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Tag interaction-site-prediction [42 articles]

Recent papers classified by the tag interaction-site-prediction.
  • meta-PPISP: a meta web server for protein-protein interaction site prediction.
    Bioinformatics, Vol. 23, No. 24. (15 December 2007), pp. 3386-3387.
    by S Qin, HX Zhou
    posted to interaction-site-prediction by bicko on 2008-01-09 17:44:01 as ** along with 2 people marti grahamc
  • 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
  • PIER: Protein interface recognition for structural proteomics
    Proteins: Structure, Function, and Bioinformatics, Vol. 67, No. 2. (2007), pp. 400-417.
    by Irina Kufareva, Levon Budagyan, Eugene Raush, Maxim Totrov, Ruben Abagyan
    posted to interaction-site-prediction by bicko on 2007-03-21 17:56:40 as ** along with 2 people choonpeng emidio_capriotti
  • An automated decision-tree approach to predicting protein interaction hot spots.
    Proteins (6 June 2007)
    by Steven J J Darnell, David Page, Julie C C Mitchell
    posted to hot-spots interaction-site-prediction by bicko on 2007-08-15 18:47:54 as ** along with 1 person cjeans
  • 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 marti gloria
  • 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 wilbur barry tjimenez chad_davis marcius structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
  • Protein-Protein Interaction Hotspots Carved into Sequences.
    PLoS Comput Biol, Vol. 3, No. 7. (13 July 2007)
    by Yanay Ofran, Burkhard Rost
    posted to hot-spots interaction-site-prediction by bicko on 2007-08-15 13:04:59 as ** along with 7 people and 3 groups higueruelo dchughes grahamc cjeans zwang Jporci Pao-Yang G4ID ParkinsonLab_at_MaRS Genetics-of-Gambling
  • Modelling interaction sites in protein domains with interaction profile hidden Markov models
    Bioinformatics, Vol. 22, No. 23. (1 December 2006), pp. 2851-2857.
    by Torben Friedrich, Birgit Pils, Thomas Dandekar, Jorg Schultz, Tobias Muller
    posted to interaction-site-prediction by bicko on 2007-01-15 11:12:33 as ** along with 1 person chad_davis
  • 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
  • Improved prediction of protein-protein binding sites using a support vector machines approach
    Bioinformatics, Vol. 21, No. 8. (15 April 2005), pp. 1487-1494.
    by James R Bradford, David R Westhead
    posted to interaction-site-prediction by bicko on 2005-12-12 14:43:42 as ** along with 8 people marti OriginalLurch sriram_s chaleil ameetsoni cjeans Evangelia phoenixzxl
  • Residue centrality, functionally important residues, and active site shape: analysis of enzyme and non-enzyme families.
    Protein Sci, Vol. 15, No. 9. (September 2006), pp. 2120-2128.
    by A del Sol, H Fujihashi, D Amoros, R Nussinov
    posted to interface-properties interaction-site-prediction by bicko on 2007-01-15 11:28:23 as ** along with 3 people drastic choonpeng massivemayhem
  • High-throughput identification of Interacting Protein-Protein Binding Sites
    BMC Bioinformatics, Vol. 8 (27 June 2007), 223.
    by Jo-Lan Chung, Wei Wang, Philip E Bourne
    posted to interaction-partner-prediction interaction-site-prediction by bicko on 2007-08-15 16:52:20 as ***** along with 3 people and 1 group grahamc zwang Evangelia ParkinsonLab_at_MaRS
  • A two-stage classifier for identification of protein-protein interface residues.
    Bioinformatics, Vol. 20 Suppl 1 (4 August 2004)
    by C Yan, D Dobbs, V Honavar
    posted to interaction-site-prediction by bicko on 2006-01-18 12:04:33 as ** along with 1 person kallberg
  • 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
  • Exploiting residue-level and profile-level interface propensities for usage in binding sites prediction of proteins
    BMC Bioinformatics, Vol. 8 (05 May 2007), 147.
    by Qiwen Dong, Xiaolong Wang, Lei Lin, Yi Guan
    posted to interaction-site-prediction interface-properties by bicko on 2007-08-15 17:12:24 as ** along with 2 people marti zwang
  • Guided docking: first step to locate potential binding sites.
