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nickolay library [137 articles]

最近 nickolay さんのライブラリ .
  • Highly accurate method for ligand-binding site prediction in unbound state (apo) protein structures.
    Proteins (1 May 2008)
    by Mizuki Morita, Shugo Nakamura, Kentaro Shimizu
    posted to strcuture protein prediction ligand energy-based apo by nickolay on 2008-07-14 20:02:25 as **
  • 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
    posted to site flexibility comparison binding by nickolay on 2008-07-08 15:05:37 as ** along with 8 people and 1 group higueruelo BragilMassoud dgruiz radestock lna yongzhao choonpeng weisblum TSRI_MGL
  • 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
    posted to site comparison classifier binding algorithm by nickolay on 2008-07-08 15:03:05 as ** along with 2 people apaydin stege
  • Analysis of binding site similarity, small-molecule similarity and experimental binding profiles in the human cytosolic sulfotransferase family.
    Bioinformatics, Vol. 23, No. 2. (15 January 2007)
    by RJ Najmanovich, A Allali-Hassani, RJ Morris, L Dombrovsky, PW Pan, M Vedadi, AN Plotnikov, A Edwards, C Arrowsmith, JM Thornton
    posted to to-be-tagged by nickolay on 2008-07-08 14:47:52 as ** along with 1 person grottenolm
  • 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.
    by Koczyk, Grzegorz, Wyrwicz, Lucjan, Rychlewski, Leszek
    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.
    by J Bostrom, A Hogner, S Schmitt
    posted to site ligand-based comparison binding by nickolay on 2008-07-08 14:24:45 as read along with 3 people schlauchi daevans superpyrin
  • 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
    posted to software site identification binding algorithm by nickolay on 2008-07-08 13:56:28 as ** along with 1 person sriram_s
  • Optimization of multiple-sequence alignment based on multiple-structure alignment.
    Proteins, Vol. 62, No. 1. (1 January 2006), pp. 209-217.
    by M Shatsky, R Nussinov, HJ Wolfson
    posted to wrmsd structure sequence protein printed alignment by nickolay on 2008-06-11 19:53:47 as ***
  • 3DCoffee: combining protein sequences and structures within multiple sequence alignments.
    J Mol Biol, Vol. 340, No. 2. (2 July 2004), pp. 385-395.
    by O O'Sullivan, K Suhre, C Abergel, DG Higgins, C Notredame
    posted to wrmsd structure sequence protein printed alignment by nickolay on 2008-06-11 19:49:44 as *** along with 4 people and 4 groups edvin ana jwm analogAI structural_bioinformatics Radiation_Damage Stressosome Bioinformatics
  • Pairwise iterative superposition of distantly related proteins and assessment of the significance of 3-D structural similarity
    Protein Eng., Vol. 9, No. 12. (1 December 1996), pp. 1093-1101.
    by Alex C May
    posted to wrmsd structure protein printed iterative alignment by nickolay on 2008-06-11 19:42:10 as ***
  • 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
    posted to structure site search review read protein printed function by nickolay on 2008-06-10 19:06:59 as *** along with 6 people and 1 group jwm BragilMassoud LeightonP chrn Einat proteasome structural_bioinformatics
  • Moment invariants as shape recognition technique for comparing protein binding sites
    Bioinformatics, Vol. 23, No. 23. (1 December 2007), pp. 3139-3146.
    by Ingolf Sommer, Oliver Muller, Francisco S Domingues, Oliver Sander, Joachim Weickert, Thomas Lengauer
    posted to no-tag by nickolay on 2007-12-04 22:23:29 as **** along with 3 people tjimenez chad_davis carlescorbi
  • 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
    posted to surface site protein printed neural networks identification function comparison binding analysis by nickolay on 2007-12-04 21:17:45 as ***** along with 3 people and 1 group higueruelo sobolevnrm carlescorbi baker-group
  • Prediction of Protein-Protein Interaction Sites using Patch Analysis
    pp. 133-143.
    by S Jones
    posted to no-tag by nickolay on 2007-08-24 01:26:42 as ***** along with 1 person npt11tpn
  • Studies of protein-protein interfaces: a statistical analysis of the hydrophobic effect.
    Protein Sci, Vol. 6, No. 1. (January 1997), pp. 53-64.
    by CJ Tsai, SL Lin, HJ Wolfson, R Nussinov
    posted to hyfrophobic-effect protein-interface protein-protein by nickolay on 2007-08-24 01:23:14 as ***** along with 3 people npt11tpn bicko chad_davis
  • Amino acid quantitative structure property relationship database: a web-based platform for quantitative investigations of amino acids
    Protein Engineering, Design and Selection, Vol. 20, No. 7. (1 July 2007), pp. 347-351.
    by Yi Lu, Blazej Bulka, Marie Desjardins, Stephen J Freeland
    posted to amino-acids database property structure web-based by nickolay on 2007-08-22 16:37:46 as **
  • Clinical phenotypes and factor VII genotype in congenital factor VII deficiency.
