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Author Nussinov [115 articles]

Recent papers posted to CiteULike by the author Nussinov.
  • Prism: Protein–Protein Interaction Prediction by Structural Matching
    Functional Proteomics (2008), pp. 505-521.
    by Ozlem Keskin, Ruth Nussinov, Attila Gursoy
    posted to no-tag by aprildh31 to the group Proteasome on 2008-07-24 23:22:27 as **
  • Allostery: Absence of a Change in Shape Does Not Imply that Allostery Is Not at Play.
    J Mol Biol (29 February 2008)
    by Chung-Jung J Tsai, Antonio Del Sol, Ruth Nussinov
    posted to review protein_dynamics energy_entropy allostery 2008 by cchang to the group group on 2008-07-23 20:21:25 as ** along with 6 people and 2 groups higueruelo barry choonpeng cactus sobolevnrm CameronNeylon McCammon structural_bioinformatics
  • Conservation of polar residues as hot spots at protein interfaces
    Proteins: Structure, Function, and Genetics, Vol. 39, No. 4. (2000), pp. 331-342.
    by Zengjian Hu, Buyong Ma, Haim Wolfson, Ruth Nussinov
    posted to values hotspot aastatistic by timg on 2008-07-17 13:29:46 as read
  • Efficient Unbound Docking of Rigid Molecules
    Algorithms in Bioinformatics (2002), pp. 185-200.
    by Dina Duhovny, Ruth Nussinov, Haim Wolfson
    posted to ghashing docking 2point by timg on 2008-07-15 17:24:10 as read
  • FireDock: Fast interaction refinement in molecular docking.
    Proteins (27 June 2007)
    by Nelly Andrusier, Ruth Nussinov, Haim J J Wolfson
    posted to vdw electrostatic docking by timg on 2008-07-15 17:20:20 as read along with 1 person bicko
  • Explicit and implicit water simulations of a &bgr;-hairpin peptide
    Proteins: Structure, Function, and Genetics, Vol. 37, No. 1. (1999), pp. 73-87.
    by Buyong Ma, Ruth Nussinov
    posted to ma1999 by msuarezdiez on 2008-07-15 17:01:45 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
  • MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions.
    Nucleic acids research (8 May 2008)
    by Alexandra Shulman-Peleg, Maxim Shatsky, Ruth Nussinov, Haim J J Wolfson
    posted to no-tag by reyez on 2008-07-07 09:40:07 as ** along with 2 people higueruelo massivemayhem
  • Analysis of ordered and disordered protein complexes reveals structural features discriminating between stable and unstable monomers.
    J Mol Biol, Vol. 341, No. 5. (27 August 2004), pp. 1327-1341.
    by K Gunasekaran, CJ Tsai, R Nussinov
    posted to interactions disordered-regions by marti on 2008-07-04 16:17:45 as ** along with 2 people allmensch chad_davis
  • 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 thesis docking by nigham on 2008-06-27 06:22:59 as ** along with 19 people and 3 groups dgruiz cantupaz apaydin bicko chad_davis yongzhao ttjoseph nickolay ima sangeetha dgront blackbart gane5h mmuecke kazemi bpagano massivemayhem cjeans Evangelia Bioinformatics TSRI_MGL insilicodrug
  • Flexible docking allowing induced fit in proteins: insights from an open to closed conformational isomers.
    Proteins, Vol. 32, No. 2. (1 August 1998), pp. 159-174.
    by B Sandak, HJ Wolfson, R Nussinov
    posted to structure docking by carlk on 2008-06-26 18:20:39 as ** along with 1 person blackbart
  • The ARTS web server for aligning RNA tertiary structures.
    Nucleic Acids Research, Vol. 34, No. Web Server issue. (1 July 2006)
    by O Dror, R Nussinov, HJ Wolfson
    posted to no-tag by reyez on 2008-06-26 15:58:25 as ** along with 1 person emidio_capriotti
  • 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 protein-protein by npt11tpn on 2008-06-16 08:03:25 as ** along with 3 people bicko chad_davis nickolay
  • 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 ***
  • Prediction of Interacting Single-Stranded RNA Bases by Protein-Binding Patterns
    Journal of Molecular Biology, Vol. 379, No. 2. (29 May 2008), pp. 299-316.
    by Alexandra Shulman-Peleg, Maxim Shatsky, Ruth Nussinov, Haim J Wolfson
    posted to rna protein molecular_biology by psique on 2008-06-10 22:52:27 as **** along with 1 person marck
  • 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 structure proj_assembly modelling download docking complexes binding algorithm by chad_davis on 2008-05-28 10:23:55 as ** along with 1 person bicko
  • Principles of Protein-Protein Interactions: What are the Preferred Ways For Proteins To Interact?
