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Tag ppi-evolution [38 articles]

Recent papers classified by the tag ppi-evolution.
  • WHISCY: What information does surface conservation yield? Application to data-driven docking.
    Proteins (31 January 2006)
    by Sjoerd J J de Vries, Aalt D J D van Dijk, Alexandre M J J M Bonvin
    posted to docking-algorithm docking-scoring-function guided-docking interaction-site-prediction ppi-evolution by bicko on 2006-02-17 16:55:08 as ** along with 2 people gloria marti
  • Characterization of protein-protein interfaces.
    The protein journal, Vol. 27, No. 1. (January 2008), pp. 59-70.
    by C Yan, F Wu, RL Jernigan, D Dobbs, V Honavar
    posted to interface-properties ppi-evolution by bicko on 2008-04-04 13:29:40 as ** along with 2 people wonaya Lombardo_7
  • Conservation helps to identify biologically relevant crystal contacts.
    J Mol Biol, Vol. 313, No. 2. (19 October 2001), pp. 399-416.
    by WS Valdar, JM Thornton
    posted to crystal-contacts interface-properties ppi-evolution quaternary-structure by bicko on 2005-11-07 15:19:01 as ** along with 3 people cjeans Evangelia jwm
  • Unraveling hot spots in binding interfaces: progress and challenges.
    Curr Opin Struct Biol, Vol. 12, No. 1. (February 2002), pp. 14-20.
    by WL DeLano
    posted to hot-spots interface-properties ppi-evolution by bicko on 2006-02-20 14:40:07 as ** along with 2 people Dualsystems higueruelo
  • 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 obligate-transient ppi-evolution ppi-review quaternary-structure by bicko on 2005-10-17 11:15:59 as ***** along with 9 people and 3 groups barry bjorns wiehe julianm chad_davis cjeans Evangelia marti higueruelo structural_bioinformatics ZLAB Bioinformatics
  • Efficient Restraints for Protein-Protein Docking by Comparison of Observed Amino Acid Substitution Patterns with those Predicted from Local Environment
    Journal of Molecular Biology, Vol. 357, No. 5. (14 April 2006), pp. 1669-1682.
    by Vijayalakshmi Chelliah, Tom L Blundell, Juan Fernandez-Recio
    posted to docking-algorithm guided-docking interaction-site-prediction ppi-evolution by bicko on 2006-06-23 01:15:08 as ** along with 3 people ima drastic cjeans
  • ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information.
    Bioinformatics, Vol. 19, No. 1. (January 2003), pp. 163-164.
    by F Glaser, T Pupko, I Paz, RE Bell, D Bechor-Shental, E Martz, N Ben-Tal
    posted to interaction-site-prediction interface-properties ppi-evolution by bicko on 2006-06-29 19:03:47 as ** along with 2 people chrn siebertm
  • Statistical analysis of domains in interacting protein pairs.
    Bioinformatics (27 October 2004)
    by Tom M W M Nye, Carlo Berzuini, Walter R R Gilks, M Madan M Babu, Sarah A A Teichmann
    posted to ppi-evolution quaternary-structure by bicko on 2005-11-15 16:46:53 as ** along with 3 people hununu satsumakenji choonpeng
  • Scoring docking models with evolutionary information.
    Proteins, Vol. 60, No. 2. (1 August 2005), pp. 275-280.
    by M Tress, D de Juan, O Graña, MJ Gómez, P Gómez-Puertas, JM González, G López, A Valencia
    posted to docking-algorithm docking-scoring-function guided-docking interface-properties ppi-evolution by bicko on 2006-06-21 15:02:12 as ** along with 3 people and 2 groups marcius ameetsoni cjeans BioinfoCIPF SGU-CIPF
  • Rate4Site: an algorithmic tool for the identification of functional regions in proteins by surface mapping of evolutionary determinants within their homologues.
    Bioinformatics, Vol. 18 Suppl 1 (2002)
    by T Pupko, RE Bell, I Mayrose, F Glaser, N Ben-Tal
    posted to interaction-site-prediction ppi-evolution by bicko on 2006-08-17 11:37:43 as ** along with 1 person sriram_s
  • Specific protein-protein binding in many-component mixtures of proteins.
    Phys Biol, Vol. 1, No. 1-2. (June 2004), pp. 53-60.
    by RP Sear
    posted to ppi-evolution protein-networks scale-free by bicko on 2006-02-17 15:27:50 as **
  • 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 guided-docking hot-spots interaction-site-prediction interface-properties ppi-evolution by bicko on 2006-02-20 14:47:25 as ** along with 3 people and 2 groups csrocha barry timg structural_bioinformatics Bioinformatics
  • Correlated sequence-signatures as markers of protein-protein interaction.
