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barry's protein_protein [55 articles]

Recent papers added to barry's library classified by the tag protein_protein. You can also see everyone's protein_protein.
  • notes Conformational dynamics of loops L11 and L12 of kinesin as revealed by spin-labeling EPR
    Biochemical and Biophysical Research Communications, Vol. 364, No. 3. (21 December 2007), pp. 620-626.
    by Masafumi D Yamada, Shinsaku Maruta, Satoshi Yasuda, Kazunori Kondo, Hidekatsu Maeda, Toshiaki Arata
    posted to protein_protein molecular_motors kinesin epr by barry on 2008-06-02 19:35:08 as read
  • 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 on 2008-04-29 19:37:04 as ** along with 1 person and 1 group cdeane Bioinformatics
  • Protein interactions in human genetic diseases
    Genome Biology, Vol. 9, No. 1. (2008)
    by Benjamin S Bockler, Alex Bateman
    posted to protein_protein protein_structure by barry on 2008-03-20 01:10:21 as read along with 9 people and 2 groups balicea frohike neils grahamc aconesa biomcgary barriot mingzhi mclarenv McCammon Bioinformatics
  • 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 on 2008-01-10 19:41:24 as ** along with 3 people and 3 groups sobolevnrm iantunbridge mikaellund structural_bioinformatics 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 on 2007-10-02 03:05:14 as read along with 3 people and 3 groups lna allmensch cursonivel1 structural_bioinformatics Bioinformatics cursonivel1
  • Assessing predictions of protein-protein interaction: the CAPRI experiment.
    Protein Sci, Vol. 14, No. 2. (February 2005), pp. 278-283.
    by J Janin
    posted to docking protein_protein by barry on 2007-09-27 19:26:18 as read along with 3 people and 1 group bicko ima drastic 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 on 2007-09-27 17:40:34 as *** along with 3 people and 2 groups jwm xdeupi Ema structural_bioinformatics 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_protein protein_sequence protein_structure by barry on 2007-09-14 01:51:37 as ** along with 5 people and 4 groups wilbur tjimenez bicko chad_davis marcius structural_bioinformatics 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 nma protein_protein protein_structure by barry on 2007-09-13 18:55:42 as ** along with 4 people and 2 groups baaden aqeel eweaver choonpeng structural_bioinformatics 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 dehydron hbond protein_packing protein_protein protein_structure by barry on 2007-09-13 18:45:52 as ** along with 2 people and 2 groups BragilMassoud Evangelia structural_bioinformatics 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 dehydron hbond protein_packing protein_protein protein_structure by barry on 2007-09-13 18:45:36 as **** along with 1 person and 2 groups BragilMassoud structural_bioinformatics 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_protein protein_sequence by barry on 2007-09-04 20:17:20 as * along with 2 groups structural_bioinformatics 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 nma protein_dynamics protein_protein by barry on 2007-09-04 20:13:14 as ***** along with 1 person and 2 groups aqeel structural_bioinformatics 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 hot_spots protein_protein protein_sequence protein_structure by barry on 2007-09-04 19:49:40 as ** along with 8 people and 2 groups mdimmic bicko lyongu nickolay choonpeng cjeans carlescorbi ladab structural_bioinformatics 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_design protein_evolution protein_protein protein_sequence protein_structure by barry on 2007-09-04 19:25:04 as ** along with 3 people and 2 groups paolomarcatili grahamc cjeans structural_bioinformatics 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 nmr protein_ligand protein_protein by barry on 2007-08-28 02:08:20 as read along with 1 person and 3 groups sobolevnrm structural_bioinformatics 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 on 2007-08-14 22:53:26 as * along with 10 people and 2 groups paolomarcatili baaden bicko nickolay j3xucite bluvsh1 xz grahamc Evangelia ladab structural_bioinformatics 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 allosteric disorder protein_dynamics protein_protein protein_structure by barry on 2007-05-25 01:36:39 as **** along with 4 people and 3 groups apaydin choonpeng cursonivel1 cactus structural_bioinformatics 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 on 2007-01-16 23:20:45 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • Interrogating protein interaction networks through structural biology.
    Proc Natl Acad Sci U S A, Vol. 99, No. 9. (30 April 2002), pp. 5896-5901.
