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Evangelia's computational [49 articles]

Recent papers added to Evangelia's library classified by the tag computational. You can also see everyone's computational.
  • A computational strategy for the prediction of functional linear peptide motifs in proteins
    Bioinformatics (31 October 2007), btm524.
    by Holger Dinkel, Heinrich Sticht
    posted to computational motif peptides statistics by Evangelia on 2008-08-25 10:39:46 as ** along with 1 person cjeans
  • Efficient representation and P-value computation for high-order Markov motifs
    Bioinformatics, Vol. 24, No. 16. (15 August 2008), pp. i160-166.
    by Paulo G da Fonseca, Katia S Guimaraes, Marie-France Sagot
    posted to computational statistics by Evangelia on 2008-08-21 10:53:28 as *** along with 1 person Stew
  • Information content of binding sites on nucleotide sequences
    Journal of Molecular Biology, Vol. 188, No. 3. (5 April 1986), pp. 415-431.
    by Thomas D Schneider, Gary D Stormo, Larry Gold, Andrzej Ehrenfeucht
    posted to computational statistics by Evangelia on 2008-08-21 10:01:52 as ***
  • Structure-Templated Predictions of Novel Protein Interactions from Sequence Information
    PLoS Computational Biology:, Vol. 3, No. 9. (September 2007), pp. 1783-9.
    by D Betel, KE Breitkreuz, R Isserlin, D Dewar-Darch, M Tyers, CW Hogue
    posted to computational interactions peptides protein by Evangelia on 2008-05-21 13:53:24 as ****
  • PEPOP: Computational design of immunogenic peptides
    BMC Bioinformatics, Vol. 9 (30 January 2008), 71.
    by Violaine Moreau, Cecile Fleury, Dominique Piquer, Christophe Nguyen, Nicolas Novali, Sylvie Villard, Daniel Laune, Claude Granier, Franck Molina
    posted to computational peptides prediction by Evangelia on 2008-05-06 14:04:59 as ** along with 1 person zgcarvalho
  • Bioinformatic analysis of the CLE signaling peptide family
    BMC Plant Biology, Vol. 8 (03 January 2008), 1.
    by Karsten Oelkers, Nicolas Goffard, Georg F Weiller, Peter M Gresshoff, Ulrike Mathesius, Tancred Frickey
    posted to computational peptides signaling by Evangelia on 2008-05-06 14:02:23 as **
  • In Silico Tools for Predicting Peptides Binding to HLA-Class II Molecules: More Confusion than Conclusion
    J. Proteome Res., Vol. 7, No. 1. (4 January 2008), pp. 154-163.
    by Uthaman Gowthaman, Javed N Agrewala
    posted to binding computational mhc peptides by Evangelia on 2008-05-06 13:59:45 as **
  • Deciphering Protein–Protein Interactions. Part II. Computational Methods to Predict Protein and Domain Interaction Partners
    PLoS Computational Biology, Vol. 3, No. 4. (1 April 2007), e43.
    by Benjamin A Shoemaker, Anna R Panchenko
    posted to domains computational interaction ppi prediction protein protein-protein review use by Evangelia on 2008-03-09 15:36:19 as read along with 14 people Yanno jyuh aalibes bicko jfr chad_davis cjeans iris_2001 zwang lpfernandes groepl carlk higueruelo phoenixzxl
  • Statistical analysis of physical-chemical properties and prediction of protein-protein interfaces
    J Mol Model, Vol. 13 (2007), pp. 1157-1167.
    by Surendra S Negi, Werner Braun
    posted to computational interaction interface prediction properties protein-protein statistics by Evangelia on 2007-12-13 08:10:23 as ***
  • Computational Design of Peptides That Target Transmembrane Helices
    Science, Vol. 315, No. 5820. (30 March 2007), pp. 1817-1822.