    J Mol Biol, Vol. 311, No. 4. (24 August 2001), pp. 681-692.
    by E Sprinzak, H Margalit
    posted to 1st-yr-report interaction-partner-prediction ppi-evolution by bicko on 2006-06-29 18:48:08 as ** along with 9 people chad_davis maryee dyermd grahamc cjeans lilith wilbur Rhys phoenixzxl
  • Prediction of protein--protein interaction sites in heterocomplexes with neural networks.
    Eur J Biochem, Vol. 269, No. 5. (March 2002), pp. 1356-1361.
    by P Fariselli, F Pazos, A Valencia, R Casadio
    posted to interaction-site-prediction interface-properties ppi-evolution by bicko on 2005-10-20 16:05:54 as ** along with 1 person cjeans
  • Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?
    Protein Sci, Vol. 13, No. 1. (January 2004), pp. 190-202.
    by DR Caffrey, S Somaroo, JD Hughes, J Mintseris, ES Huang
    posted to interface-properties ppi-evolution by bicko on 2005-11-04 17:13:35 as ** along with 3 people cjeans Evangelia higueruelo
  • Physicochemical and residue conservation calculations to improve the ranking of protein-protein docking solutions
    Protein Sci, Vol. 14, No. 2. (1 February 2005), pp. 316-328.
    by Yuhua Duan, Boojala V Reddy, Yiannis N Kaznessis
    posted to ppi-evolution guided-docking docking-scoring-function docking-algorithm by bicko on 2007-01-15 11:08:21 as ** along with 2 people ameetsoni carlescorbi
  • The relationship between sequence and interaction divergence in proteins.
    J Mol Biol, Vol. 332, No. 5. (3 October 2003), pp. 989-998.
    by P Aloy, H Ceulemans, A Stark, RB Russell
    posted to interface-properties ppi-evolution quaternary-structure by bicko on 2005-10-14 10:33:46 as *** along with 5 people karbak chad_davis drastic ruvido RebeccaHamer
  • Conservation of polar residues as hot spots at protein interfaces.
    Proteins, Vol. 39, No. 4. (1 June 2000), pp. 331-342.
    by Z Hu, B Ma, H Wolfson, R Nussinov
    posted to hot-spots interface-properties ppi-evolution by bicko on 2006-02-20 14:54:13 as **
  • Design of Multi-Specificity in Protein Interfaces
    PLoS Computational Biology, Vol. 3, No. 8. (1 August 2007), e164.
    by Elisabeth L Humphris, Tanja Kortemme
    posted to ppi-evolution promiscuous-ppis protein-design by bicko on 2007-09-18 14:12:51 as ** along with 7 people and 3 groups msuarezdiez jwm Einat dpollard Scis0000002 phoenixzxl marck structural_bioinformatics Bioinformatics EisenLab
  • 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 hot-spots interface-properties ppi-evolution by bicko on 2006-06-21 14:55:39 as ** along with 10 people and 2 groups barry baaden nickolay j3xucite bluvsh1 xz grahamc Evangelia ladab paolomarcatili structural_bioinformatics Bioinformatics
  • Exploiting sequence and structure homologs to identify protein-protein binding sites.
    Proteins, Vol. 62, No. 3. (15 March 2006), pp. 630-640.
    by JL Chung, W Wang, PE Bourne
    posted to ppi-evolution interaction-site-prediction by bicko on 2007-01-09 11:47:27 as ** along with 2 people and 2 groups marcius ameetsoni BioinfoCIPF SGU-CIPF
  • The origins and evolution of functional modules: lessons from protein complexes.
    Philos Trans R Soc Lond B Biol Sci, Vol. 361, No. 1467. (29 March 2006), pp. 507-517.
    by JB Pereira-Leal, ED Levy, SA Teichmann
    posted to quaternary-structure ppi-evolution ppi-database by bicko on 2007-01-19 12:05:05 as ** along with 4 people agustinarce choonpeng cjeans cmzmasek
  • Biochemistry. Proteins in a small world.
    Science, Vol. 314, No. 5807. (22 December 2006), pp. 1882-1883.
    by TO Yeates, M Beeby
    posted to quaternary-structure protein-networks ppi-review ppi-evolution by bicko on 2007-01-12 18:45:24 as ** along with 1 person and 1 group lfriedl kdl
  • Identification of protein oligomerization states by analysis of interface conservation.
    Proc Natl Acad Sci U S A, Vol. 98, No. 6. (13 March 2001), pp. 2990-2994.
    by AH Elcock, JA McCammon
    posted to crystal-contacts interface-properties ppi-evolution quaternary-structure by bicko on 2005-11-07 15:15:31 as ** along with 2 people Evangelia marti
  • 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 interaction-partner-prediction ppi-evolution by bicko on 2005-11-01 10:39:16 as ** along with 2 people and 2 groups barry baldo structural_bioinformatics Bioinformatics
  • Highly specific protein-protein interactions, evolution and negative design.