    Proteins, Vol. 52, No. 1. (1 July 2003), pp. 28-32.
    by PW Fitzjohn, PA Bates
    posted to docking-algorithm docking-scoring-function guided-docking interaction-site-prediction by bicko on 2005-10-21 10:47:16 as **
  • 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
  • SHARP2: protein-protein interaction predictions using patch analysis
    Bioinformatics, Vol. 22, No. 14. (15 July 2006), pp. 1794-1795.
    by Yoichi Murakami, Susan Jones
    posted to interaction-site-prediction by bicko on 2008-01-17 14:00:06 as ** along with 1 person ameetsoni
  • Interaction-Site Prediction for Protein Complexes: a Critical Assessment
    Bioinformatics (22 June 2007), btm323.
    by Huan-Xiang Zhou, Sanbo Qin
    posted to interaction-site-prediction by bicko on 2007-09-18 14:48:39 as ** along with 10 people kintoki higueruelo tjimenez malcook zwang cabbagezs niallhaslam carlescorbi marti phoenixzxl
  • An algorithm for predicting protein-protein interaction sites: Abnormally exposed amino acid residues and secondary structure elements.
    Protein Sci, Vol. 15, No. 5. (May 2006), pp. 1017-1029.
    by J Hoskins, S Lovell, TL Blundell
    posted to blundell-group interaction-site-prediction interface-properties by bicko on 2006-06-29 19:05:26 as ** along with 2 people higueruelo drastic
  • Predicting protein interaction sites: binding hot-spots in proteinprotein and proteinligand interfaces
    Bioinformatics, Vol. 22, No. 11. (1 June 2006), pp. 1335-1342.
    by Burgoyne, J Nicholas, Jackson, M Richard
    posted to interaction-site-prediction by bicko on 2007-08-24 15:25:49 as ** along with 5 people chad_davis nickolay conkymacro marti ladab
  • Small-world network approach to identify key residues in protein-protein interaction.
    Proteins, Vol. 58, No. 3. (15 February 2005), pp. 672-682.
    by A del Sol, P O'Meara
    posted to hot-spots interaction-site-prediction interface-properties proteins-as-graphs scale-free by bicko on 2006-01-29 12:21:34 as ***** along with 2 people higueruelo choonpeng
  • Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking.
    J Mol Biol, Vol. 311, No. 2. (10 August 2001), pp. 395-408.
    by P Aloy, E Querol, FX Aviles, MJ Sternberg
    posted to evolutionary-trace guided-docking interaction-site-prediction by bicko on 2006-02-20 14:14:10 as ** along with 5 people kaarsinogen chrn chad_davis sriram_s 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
  • 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 Lombardo_7 gbart ramensky cjeans tale mingzhi friendpine
  • Protein-Protein Binding-Sites Prediction by Protein Surface Structure Conservation.
    J Chem Inf Model (28 March 2007)
    by Janez Konc, Dušanka Janežič
    posted to interaction-site-prediction by bicko on 2007-03-30 15:03:51 as ** along with 1 person chad_davis
  • Predicting protein interaction interfaces from protein sequences: Case studies of subtilisin and phycocyanin
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Bin-Bin Xie, Xiu-Lan Chen, Xi-Ying Zhang, Hai-Lun He, Yu-Zhong Zhang, Bai-Cheng Zhou
    posted to interaction-site-prediction by bicko on 2008-01-09 17:46:53 as **
  • Intramolecular surface contacts contain information about protein-protein interface regions.
    Bioinformatics (9 June 2006)
    by Sjoerd J J de Vries, Alexandre M J J M Bonvin
    posted to evolution interaction-partner-prediction interaction-site-prediction interface-properties by bicko on 2007-05-18 13:48:53 as ***** along with 2 people chad_davis choonpeng
  • HotPatch: A Statistical Approach to Finding Biologically Relevant Features on Protein Surfaces.