    by Hang Yin, Joanna S Slusky, Bryan W Berger, Robin S Walters, Gaston Vilaire, Rustem I Litvinov, James D Lear, Gregory A Caputo, Joel S Bennett, William F Degrado
    posted to computational design geometry-based peptides by Evangelia on 2007-10-31 15:09:06 as read along with 4 people chad_davis zwang xxh0541 chgjb
  • Structural systems biology: modelling protein interactions
    Nature Reviews Molecular Cell Biology, Vol. 7, No. 3., pp. 188-197.
    by Patrick Aloy, Robert B Russell
    posted to computational interaction model protein protein-protein review structure systems by Evangelia on 2007-10-02 10:39:18 as read along with 19 people and 3 groups ana aalibes bicko xico dgront drastic choonpeng henschel ruvido massivemayhem cat_worth fishtank iris_2001 gvuister lpfernandes andreas_foersch higueruelo chad_davis jteyra structural_bioinformatics Bioinformatics WetBiology
  • Detection of protein three-dimensional side-chain patterns: new examples of convergent evolution
    Journal of Molecular Biology, Vol. 279, No. 5. (26 June 1998), pp. 1211-1227.
    by Robert B Russell
    posted to bioinformatics computational evolution patterns profile structure by Evangelia on 2007-10-02 10:23:34 as read along with 2 people shadowman jwm
  • Three-dimensional profiles: a new tool to identify protein surface similarities
    Journal of Molecular Biology, Vol. 284, No. 4. (11 December 1998), pp. 1211-1221.
    by Manuel de Rinaldis, Gabriele Ausiello, Gianni Cesareni, Manuela Helmer-Citterich
    posted to binding computational domains grid interaction pattern prediction profile protein sh2 sh3 structure surface by Evangelia on 2007-10-02 09:57:29 as read along with 2 people nickolay carlescorbi
  • Sequence, Structure and Energetic Determinants of Phosphopeptide Selectivity of SH2 Domains
    Journal of Molecular Biology, Vol. 334, No. 4. (5 December 2003), pp. 823-841.
    by Felix B Sheinerman, Bissan Al-Lazikani, Barry Honig
    posted to bioinformatics computational domains peptides phospho_peptides prediction sh2 specificity structure by Evangelia on 2007-10-02 09:53:17 as read along with 1 person carlescorbi
  • A regularized discriminative model for the prediction of protein–peptide interactions
    Bioinformatics, Vol. 22, No. 5. (2006), pp. 532-540.
    by Wolfgang P Lehrach, Dirk Husmeier, Christopher KI Williams
    posted to bioinformatics computational interaction peptides prediction protein by Evangelia on 2007-10-02 09:48:11 as read
  • Predicting protein–peptide interactions via a network-based motif sampler
    Bioinformatics, Vol. 20, No. Suppl.1. (2004), pp. i274-i282.
    by David J Reiss, Benno Schwikowski
    posted to bioinformatics computational interaction motifs peptides prediction protein by Evangelia on 2007-10-02 09:44:39 as read
  • Ranking potential binding peptides to MHC molecules by a computational threading approach
    Journal of Molecular Biology, Vol. 249, No. 2. (1995), pp. 244-250.
    by Yael Altuvia, Ora Schueler, Hanah Margalit
    posted to algorithm binding computational mhc peptides prediction by Evangelia on 2007-10-01 18:56:25 as read
  • Computational classification of classically secreted proteins
    Drug Discovery Today, Vol. 12, No. 5-6. (March 2007), pp. 234-240.
    by Eric W Klee, Carlos P Sosa
    posted to computational prediction signal_peptides by Evangelia on 2007-10-01 18:48:27 as read
  • Automatic generation of 3D motifs for classification of protein binding sites
    BMC Bioinformatics, Vol. 8 (30 August 2007), 321.
    by Jean-Christophe Nebel, Pawel Herzyk, David R Gilbert
    posted to computational motifs patterns prediction structure algorithm binding binding_site by Evangelia on 2007-10-01 18:45:14 as read along with 3 people shadowman carlescorbi Minty
  • A combined experimental and computational strategy to define protein interaction networks for peptide recognition modules.