    Chem. Rev. (21 March 2008)
    by O Keskin, A Gursoy, B Ma, R Nussinov
    posted to no-tag by GermanErlenkamp on 2008-05-27 13:11:02 as ** along with 4 people and 1 group higueruelo allmensch winterschlaefer jmrivort Supramolecular
  • 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 structure interaction docking by paolomarcatili on 2008-05-23 17:23:18 as ** along with 10 people and 2 groups barry baaden bicko nickolay j3xucite bluvsh1 xz grahamc Evangelia ladab structural_bioinformatics Bioinformatics
  • Extended disordered proteins: targeting function with less scaffold
    Trends in Biochemical Sciences, Vol. 28, No. 2. (February 2003), pp. 81-85.
    by Kannan Gunasekaran, Chung-Jung Tsai, Sandeep Kumar, David Zanuy, Ruth Nussinov
    posted to usa by allmensch on 2008-05-07 16:23:54 as ** along with 1 person Evangelia
  • Principles of nanostructure design with protein building blocks.
    Proteins, Vol. 68, No. 1. (3 April 2007), pp. 1-12.
    by Chung-Jung J Tsai, Jie Zheng, David Zanuy, Nurit Haspel, Haim Wolfson, Carlos Alemán, Ruth Nussinov
    posted to review origami-alternatives origami by dna on 2008-05-06 21:24:17 as ** along with 1 person choonpeng
  • Constructing templates for protein structure prediction by simulation of protein folding pathways
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by Ilona Kifer, Ruth Nussinov, Haim J Wolfson
    posted to structure simulation protein prediction modelling folding by neils on 2008-04-25 01:52:40 as **
  • A computer vision based technique for 3-D sequence-independent structural comparison of proteins.
    Protein engineering, Vol. 6, No. 3. (April 1993), pp. 279-288.
    by O Bachar, D Fischer, R Nussinov, H Wolfson
    posted to geometric_hashing protein_design by jwm on 2008-04-11 18:34:35 as **
  • 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 2007 hotspots interface ppi xf by higueruelo on 2008-03-26 10:36:04 as *** along with 3 people marti bicko IrinaMoreira
  • 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 correlated mutation by friendpine on 2008-03-23 14:16:12 as ** along with 6 people bicko gbart ramensky cjeans tale mingzhi
  • Three-dimensional, sequence order-independent structural comparison of a serine protease against the crystallographic database reveals active site similarities: potential implications to evolution and to protein folding.
    Protein Sci, Vol. 3, No. 5. (May 1994), pp. 769-778.
    by D Fischer, H Wolfson, SL Lin, R Nussinov
    posted to evo_502 structure-comparison by chrys on 2008-03-18 15:13:35 as ** along with 4 people and 2 groups barry aalibes shadowman tjimenez structural_bioinformatics Bioinformatics
  • 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 no-tag by jlh64 on 2008-03-13 20:40:14 as ** along with 4 people higueruelo bicko chad_davis 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 salt-bridge by choonpeng on 2008-03-10 13:16:59 as *** along with 2 people bicko onufriev
  • Conservation and persistence of spin currents and their relation to the Lieb-Schulz-Mattis twist operators
    arXiv:0803.0984 (7 Mar 2008)
    by N Bray-Ali, Z Nussinov
    posted to spin-hall spin-orbit spin_transport by misha on 2008-03-10 01:18:11 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 database interaction protein-protein by ladab on 2008-02-29 16:14:10 as *** along with 5 people baaden bicko chad_davis nickolay henschel
  • 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 interaction protein-protein by ladab on 2008-02-29 16:10:08 as *** along with 8 people and 2 groups mdimmic barry bicko lyongu nickolay choonpeng cjeans carlescorbi structural_bioinformatics Bioinformatics
  • Reducing the computational complexity of protein folding via fragment folding and assembly.
    Protein Sci, Vol. 12, No. 6. (June 2003), pp. 1177-1187.
    by N Haspel, CJ Tsai, H Wolfson, R Nussinov
    posted to no-tag by iantunbridge on 2008-02-29 11:23:43 as ** along with 2 people and 2 groups marcius biehl BioinfoCIPF SGU-CIPF
  • Interdomain Interactions in Hinge-Bending Transitions
    Structure, Vol. 9, No. 12. (December 2001), pp. 1165-1181.
    by Neeti Sinha, Sandeep Kumar, Ruth Nussinov
    posted to 2001 flexibility hinge xf by higueruelo on 2008-02-28 10:35:12 as ***
  • Interdomain Interactions in Hinge-Bending Transitions
    Structure, Vol. 10, No. 3. (March 2002), 441.