    Phys Biol, Vol. 1, No. 3-4. (December 2004), pp. 166-172.
    by RP Sear
    posted to ppi-evolution ppi-review by bicko on 2006-02-17 15:31:50 as **
  • Convergent solutions to binding at a protein-protein interface.
    Science, Vol. 287, No. 5456. (18 February 2000), pp. 1279-1283.
    by WL DeLano, MH Ultsch, AM de Vos, JA Wells
    posted to interface-properties ppi-evolution ppi-experimental-methods by bicko on 2006-02-20 15:19:27 as ** along with 2 people matzke higueruelo
  • Relating three-dimensional structures to protein networks provides evolutionary insights.
    Science, Vol. 314, No. 5807. (22 December 2006), pp. 1938-1941.
    by PM Kim, LJ Lu, Y Xia, MB Gerstein
    posted to quaternary-structure protein-networks ppi-review ppi-evolution by bicko on 2007-01-09 18:06:43 as ** along with 18 people and 2 groups cerca lfriedl chad_davis Einat tny choonpeng timflutre grahamc ramensky massivemayhem efge lpfernandes cdeane Pao-Yang phoenixzxl carlk paolomarcatili saket structural_bioinformatics kdl
  • Diversity of protein-protein interactions.
    EMBO J, Vol. 22, No. 14. (15 July 2003), pp. 3486-3492.
    by IM Nooren, JM Thornton
    posted to ppi-evolution ppi-review quaternary-structure by bicko on 2005-10-14 12:31:01 as ** along with 4 people chad_davis drastic Evangelia higueruelo
  • A hot spot of binding energy in a hormone-receptor interface.
    Science, Vol. 267, No. 5196. (20 January 1995), pp. 383-386.
    by T Clackson, JA Wells
    posted to hot-spots interface-properties ppi-evolution by bicko on 2006-02-20 15:23:00 as **
  • Co-evolutionary analysis reveals insights into protein-protein interactions.
    J Mol Biol, Vol. 324, No. 1. (15 November 2002), pp. 177-192.
    by CS Goh, FE Cohen
    posted to 1st-yr-report interaction-partner-prediction ppi-evolution by bicko on 2006-06-29 18:17:39 as ** along with 1 person ruvido
  • 3D complex: a structural classification of protein complexes.
    PLoS Comput Biol, Vol. 2, No. 11. (17 November 2006)
    by ED Levy, JB Pereira-Leal, C Chothia, SA Teichmann
    posted to quaternary-structure protein-networks ppi-evolution ppi-database by bicko on 2007-01-09 15:43:33 as ** along with 2 people and 1 group chad_davis Einat structural_bioinformatics
  • Distinguishing structural and functional restraints in evolution in order to identify interaction sites.
    J Mol Biol, Vol. 342, No. 5. (1 October 2004), pp. 1487-1504.
    by V Chelliah, L Chen, TL Blundell, SC Lovell
    posted to blundell-group docking-algorithm guided-docking interaction-site-prediction ppi-evolution by bicko on 2006-06-29 19:07:59 as ** along with 8 people and 1 group chrn rabio massivemayhem cat_worth MaggieYe medic0747 cjeans zwang 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 interaction-partner-prediction ppi-evolution by bicko on 2005-11-01 10:40:46 as ** along with 4 people and 2 groups apaydin barry j3xucite dyermd structural_bioinformatics Bioinformatics
  • Character and evolution of protein-protein interfaces.
    Phys Biol, Vol. 2, No. 1-2. (June 2005)
    by I Res, O Lichtarge
    posted to evolutionary-trace hot-spots interface-properties ppi-evolution by bicko on 2006-02-20 14:20:30 as ** along with 2 people beeblebrox higueruelo
  • An accurate, sensitive, and scalable method to identify functional sites in protein structures.
    J Mol Biol, Vol. 326, No. 1. (7 February 2003), pp. 255-261.
    by H Yao, DM Kristensen, I Mihalek, ME Sowa, C Shaw, M Kimmel, L Kavraki, O Lichtarge
    posted to 1st-yr-report evolutionary-trace interaction-site-prediction ppi-evolution by bicko on 2006-06-29 18:24:21 as ** along with 4 people chrn beeblebrox nickolay sriram_s
  • 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 interaction-site-prediction ppi-evolution structure-comparison by bicko on 2008-01-09 16:16:30 as ** along with 5 people and 4 groups barry tjimenez chad_davis marcius wilbur structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
  • Correlated mutations: Advances and limitations. A study on fusion proteins and on the Cohesin-Dockerin families.
    Proteins (28 February 2006)
    by Inbal Halperin, Haim Wolfson, Ruth Nussinov
    posted to evolutionary-trace guided-docking interaction-site-prediction ppi-evolution by bicko on 2006-03-03 11:28:32 as ** along with 7 people gbart ramensky cjeans tale mingzhi friendpine Lombardo_7
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