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bicko's Nussinov [31 articles]

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  • A geometry-based suite of molecular docking processes.
    J Mol Biol, Vol. 248, No. 2. (28 April 1995), pp. 459-477.
    by D Fischer, SL Lin, HL Wolfson, R Nussinov
    posted to contact-pairing-preferences by bicko on 2008-08-01 16:25:21 as ** along with 1 person tjimenez
  • RESTRICTED MOBILITY OF CONSERVED RESIDUES IN PROTEIN-PROTEIN INTERFACES IN MOLECULAR SIMULATIONS.
    Biophys J (28 January 2008)
    by S Bora B Erdemli, O Nuri N Yogurtcu, Metin Turkay, Ruth Nussinov, Ozlem Keskin
    posted to hot-spots interface-properties by bicko on 2008-02-06 16:31:58 as ** along with 3 people jlh64 marti higueruelo
  • Spatial chemical conservation of hot spot interactions in protein-protein complexes
    BMC Biology, Vol. 5 (09 October 2007), 43.
    by Alexandra Shulman-Peleg, Maxim Shatsky, Ruth Nussinov, Haim J Wolfson
    posted to hot-spots by bicko on 2007-10-22 23:16:44 as ** along with 3 people IrinaMoreira higueruelo marti
  • Salt bridge stability in monomeric proteins,
    Journal of Molecular Biology, Vol. 293, No. 5. (12 November 1999), pp. 1241-1255.
    by Sandeep Kumar, Ruth Nussinov
    posted to ion-pairs by bicko on 2007-10-16 16:09:51 as ** along with 2 people choonpeng onufriev
  • Relationship between ion pair geometries and electrostatic strengths in proteins.
    Biophys J, Vol. 83, No. 3. (September 2002), pp. 1595-1612.
    by S Kumar, R Nussinov
    posted to ion-pairs by bicko on 2007-10-16 16:09:09 as ** along with 1 person and 2 groups barry structural_bioinformatics Bioinformatics
  • Modular architecture of protein structures and allosteric communications: potential implications for signaling proteins and regulatory linkages
    Genome Biology, Vol. 8 (25 May 2007), R92.
    by Antonio D Sol, Marcos J Arauzo-Bravo, Dolors A Moya, Ruth Nussinov
    posted to proteins-as-graphs by bicko on 2007-08-15 18:00:52 as ** along with 2 people choonpeng echcram
  • Trp/Met/Phe hot spots in protein-protein interactions: potential targets in drug design.
    Curr Top Med Chem, Vol. 7, No. 10. (2007), pp. 999-1005.
    by B Ma, R Nussinov
    posted to drug-discovery hot-spots interface-properties by bicko on 2007-08-15 17:48:31 as **
  • Towards drugs targeting multiple proteins in a systems biology approach.
    Curr Top Med Chem, Vol. 7, No. 10. (2007), pp. 943-951.
    by O Keskin, A Gursoy, B Ma, R Nussinov
    posted to drug-discovery protein-networks systems-biology by bicko on 2007-08-15 17:23:18 as ** along with 1 person higueruelo
  • Similar binding sites and different partners: implications to shared proteins in cellular pathways.
    Structure, Vol. 15, No. 3. (March 2007), pp. 341-354.
    by O Keskin, R Nussinov
    posted to interaction-partner-prediction interface-properties promiscuous-ppis by bicko on 2007-08-15 17:19:27 as ** along with 3 people choonpeng higueruelo marti
  • FireDock: Fast interaction refinement in molecular docking.
    Proteins (27 June 2007)
    by Nelly Andrusier, Ruth Nussinov, Haim J J Wolfson
    posted to docking-algorithm by bicko on 2007-07-04 19:20:50 as ** along with 1 person timg
  • Hydrogen bonds and salt bridges across protein-protein interfaces.
    Protein Eng, Vol. 10, No. 9. (September 1997), pp. 999-1012.
    by D Xu, CJ Tsai, R Nussinov
    posted to interface-properties by bicko on 2007-05-18 15:24:39 as ** along with 1 person gisle
  • 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 residue-contacts interface-properties by bicko on 2007-05-18 15:10:28 as ** along with 2 people nickolay npt11tpn
  • A set of van der Waals and coulombic radii of protein atoms for molecular and solvent-accessible surface calculation, packing evaluation, and docking.
    Proteins, Vol. 32, No. 1. (1 July 1998), pp. 111-127.
    by AJ Li, R Nussinov
    posted to interface-properties atomic-radii by bicko on 2007-02-05 18:09:57 as **
  • 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 4 people neils drastic choonpeng massivemayhem
  • 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
  • Combinatorial docking approach for structure prediction of large proteins and multi-molecular assemblies.
