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nickolay's site [20 articles]

Recent papers added to nickolay's library classified by the tag site. You can also see everyone's site.
  • Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites
    Bioinformatics, Vol. 24, No. 16. (15 August 2008), pp. i105-111.
    by Rafael Najmanovich, Natalja Kurbatova, Janet Thornton
  • How Different are Structurally Flexible and Rigid Binding Sites? Sequence and Structural Features Discriminating Proteins that Do and Do not Undergo Conformational Change upon Ligand Binding.
    J Mol Biol (29 September 2006)
    by Kannan Gunasekaran, Ruth Nussinov
  • From the Similarity Analysis of Protein Cavities to the Functional Classification of Protein Families Using Cavbase
    Journal of Molecular Biology, Vol. 359, No. 4. (16 June 2006), pp. 1023-1044.
    by Daniel Kuhn, Nils Weskamp, Stefan Schmitt, Eyke Hullermeier, Gerhard Klebe
  • LigProf: A simple tool for in silico prediction of ligand-binding sites
    Journal of Molecular Modeling, Vol. 13, No. 3. (March 2007), pp. 445-455.
    posted to software site server motif comparison binding by nickolay on 2008-07-08 14:38:30 as **
  • Do Structurally Similar Ligands Bind in a Similar Fashion?
    J. Med. Chem., Vol. 49, No. 23. (16 November 2006), pp. 6716-6725.
  • Structure-based identification of binding sites, native ligands and potential inhibitors for G-protein coupled receptors.
    Proteins, Vol. 51, No. 3. (15 May 2003), pp. 423-433.
    by CN Cavasotto, AJ Orry, RA Abagyan
    posted to small site identification gpcr binding algorithm by nickolay on 2008-07-08 14:04:41 as **
  • Comprehensive identification of "druggable" protein ligand binding sites.
    Genome Inform Ser Workshop Genome Inform, Vol. 15, No. 2. (2004), pp. 31-41.
    by J An, M Totrov, R Abagyan
  • Searching for functional sites in protein structures
    Current Opinion in Chemical Biology, Vol. 8, No. 1. (February 2004), pp. 3-7.
    by Susan Jones, Janet M Thornton
  • Large scale analysis of protein-binding cavities using self-organizing maps and wavelet-based surface patches to describe functional properties, selectivity discrimination, and putative cross-reactivity
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Katrin Kupas, Alfred Ultsch, Gerhard Klebe
  • On the nature of cavities on protein surfaces: Application to the identification of drug-binding sites.
    Proteins (13 February 2006)
    by Murad Nayal, Barry Honig
  • Localization of binding sites in protein structures by optimization of a composite scoring function.
    Protein Sci, Vol. 15, No. 10. (October 2006), pp. 2366-2380.
    by A Rossi, MA Marti-Renom, A Sali
  • LIGSITEcsc: Predicting ligand binding sites using the Connolly surface and degree of conservation
    BMC Structural Biology, Vol. 6 (24 September 2006), 19.
    by Bingding Huang, Michael Schroeder
  • Recognition of docking sites on a protein using [beta]-shape based on Voronoi diagram of atoms
    Computer-Aided Design, Vol. 38, No. 5. (May 2006), pp. 431-443.
    by Deok-Soo Kim, Cheol-Hyung Cho, Donguk Kim, Youngsong Cho
    posted to site protein identification geometric binding algorithm by nickolay on 2007-01-18 18:56:02 as **
  • Pattern recognition strategies for molecular surfaces: III. Binding site prediction with a neural network.
    J Comput Chem, Vol. 25, No. 6. (30 April 2004), pp. 779-789.
    by M Keil, TE Exner, J Brickmann
  • Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites
    Bioinformatics, Vol. 21, No. 9. (1 May 2005), pp. 1908-1916.
    by Alasdair T Laurie, Richard M Jackson
  • Fast prediction and visualization of protein binding pockets with PASS.
    J Comput Aided Mol Des, Vol. 14, No. 4. (May 2000), pp. 383-401.
    by GP Brady, PF Stouten
  • Characterization of protein-ligand interaction sites using experimental and computational methods.
    Curr Opin Drug Discov Devel, Vol. 9, No. 3. (May 2006), pp. 354-362.
  • Identification and mapping of small-molecule binding sites in proteins: computational tools for structure-based drug design
    Il Farmaco, Vol. 57, No. 3. (1 March 2002), pp. 243-251.
    by Christoph Sotriffer, Gerhard Klebe
    posted to site review indentification comparison binding algorithm by nickolay on 2006-12-05 21:36:58 as read
  • LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins.
    J Mol Graph Model, Vol. 15, No. 6. (December 1997)
  • The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria.
    J Mol Biol, Vol. 256, No. 1. (16 February 1996), pp. 201-213.
    by KP Peters, J Fauck, C Frömmel
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