    J Mol Biol (21 March 2007)
    by Frank K K Pettit, Emiko Bare, Albert Tsai, James U U Bowie
    posted to interaction-site-prediction by bicko on 2007-08-24 15:24:43 as ** along with 1 person cjeans
  • 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 docking-algorithm guided-docking hot-spots interaction-site-prediction interface-properties by bicko on 2005-10-14 12:40:50 as **** along with 2 people and 2 groups barry Evangelia structural_bioinformatics Bioinformatics
  • 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
  • Prediction-based fingerprints of protein-protein interactions
    Proteins: Structure, Function, and Bioinformatics, Vol. 66, No. 3. (2007), pp. 630-645.
    by Aleksey Porollo, Jarosław Meller
    posted to interaction-site-prediction by bicko on 2007-05-18 14:41:21 as ** along with 2 people marti choonpeng
  • Network Analysis of Protein Structures Identifies Functional Residues
    Journal of Molecular Biology, Vol. 344, No. 4. (3 December 2004), pp. 1135-1146.
    by Gil Amitai, Arye Shemesh, Einat Sitbon, Maxim Shklar, Dvir Netanely, Ilya Venger, Shmuel Pietrokovski
    posted to interaction-site-prediction proteins-as-graphs by bicko on 2006-08-17 11:24:18 as ** along with 7 people and 1 group chrn vavi Einat amitai sriram_s massivemayhem siebertm structural_bioinformatics
  • InterProSurf: a web server for predicting interacting sites on protein surfaces.
    Bioinformatics (12 October 2007)
    by Surendra S S Negi, Catherine H H Schein, Numan Oezguen, Trevor D D Power, Werner Braun
    posted to interaction-site-prediction by bicko on 2008-01-09 17:45:34 as ** along with 2 people Ema grahamc
  • Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design.
    Nucleic Acids Res, Vol. 33, No. 18. (2005), pp. 5861-5867.
    by Gong Cheng, Bin Qian, Ram Samudrala, David Baker
    posted to interaction-site-prediction interface-properties by bicko on 2006-08-17 11:23:31 as ** along with 6 people and 3 groups Einat marcius alexg nickolay sriram_s ladab structural_bioinformatics BioinfoCIPF SGU-CIPF
  • In silico identification of functional regions in proteins.
    Bioinformatics, Vol. 21 Suppl 1 (1 June 2005)
    by G Nimrod, F Glaser, D Steinberg, N Ben-Tal, T Pupko
    posted to interaction-site-prediction by bicko on 2006-08-17 11:38:05 as ** along with 1 person sriram_s
  • 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
  • Identification of domains and domain interface residues in multidomain proteins from graph spectral method.
    Proteins, Vol. 59, No. 3. (15 May 2005), pp. 616-626.
    by RK Sistla, B K V, S Vishveshwara
    posted to interaction-site-prediction proteins-as-graphs by bicko on 2007-08-15 17:51:59 as ** along with 1 person choonpeng
  • 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 interaction-site-prediction interface-properties quaternary-structure by bicko on 2005-10-17 18:00:30 as ** along with 6 people and 2 groups barry lyongu ameetsoni cjeans Evangelia marti structural_bioinformatics Bioinformatics
  • ProMate: a structure based prediction program to identify the location of protein-protein binding sites.
    J Mol Biol, Vol. 338, No. 1. (16 April 2004), pp. 181-199.
    by H Neuvirth, R Raz, G Schreiber
    posted to interaction-site-prediction by bicko on 2006-01-12 12:30:08 as ** along with 4 people ameetsoni cjeans Ema marti
  • 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 2 people and 2 groups timg barry structural_bioinformatics Bioinformatics
  • Optimal docking area: a new method for predicting protein-protein interaction sites.
    Proteins, Vol. 58, No. 1. (1 January 2005), pp. 134-143.
    by J Fernandez-Recio, M Totrov, C Skorodumov, R Abagyan
    posted to blundell-group docking-scoring-function energy-landscapes guided-docking interaction-site-prediction by bicko on 2006-02-20 14:45:16 as ** along with 4 people and 2 groups jwm schlauchi cjeans marti Radiation_Damage Stressosome
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