    by P Aloy, RB Russell
    posted to protein_protein protein_structure by barry on 2006-09-29 19:14:25 as ** along with 10 people and 3 groups ana baaden bicko lfriedl chad_davis henschel ruvido cjeans tale Evangelia structural_bioinformatics kdl 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 on 2006-08-28 18:00:47 as ** along with 7 people and 2 groups paolomarcatili marti conkymacro ameetsoni grahamc massivemayhem phoenixzxl structural_bioinformatics Bioinformatics
  • notes 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 on 2006-07-07 19:57:04 as **** along with 2 people and 5 groups marcius sobolevnrm structural_bioinformatics 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 on 2006-05-22 19:20:49 as ** along with 4 people and 2 groups pansapiens lna aqeel allmensch structural_bioinformatics 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 on 2006-05-08 20:05:12 as *** along with 1 person and 5 groups joergkurtwegner structural_bioinformatics 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 on 2006-03-06 22:20:06 as ** along with 2 people and 2 groups bicko baldo structural_bioinformatics 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 on 2006-03-06 22:03:40 as ** along with 4 people and 2 groups apaydin bicko j3xucite dyermd structural_bioinformatics 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 on 2006-03-02 22:37:16 as ** along with 6 people and 2 groups pansapiens sriram_s cjeans mingzhi Pao-Yang marti structural_bioinformatics Bioinformatics
  • notes 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 on 2005-12-07 23:56:00 as ***** along with 4 people and 6 groups skoddet sangeetha blackbart joergkurtwegner structural_bioinformatics Bioinformatics Molecular-Modelling Drug-Design Cheminformatics insilicodrug
  • notes 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 on 2005-12-07 23:47:30 as *** along with 2 people and 5 groups chad_davis joergkurtwegner structural_bioinformatics 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 on 2005-10-17 18:55:00 as ** along with 9 people and 3 groups higueruelo bjorns wiehe julianm bicko chad_davis cjeans Evangelia marti structural_bioinformatics ZLAB Bioinformatics
  • 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 on 2005-10-17 18:53:58 as ** along with 9 people and 3 groups aqeel jwm bicko yongzhao blackbart bluvsh1 hmk selrac Evangelia structural_bioinformatics 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 on 2005-10-17 18:52:59 as ** along with 3 people and 2 groups jwm bicko bluvsh1 structural_bioinformatics 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 on 2005-10-17 18:51:04 as ** along with 3 people and 2 groups bicko bluvsh1 boris_aguilar structural_bioinformatics 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 on 2005-10-17 18:49:54 as ** along with 5 people and 2 groups bicko bluvsh1 cjeans selrac wilbur structural_bioinformatics 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 on 2005-10-17 18:44:16 as ** along with 6 people and 2 groups bicko lyongu ameetsoni cjeans Evangelia marti structural_bioinformatics 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 on 2005-10-08 00:59:52 as ** along with 3 people and 3 groups BragilMassoud apaydin yongzhao structural_bioinformatics Bioinformatics TSRI_MGL
  • The Relationship between the Flexibility of Proteins and their Conformational States on Forming Protein-Protein Complexes with an Application to Protein-Protein Docking
    Journal of Molecular Biology, Vol. 347, No. 5. (15 April 2005), pp. 1077-1101.
    by Graham R Smith, Michael Sternberg, Paul A Bates
    posted to protein_dynamics protein_protein structural_bioinformatics by barry on 2005-06-27 18:42:57 as ** along with 6 people and 3 groups jteyra ana aqeel bicko yongzhao ttjoseph structural_bioinformatics Bioinformatics TSRI_MGL
  • Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues.
    J Mol Biol, Vol. 345, No. 5. (4 February 2005), pp. 1281-1294.
    by O Keskin, B Ma, R Nussinov
    posted to protein_protein structural_bioinformatics by barry on 2005-06-27 18:39:01 as **** along with 8 people and 2 groups mdimmic ana baaden okarsligil bicko j3xucite bilab xz structural_bioinformatics 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 on 2005-06-24 23:26:22 as ***** along with 1 person and 2 groups qwermish structural_bioinformatics 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 on 2005-06-24 23:23:02 as ***** along with 2 people and 2 groups shuns qwermish structural_bioinformatics Bioinformatics
  • notes 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 on 2005-06-24 23:20:59 as ***** along with 2 groups structural_bioinformatics 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 on 2005-04-25 22:46:34 as ** along with 4 people and 2 groups chad_davis karbak lyongu biosv structural_bioinformatics 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 on 2005-04-14 20:14:54 as *** along with 2 groups structural_bioinformatics Bioinformatics
  • notes 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 on 2005-04-14 20:11:47 as ***** along with 2 groups structural_bioinformatics Bioinformatics
  • notes 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 on 2005-04-14 20:08:28 as ***** along with 2 groups structural_bioinformatics Bioinformatics
  • notes 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 on 2005-04-14 19:52:37 as ***** along with 2 groups structural_bioinformatics 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 on 2005-04-14 19:51:11 as ** along with 2 people and 2 groups bicko Evangelia structural_bioinformatics Bioinformatics
  • notes 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 on 2005-04-14 19:49:45 as ***** along with 2 people and 2 groups timg bicko structural_bioinformatics 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 on 2005-04-14 19:47:32 as ***** along with 1 person and 2 groups selrac structural_bioinformatics 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 on 2005-04-14 19:42:27 as ** along with 2 groups structural_bioinformatics Bioinformatics
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