    Science, Vol. 295, No. 5553. (11 January 2002), pp. 321-324.
    by AH Tong, B Drees, G Nardelli, GD Bader, B Brannetti, L Castagnoli, M Evangelista, S Ferracuti, B Nelson, S Paoluzi, M Quondam, A Zucconi, CW Hogue, S Fields, C Boone, G Cesareni
    posted to computational domains experimental networks pathways peptides prediction rev_ref y2h by Evangelia on 2007-10-01 18:31:35 as read along with 4 people chad_davis balajis roys carlk
  • Bioinformatic discovery of novel bioactive peptides
    Nat Chem Biol, Vol. 3, No. 2. (February 2007), pp. 108-112.
    by Richard J Edwards, Niamh Moran, Marc Devocelle, Aoife Kiernan, Gerardene Meade, William Signac, Martina Foy, Stephen D Park, Eimear Dunne, Dermot Kenny, Denis C Shields
    posted to binding bioinformatics computational interaction peptides prediction rev_ref by Evangelia on 2007-10-01 18:26:47 as read along with 1 person zwang
  • Reduced surface: An efficient way to compute molecular surfaces
    Biopolymers, Vol. 38, No. 3. (6 December 1998), pp. 305-320.
    by Michel F Sanner, Arthur J Olson, Jean-Claude Spehner
    posted to computational properties surface by Evangelia on 2007-10-01 18:16:17 as read along with 1 person mleis
  • An intuitive approach to measuring protein surface curvature.
    Proteins, Vol. 61, No. 4. (1 December 2005), pp. 1068-1074.
    by RG Coleman, MA Burr, DL Souvaine, AC Cheng
    posted to computational curvature geometry-based surface by Evangelia on 2007-10-01 18:13:07 as read along with 1 person nickolay
  • Fast and Robust Computation of Molecular Surfaces
    (1995)
    by Michel F Sanner, Arthur J Olson, Jean-Claude Spehner
    posted to accessibility computational properties surface by Evangelia on 2007-10-01 18:10:35 as read
  • Computational analyses of the surface properties of protein-protein interfaces
    Acta Crystallographica Section D, Vol. 63, No. 1. (January 2007), pp. 50-57.
    by J Gruber, A Zawaira, R Saunders, CP Barrett, MEM Noble
    posted to computational interface properties protein-protein surface by Evangelia on 2007-10-01 18:07:32 as read
  • MULTIPRED: a computational system for prediction of promiscuous HLA binding peptides.
    Nucleic Acids Res, Vol. 33, No. Web Server issue. (1 July 2005)
    by GL Zhang, AM Khan, KN Srinivasan, JT August, V Brusic
    posted to algorithm binding computational hla peptides prediction by Evangelia on 2007-10-01 18:02:09 as *** along with 1 person sci91078
  • A structure-based approach for prediction of MHC-binding peptides
    Methods, Vol. 34, No. 4. (December 2004), pp. 454-459.
    by Yael Altuvia, Hanah Margalit
    posted to algorithm binding bioinformatics computational mhc peptides prediction structure by Evangelia on 2007-10-01 18:00:42 as read
  • SH3-SPOT: an algorithm to predict preferred ligands to different members of the SH3 gene family
    Journal of Molecular Biology, Vol. 298, No. 2. (28 April 2000), pp. 313-328.
    by Barbara Brannetti, Allegra Via, Gianluca Cestra, Gianni Cesareni, Manuela H Citterich
    posted to algorithm bioinformatics complexes computational domains motifs prediction rev_ref sh3 specificity structure by Evangelia on 2007-10-01 17:58:07 as read along with 2 people carlescorbi biehl
  • A computational method for the analysis and prediction of protein:phosphopeptide-binding sites
    Protein Sci, Vol. 14, No. 1. (1 January 2005), pp. 131-139.
    by Brian A Joughin, Bruce Tidor, Michael B Yaffe
    posted to algorithm computational peptides phospho_peptides prediction protein by Evangelia on 2007-10-01 17:53:50 as read
  • Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain.