    Phys Biol, Vol. 2, No. 4. (November 2005)
    by Y Inbar, H Benyamini, R Nussinov, HJ Wolfson
    posted to docking-algorithm docking-applications docking-symmetry guided-docking quaternary-structure systems-biology by bicko on 2006-06-15 01:39:07 as ** along with 1 person chad_davis
  • Protein-protein interactions: organization, cooperativity and mapping in a bottom-up Systems Biology approach.
    Phys Biol, Vol. 2, No. 1-2. (June 2005)
    by Ozlem Keskin, Buyong Ma, Kristina Rogale, K Gunasekaran, Ruth Nussinov
    posted to interface-properties ppi-review protein-networks systems-biology by bicko on 2006-06-14 12:22:26 as ** along with 2 people choonpeng higueruelo
  • Examination of shape complementarity in docking of unbound proteins.
    Proteins, Vol. 36, No. 3. (15 August 1999), pp. 307-317.
    by R Norel, D Petrey, HJ Wolfson, R Nussinov
    posted to docking-benchmark docking-scoring-function interface-properties ppi-database by bicko on 2006-05-11 14:57:42 as ** along with 1 person blackbart
  • 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
  • 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 **
  • A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique.
    J Mol Biol, Vol. 260, No. 4. (26 July 1996), pp. 604-620.
    by CJ Tsai, SL Lin, HJ Wolfson, R Nussinov
    posted to docking-benchmark interface-properties ppi-database by bicko on 2006-02-20 12:23:46 as **
  • Geometry-based flexible and symmetric protein docking.
    Proteins, Vol. 60, No. 2. (1 August 2005), pp. 224-231.
    by D Schneidman-Duhovny, Y Inbar, R Nussinov, HJ Wolfson
    posted to docking-algorithm docking-symmetry by bicko on 2005-10-21 10:21:14 as ** along with 2 people and 2 groups vavi marcius BioinfoCIPF SGU-CIPF
  • 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 hot-spots interface-properties by bicko on 2005-10-20 16:02:13 as ** along with 8 people and 2 groups mdimmic barry lyongu nickolay choonpeng cjeans carlescorbi ladab structural_bioinformatics Bioinformatics
  • PatchDock and SymmDock: servers for rigid and symmetric docking.
    Nucleic Acids Res, Vol. 33, No. Web Server issue. (1 July 2005)
    by D Schneidman-Duhovny, Y Inbar, R Nussinov, HJ Wolfson
    posted to docking-algorithm docking-symmetry by bicko on 2005-10-20 13:15:40 as **
  • 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 ppi-database by bicko on 2005-10-20 12:33:00 as ** along with 6 people thomaskelder baaden chad_davis nickolay henschel ladab
  • SiteEngines: recognition and comparison of binding sites and protein-protein interfaces.
    Nucleic Acids Res, Vol. 33, No. Web Server issue. (1 July 2005)
    by A Shulman-Peleg, R Nussinov, HJ Wolfson
    posted to interface-properties modelling-interactions ppi-database by bicko on 2005-10-20 12:31:41 as ** along with 1 person nickolay
  • PRISM: protein interactions by structural matching.
    Nucleic Acids Res, Vol. 33, No. Web Server issue. (1 July 2005)
    by U Ogmen, O Keskin, AS Aytuna, R Nussinov, A Gursoy
    posted to modelling-interactions ppi-database by bicko on 2005-10-18 16:28:32 as ** along with 4 people chad_davis apaydin j3xucite henschel
  • Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues.
    J Mol Biol, Vol. 345, No. 5. (4 February 2005), pp. 1281-1294.
    by O Keskin, B Ma, R Nussinov
    posted to hot-spots interface-properties by bicko on 2005-10-18 16:27:58 as ** along with 8 people and 2 groups mdimmic ana barry baaden okarsligil j3xucite bilab xz structural_bioinformatics Bioinformatics
  • Generation and analysis of a protein-protein interface data set with similar chemical and spatial patterns of interactions
    Proteins: Structure, Function, and Bioinformatics, Vol. 61, No. 1. (3 August 2005), pp. 6-20.
    by Shira Mintz, Alexandra Shulman-Peleg, Haim J Wolfson, Ruth Nussinov
    posted to interface-properties ppi-database by bicko on 2005-10-17 17:56:55 as **
  • 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
  • Principles of docking: An overview of search algorithms and a guide to scoring functions.
    Proteins, Vol. 47, No. 4. (1 June 2002), pp. 409-443.
    by I Halperin, B Ma, H Wolfson, R Nussinov
    posted to docking-algorithm docking-scoring-function ppi-review by bicko on 2005-10-14 12:33:54 as **** along with 20 people and 3 groups timg dgruiz cantupaz apaydin chad_davis yongzhao ttjoseph nickolay ima sangeetha dgront blackbart gane5h mmuecke kazemi bpagano massivemayhem cjeans Evangelia nigham Bioinformatics TSRI_MGL insilicodrug
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