    Thromb Haemost, Vol. 93, No. 3. (March 2005), pp. 481-487.
    by G Mariani, FH Herrmann, A Dolce, A Batorova, D Etro, F Peyvandi, K Wulff, JF Schved, G Auerswald, J Ingerslev, F Bernardi,
    posted to ontology by nickolay on 2007-07-18 02:29:52 as **
  • Towards Fully Automated Structure-based Function Prediction in Structural Genomics: A Case Study
    Journal of Molecular Biology, Vol. 367, No. 5. (13 April 2007), pp. 1511-1522.
    by James D Watson, Steve Sanderson, Alexandra Ezersky, Alexei Savchenko, Aled Edwards, Christine Orengo, Andrzej Joachimiak, Roman A Laskowski, Janet M Thornton
    posted to no-tag by nickolay on 2007-05-02 15:31:25 as ***** along with 4 people and 2 groups jwm ana tjimenez grottenolm structural_bioinformatics Bioinformatics
  • 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
    posted to small site identification classifier binding by nickolay on 2007-01-18 19:09:10 as ** along with 4 people and 1 group BragilMassoud pansapiens tjimenez Einat structural_bioinformatics
  • Looking at enzymes from the inside out: the proximity of catalytic residues to the molecular centroid can be used for detection of active sites and enzyme-ligand interfaces.
    J Mol Biol, Vol. 351, No. 2. (12 August 2005), pp. 309-326.
    by A Ben-Shimon, M Eisenstein
    posted to to-be-tagged by nickolay on 2007-01-18 19:07:34 as ** along with 3 people and 1 group baaden Einat Evangelia structural_bioinformatics
  • 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
    posted to structure site scoring protein printed localization function binding by nickolay on 2007-01-18 19:05:03 as ** along with 2 people tjimenez MaggieYe
  • 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
    posted to software site server identification geometric binding algorithm by nickolay on 2007-01-18 18:58:13 as ***** along with 1 person tjimenez
  • 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
    posted to surface site protein prediction neural network identification binding by nickolay on 2007-01-18 18:51:41 as *** along with 1 person kaarsinogen
  • 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
    posted to site protein printed prediction method binding by nickolay on 2007-01-18 18:49:52 as *** along with 1 person sriram_s
  • What makes a binding site a binding site?
    Curr Opin Struct Biol, Vol. 5, No. 6. (December 1995), pp. 825-829.
    by D Ringe
    posted to to-be-tagged by nickolay on 2007-01-17 20:28:20 as **
  • 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
    posted to visualization site protein printed prediction method binding by nickolay on 2007-01-17 20:22:25 as *** along with 1 person tjimenez
  • 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.
    by S Vajda, F Guarnieri
    posted to solvent site review mc mapping identification computational binding by nickolay on 2007-01-03 15:16:19 as ** along with 2 people and 1 group kentsis caporaso biomedical-nlp
  • 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
  • POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids.
    J Mol Graph, Vol. 10, No. 4. (December 1992), pp. 229-234.
    by DG Levitt, LJ Banaszak
    posted to to-be-tagged by nickolay on 2006-12-04 21:16:26 as ** along with 2 people tjimenez sriram_s
  • LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins.
    J Mol Graph Model, Vol. 15, No. 6. (December 1997)
    by M Hendlich, F Rippmann, G Barnickel
    posted to site identification geometric binding algorithm by nickolay on 2006-12-04 21:14:14 as ** along with 1 person tjimenez
  • In silico identification of novel EGFR inhibitors with antiproliferative activity against cancer cells
    Bioorganic & Medicinal Chemistry Letters, Vol. 16, No. 7. (1 April 2006), pp. 1969-1974.
    by Claudio N Cavasotto, Maria A Ortiz, Ruben A Abagyan, Javier F Piedrafita
    posted to to-be-tagged by nickolay on 2006-12-04 21:05:53 as **
  • Complexity of free energy landscapes of peptides revealed by nonlinear principal component analysis
    Proteins: Structure, Function, and Bioinformatics, Vol. 65, No. 4. (2006), pp. 898-913.
    by Phuong H Nguyen
    posted to to-be-tagged by nickolay on 2006-11-29 16:29:46 as ** along with 3 people Diego_Prada npt11tpn ladab
  • Residue frequencies and pairing preferences at protein-protein interfaces
    Proteins: Structure, Function, and Genetics, Vol. 43, No. 2. (2001), pp. 89-102.
    by Fabian Glaser, David M Steinberg, Ilya A Vakser, Nir Ben-Tal
    posted to aa-propensity binding-site-analysis protein-interface protein-protein by nickolay on 2006-11-17 16:26:47 as *** along with 3 people timg Evangelia ladab
  • Travel depth, a new shape descriptor for macromolecules: application to ligand binding.