    PLoS Comput Biol, Vol. 2, No. 1. (January 2006)
    by T Hou, K Chen, WA McLaughlin, B Lu, W Wang
    posted to algorithm binding computational domains motifs prediction sh3 by Evangelia on 2007-10-01 17:51:23 as read along with 4 people neils carlescorbi biehl jteyra
  • PepDist: a new framework for protein-peptide binding prediction based on learning peptide distance functions.
    BMC Bioinformatics, Vol. 7 Suppl 1 (2006)
    by T Hertz, C Yanover
    posted to algorithm binding bioinformatics computational interaction peptides prediction protein by Evangelia on 2007-10-01 17:49:32 as read
  • Structural prediction of peptides binding to MHC class I molecules
    Proteins: Structure, Function, and Bioinformatics, Vol. 63, No. 1. (2006), pp. 43-52.
    by Huynh-Hoa Bui, Alexandra J Schiewe, Hermann von Grafenstein, Ian S Haworth
    posted to bioinformatics computational mhc peptides prediction structure by Evangelia on 2007-10-01 17:47:58 as read
  • Data-driven docking for the study of biomolecular complexes.
    FEBS J, Vol. 272, No. 2. (January 2005), pp. 293-312.
    by AD van Dijk, R Boelens, AM Bonvin
    posted to complexes computational docking interaction protein-protein by Evangelia on 2007-10-01 16:51:22 as * along with 5 people and 1 group dgruiz bicko anita gloria higueruelo structure-bii
  • 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 binding bioinformatics computational interaction potential prediction protein protein-protein statistics by Evangelia on 2007-10-01 16:40:10 as read along with 6 people and 2 groups barry bicko lyongu ameetsoni cjeans marti structural_bioinformatics Bioinformatics
  • A new program to compute the surface properties of biomolecules
    (2003), pp. 29-34.
    by Dan V Nicolau, Florin Fulga, Dan V Nicolau
    posted to bioinformatics biology computational properties surface by Evangelia on 2007-10-01 16:24:53 as read
  • Searching for protein-protein interaction sites and docking by the methods of molecular dynamics, grid scoring, and the pairwise interaction potential of amino acid residues.
    Proteins, Vol. 60, No. 2. (1 August 2005), pp. 289-295.
    by G Terashi, M Takeda-Shitaka, D Takaya, K Komatsu, H Umeyama
    posted to computational docking grid_scoring interaction molecular_dynamics potential prediction protein-protein by Evangelia on 2007-10-01 15:57:36 as *** along with 1 person and 1 group qzhang TSRI_MGL
  • Scores for sequence searches and alignments
    Current Opinion in Structural Biology, Vol. 6, No. 3. (June 1996), pp. 353-360.
    by Steven Henikoff
    posted to alignment bioinformatics biology computational score by Evangelia on 2007-10-01 15:45:50 as **
  • Can we infer peptide recognition specificity mediated by SH3 domains?
    FEBS Letters, Vol. 513, No. 1. (20 February 2002), pp. 38-44.
    by Gianni Cesareni, Simona Panni, Giuliano Nardelli, Luisa Castagnoli
    posted to binding computational domains peptides prediction proline-rich protein sh3 specificity surface by Evangelia on 2007-10-01 15:18:04 as **** along with 1 person biehl
  • Structure-based assembly of protein complexes in yeast.
