining by setar on 2005-05-31 16:53:34 as read along with 18 people and 4 groups ggallone yaredo tmmurali dragonrez okarsligil lfriedl ccots balajis maryee brant opheliav davidandrzej wnpx rlhsiao bundschu mikaelhuss raiyar grahamc Jarman Lab kdl Bioinformatics generif_paper
  • 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
  • notes Understanding mechanisms governing protein-protein interactions from synthetic binding interfaces
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Anthony A Kossiakoff, Shohei Koide
    posted to review protein_protein protein_dynamics by barry to the group Bioinformatics on 2008-10-02 19:21:01 as ** along with 2 people and 2 groups grahamc paulschlesinger structural_bioinformatics McCammon
  • 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
  • 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
  • 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
  • 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
  • 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 3 people and 1 group csrocha bicko timg 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
  • 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
  • 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 6 people and 1 group hmk raik pansapiens lna aqeel allmensch structural_bioinformatics
  • 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 4 people and 1 group csrocha jwm xdeupi Ema 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
  • 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
  • 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
  • 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
  • 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 21 people and 5 groups camster dragonrez bicko lfriedl chad_davis alexg j3xucite bundschu yeastyboy ruvido raiyar grahamc iris_2001 cmor shu Evangelia shikin Pao-Yang carlk cerca ethkim dbk-lab structural_bioinformatics kdl generif_paper GeneGo
  • 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 10 people and 2 groups csrocha aqeel jwm bicko yongzhao blackbart bluvsh1 hmk selrac Evangelia structural_bioinformatics TSRI_MGL
  • 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
  • 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
  • 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
  • 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 bjorns wiehe julianm bicko chad_davis cjeans Evangelia marti higueruelo structural_bioinformatics ZLAB
  • 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 sangeetha blackbart joergkurtwegner skoddet structural_bioinformatics Molecular-Modelling Drug-Design Cheminformatics insilicodrug
  • 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
  • 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 7 people and 1 group kshameer mdimmic chad_davis choonpeng massivemayhem antonkratz kintoki structural_bioinformatics
  • 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 baaden bicko nickolay j3xucite bluvsh1 xz grahamc Evangelia ladab paolomarcatili 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 karbak lyongu biosv chad_davis 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
  • 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 4 people and 4 groups viktor21614 bicko chad_davis joergkurtwegner structural_bioinformatics Molecular-Modelling Drug-Design Cheminformatics
  • Protein co-evolution, co-adaptation and interactions
    The EMBO Journal, Vol. aop, No. current. (25 September 2008)
    by Florencio Pazos, Alfonso Valencia
    posted to review protein_protein phylogeny correlated_mutations by barry to the group Bioinformatics on 2008-10-02 20:24:17 as ***** along with 5 people and 2 groups balicea grahamc fhsantanna marti sjcockell structural_bioinformatics McCammon
  • 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
  • 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 4 people and 2 groups raik lna allmensch cursonivel1 structural_bioinformatics cursonivel1
  • 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
  • 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
  • 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 4 people and 1 group grahamc cjeans paolomarcatili phoenixzxl 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
  • 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
  • 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
  • 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 4 people and 3 groups tjimenez bicko marcius wilbur structural_bioinformatics BioinfoCIPF SGU-CIPF
  • 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
  • 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 mts protein_protein tubulin 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
  • 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
  • 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
  • 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
  • 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 5 people and 2 groups apaydin choonpeng cursonivel1 cactus allmensch structural_bioinformatics cursonivel1
  • 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
  • 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 conkymacro ameetsoni grahamc massivemayhem phoenixzxl marti paolomarcatili structural_bioinformatics
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