    J Mol Biol, Vol. 362, No. 3. (22 September 2006), pp. 441-458.
    by RG Coleman, KA Sharp
    posted to to-be-tagged by nickolay on 2006-11-11 22:06:34 as ** along with 1 person and 2 groups barry structural_bioinformatics Bioinformatics
  • 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 to-be-tagged by nickolay on 2006-10-26 01:40:54 as ***** along with 6 people and 3 groups bicko Einat marcius alexg sriram_s ladab structural_bioinformatics BioinfoCIPF SGU-CIPF
  • Variation in structural location and amino acid conservation of functional sites in protein domain families.
    BMC Bioinformatics, Vol. 6 (2005)
    by B Pils, RR Copley, J Schultz
    posted to binding-site-analysis conservation protein-protein residue-conservation structural structure-function by nickolay on 2006-10-24 21:21:27 as read
  • A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications.
    Protein Sci, Vol. 13, No. 4. (April 2004), pp. 1043-1055.
    by O Keskin, CJ Tsai, H Wolfson, R Nussinov
    posted to database protein-interface protein-protein by nickolay on 2006-10-24 21:18:12 as read along with 5 people baaden bicko chad_davis henschel ladab
  • 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 aa-propensity binding-site-analysis hot-spots surface by nickolay on 2006-10-24 21:09:45 as read along with 10 people and 2 groups paolomarcatili barry baaden bicko j3xucite bluvsh1 xz grahamc Evangelia ladab 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 binding-site-analysis residue-conservation surface by nickolay on 2006-10-24 21:07:11 as read along with 8 people and 2 groups mdimmic barry bicko lyongu choonpeng cjeans carlescorbi ladab structural_bioinformatics Bioinformatics
  • 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
    posted to site identification geometric binding algorithm by nickolay on 2006-10-04 17:22:44 as ** along with 2 people tjimenez sriram_s
  • notes 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 to-be-tagged by nickolay on 2006-10-04 17:19:48 as ** along with 5 people bicko chad_davis conkymacro marti ladab
  • Functional restraints on the patterns of amino acid substitutions: Application to sequence-structure homology recognition
    Proteins: Structure, Function, and Bioinformatics, Vol. 61, No. 4. (2005), pp. 722-731.
    by Vijayalakshmi Chelliah, Tom Blundell, Kenji Mizuguchi
    posted to to-be-tagged by nickolay on 2006-10-04 17:15:41 as ** along with 1 person michaelbarton
  • Are acidic and basic groups in buried proteins predicted to be ionized?
    J Mol Biol, Vol. 348, No. 5. (20 May 2005), pp. 1283-1298.
    by J Kim, J Mao, MR Gunner
    posted to to-be-tagged by nickolay on 2006-10-04 17:14:00 as **
  • An amino acid has two sides: a new 2D measure provides a different view of solvent exposure.
    Proteins, Vol. 59, No. 1. (1 April 2005), pp. 38-48.
    by T Hamelryck
    posted to to-be-tagged by nickolay on 2006-10-04 17:09:24 as ** along with 3 people karbak massivemayhem gisle
  • Catalysing new reactions during evolution: economy of residues and mechanism.
    J Mol Biol, Vol. 331, No. 4. (22 August 2003), pp. 829-860.
    by GJ Bartlett, N Borkakoti, JM Thornton
    posted to to-be-tagged by nickolay on 2006-10-04 16:46:28 as ** along with 2 people jwm gbart
  • Correlation between sequence hydrophobicity and surface-exposure pattern of database proteins
    Protein Sci, Vol. 13, No. 3. (1 March 2004), pp. 752-762.
    by Susanne Moelbert, Eldon Emberly, Chao Tang
    posted to aa-propensity binding-site-analysis residue-conservation surface by nickolay on 2006-10-04 16:10:06 as read
  • Functional annotation of proteomic sequences based on consensus of sequence and structural analysis
    Brief Bioinform, Vol. 3, No. 1. (1 January 2002), pp. 32-44.
    by David H Kitson, Azat Badretdinov, Zhan-Yang Zhu, Mikhail Velikanov, David J Edwards, Krzysztof Olszewski, Sandor Szalma, Lisa Yan
    posted to to-be-tagged by nickolay on 2006-09-05 19:32:29 as **
  • A novel statistical ligand-binding site predictor: application to ATP-binding sites
    Protein Engineering, Design and Selection, Vol. 18, No. 2. (February 2005), pp. 65-70.
    by Ting Guo, Yanxin Shi, Zhirong Sun
    posted to to-be-tagged by nickolay on 2006-09-05 19:31:14 as ** along with 1 person srdshigella
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