    Science, Vol. 303, No. 5666. (26 March 2004), pp. 2026-2029.
    by P Aloy, B Böttcher, H Ceulemans, C Leutwein, C Mellwig, S Fischer, AC Gavin, P Bork, G Superti-Furga, L Serrano, RB Russell
    posted to complexes computational interaction model structure by Evangelia on 2007-10-01 15:02:24 as read along with 4 people chad_davis koller ruvido mingzhi
  • Novel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvature
    Journal of Computational Chemistry, Vol. 23, No. 6. (2002), pp. 600-609.
    by Oleg V Tsodikov, Thomas M Record, Yuri V Sergeev
    posted to accessibility bioinformatics biology computational curvature surface by Evangelia on 2007-10-01 14:03:51 as read
  • 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 binding biology computational docking interaction protein-protein by Evangelia on 2007-10-01 13:52:10 as ** along with 9 people and 3 groups barry aqeel jwm bicko yongzhao blackbart bluvsh1 hmk selrac structural_bioinformatics Bioinformatics TSRI_MGL
  • A structural perspective on protein-protein interactions.
    Curr Opin Struct Biol, Vol. 14, No. 3. (June 2004), pp. 313-324.
    by RB Russell, F Alber, P Aloy, FP Davis, D Korkin, M Pichaud, M Topf, A Sali
    posted to bioinformatics biology complexes computational docking interaction protein-protein structure by Evangelia on 2007-10-01 13:48:48 as read along with 13 people and 1 group baaden bicko anita chad_davis dgront sriram_s ruvido cjeans Pao-Yang marti higueruelo jteyra timg structure-bii
  • 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 binding bioinformatics biology computational prediction protein-protein surface svm by Evangelia on 2007-10-01 13:34:19 as ** along with 8 people bicko sriram_s chaleil ameetsoni cjeans phoenixzxl marti OriginalLurch
  • Use of pair potentials across protein interfaces in screening predicted docked complexes
    Proteins: Structure, Function, and Genetics, Vol. 35, No. 3. (1999), pp. 364-373.
    by Gidon Moont, Henry A Gabb, Michael JE Sternberg
    posted to bioinformatics biology complexes computational docking interaction protein protein-protein score statistics by Evangelia on 2007-10-01 13:14:58 as read
  • 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 binding bioinformatics biology computational interaction networks prediction protein protein-protein structure by Evangelia on 2007-10-01 13:11:17 as read along with 10 people and 3 groups ana barry baaden bicko lfriedl chad_davis henschel ruvido cjeans tale structural_bioinformatics kdl Bioinformatics
  • Virtual Screening against Metalloenzymes for Inhibitors and Substrates.
    Biochemistry, Vol. 44, No. 37. (20 September 2005), pp. 12316-12328.
    by JJ Irwin, FM Raushel, BK Shoichet
    posted to biology computational docking prediction by Evangelia on 2007-10-01 12:42:27 as ** along with 2 people and 3 groups yongzhao sangeetha Bioinformatics TSRI_MGL insilicodrug
  • A pharmacophore-based evolutionary approach for screening selective estrogen receptor modulators
    Proteins: Structure, Function, and Bioinformatics, Vol. 59, No. 2. (2005), pp. 205-220.
    by Jinn-Moon Yang, Tsai-Wei Shen
    posted to biology computational docking by Evangelia on 2007-10-01 12:39:02 as *
  • Semi-rational approaches to engineering enzyme activity: combining the benefits of directed evolution and rational design
    Current Opinion in Biotechnology, Vol. 16, No. 4. (August 2005), pp. 378-384.
    by Roberto A Chica, Nicolas Doucet, Joelle N Pelletier
    posted to biology computational drug-design enzyme by Evangelia on 2007-10-01 12:35:29 as ** along with 1 person aalibes
  • Systematic Discovery of New Recognition Peptides Mediating Protein Interaction Networks.
    PLoS Biol, Vol. 3, No. 12. (15 November 2005)
    by Victor Neduva, Rune Linding, Isabelle Su-Angrand, Alexander Stark, Federico de D Masi, Toby J J Gibson, Joe Lewis, Luis Serrano, Robert B B Russell
    posted to bioinformatics biology computational motifs peptides prediction rev_ref by Evangelia on 2007-10-01 12:31:24 as read along with 10 people and 2 groups rklancer okarsligil bicko Ayest xwbcn drastic ezotenko grahamc oelemento chad_davis Bioinformatics ParkinsonLab_at_MaRS
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