    by Neeti Sinha, Sandeep Kumar, Ruth Nussinov
    posted to 2002 flexibility hinge xf by higueruelo on 2008-02-28 10:34:21 as ***
  • HingeProt: Automated prediction of hinges in protein structures
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Ugur Emekli, Dina Schneidman-Duhovny, Haim J Wolfson, Ruth Nussinov, Turkan Haliloglu
    posted to hinges by willpitt on 2008-02-27 16:54:32 as ** along with 3 people and 1 group higueruelo barry sobolevnrm baker-group
  • 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 2007 interface ppi xf by higueruelo on 2008-02-25 12:59:14 as *** along with 3 people bicko choonpeng marti
  • Favorable scaffolds: proteins with different sequence, structure and function may associate in similar ways
    Protein Engineering, Design and Selection, Vol. 18, No. 1. (January 2005), pp. 11-24.
    by Ozlem Keskin, Ruth Nussinov
    posted to 2005 interface ppi xf by higueruelo on 2008-02-25 12:57:45 as *** along with 1 person conkymacro
  • Allosteric effects in the marginally stable von Hippel-Lindau tumor suppressor protein and allostery-based rescue mutant design
    Proceedings of the National Academy of Sciences, Vol. 105, No. 3. (22 January 2008), pp. 901-906.
    by Jin Liu, Ruth Nussinov
    posted to allostery molecular_dynamics by sobolevnrm to the group baker-group on 2008-02-21 12:30:30 as read along with 1 person cactus
  • 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 2005 hotspots interface review systemsbio by higueruelo on 2008-02-03 11:07:23 as read along with 2 people bicko choonpeng
  • 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 2007 druggable systemsbio by higueruelo on 2008-02-03 11:06:12 as ** along with 1 person bicko
  • Comprehensive analysis of co-occurring domain sets in yeast proteins
    BMC Genomics, Vol. 8 (11 June 2007), 161.
    by Inbar Cohen-Gihon, Ruth Nussinov, Roded Sharan
    posted to protein domain co-occurrence interaction yeast by neils on 2008-01-10 05:32:08 as **
  • Recognition of functional sites in protein structures.
    J Mol Biol, Vol. 339, No. 3. (4 June 2004), pp. 607-633.
    by A Shulman-Peleg, R Nussinov, HJ Wolfson
    posted to active site by ssgong on 2008-01-03 17:26:50 as ** along with 1 person tjimenez
  • How do thermophilic proteins deal with heat?
    Cellular and Molecular Life Sciences (CMLS), Vol. 58, No. 9. (2001), pp. 1216-1233.
    by S Kumar, R Nussinov
    posted to no-tag by saravan on 2007-12-25 03:00:37 as **
  • Multiple diverse ligands binding at a single protein site: A matter of pre-existing populations
    Protein Sci, Vol. 11, No. 2. (1 February 2002), pp. 184-197.
    by Buyong Ma, Maxim Shatsky, Haim J Wolfson, Ruth Nussinov
    posted to no-tag by jlh64 on 2007-12-12 23:42:01 as ** along with 2 people and 1 group yongzhao ruvido TSRI_MGL
  • Discovery of Protein Substructures in EM Maps
    Algorithms in Bioinformatics (2005), pp. 423-434.
    by Keren Lasker, Oranit Dror, Ruth Nussinov, Haim Wolfson
    posted to dynamic_molecular_shape by tmmurali on 2007-12-02 20:57:26 as **
  • Flexible docking allowing induced fit in proteins: Insights from an open to closed conformational isomers
    Proteins: Structure, Function, and Genetics, Vol. 32, No. 2. (1998), pp. 159-174.
    by Bilha Sandak, Haim J Wolfson, Ruth Nussinov
    posted to conformers docking flexibility by LamBras on 2007-11-23 12:40:10 as ** along with 1 person kazemi
  • Fast Algorithm for Predicting the Secondary Structure of Single-Stranded RNA
    PNAS, Vol. 77, No. 11. (1 November 1980), pp. 6309-6313.
    by Ruth Nussinov, Ann B Jacobson
    posted to review by Hosna on 2007-11-05 20:30:04 as ** along with 2 people and 1 group arcticrasta condon beta
  • A method for simultaneous alignment of multiple protein structures.
    Proteins, Vol. 56, No. 1. (1 July 2004), pp. 143-156.
    by M Shatsky, R Nussinov, HJ Wolfson
    posted to project1 protein structures by carlescorbi on 2007-10-21 17:48:14 as **** along with 3 people nachtalp analogAI j3xucite
  • 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
  • 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 bioinformatics conservation docking interaction protein-protein structure by Evangelia on 2007-10-01 13:40:35 as ** along with 2 people and 2 groups barry bicko structural_bioinformatics Bioinformatics
  • Stability of Tubular Structures Based on β-Helical Proteins: Self-Assembled versus Polymerized Nanoconstructs and Wild-Type versus Mutated Sequences
    Biomacromolecules (14 September 2007)
    by D Zanuy, F Rodriguez-Ropero, N Haspel, J Zheng, R Nussinov, C Aleman
    posted to computational-studies peptide sa-in-nature self-assembly supramolecular by jmrivort to the group Supramolecular on 2007-09-23 17:45:44 as ****
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