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Tag loop [101 articles]

Recent papers classified by the tag loop.
  • A kinematic view of loop closure.
    J Comput Chem, Vol. 25, No. 4. (March 2004), pp. 510-528.
    by EA Coutsias, C Seok, MP Jacobson, KA Dill
    posted to loop by yongzhao on 2006-02-19 07:18:22 as ** along with 1 person and 1 group nigham TSRI_MGL
  • Predicting antibody hypervariable loop conformations. II: Minimization and molecular dynamics studies of MCPC603 from many randomly generated loop conformations.
    Proteins, Vol. 1, No. 4. (December 1986), pp. 342-362.
    by RM Fine, H Wang, PS Shenkin, DL Yarmush, C Levinthal
    posted to loop by yongzhao on 2006-04-03 23:31:47 as *** along with 1 group TSRI_MGL
  • A hierarchical approach to all-atom protein loop prediction.
    Proteins, Vol. 55, No. 2. (1 May 2004), pp. 351-367.
    by MP Jacobson, DL Pincus, CS Rapp, TJ Day, B Honig, DE Shaw, RA Friesner
    posted to loop by yongzhao on 2006-02-19 07:14:04 as ** along with 3 people and 1 group vavi sschurer allmensch TSRI_MGL
  • Modeling protein conformational ensembles: From missing loops to equilibrium fluctuations
    Proteins: Structure, Function, and Bioinformatics, Vol. 65, No. 1. (2006), pp. 164-179.
    by Amarda Shehu, Cecilia Clementi, Lydia E Kavraki
    posted to loop by yongzhao on 2006-08-25 23:23:58 as ** along with 6 people and 2 groups apaydin nigham aqeel elham hmk sobolevnrm TSRI_MGL baker-group
  • Predicting antibody hypervariable loop conformation. I. Ensembles of random conformations for ringlike structures.
    Biopolymers, Vol. 26, No. 12. (December 1987), pp. 2053-2085.
    by PS Shenkin, DL Yarmush, RM Fine, HJ Wang, C Levinthal
    posted to loop by yongzhao on 2006-04-03 23:27:55 as ** along with 1 group TSRI_MGL
  • Evaluating conformational free energies: the colony energy and its application to the problem of loop prediction.
    Proc Natl Acad Sci U S A, Vol. 99, No. 11. (28 May 2002), pp. 7432-7437.
    by Z Xiang, CS Soto, B Honig
    posted to colony_energy loop by yongzhao on 2006-04-03 23:24:09 as ** along with 1 person and 1 group vavi TSRI_MGL
  • 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 potential_app loop by yongzhao on 2006-11-21 19:00:57 as *** along with 8 people and 1 group BragilMassoud dgruiz radestock lna choonpeng weisblum higueruelo nickolay TSRI_MGL
  • Cyclic coordinate descent: A robotics algorithm for protein loop closure.
    Protein Sci, Vol. 12, No. 5. (May 2003), pp. 963-972.
    by AA Canutescu, RL Dunbrack
    posted to loop by yongzhao on 2006-02-19 07:17:09 as ** along with 4 people and 1 group vavi j3xucite dgront mijam TSRI_MGL
  • Prediction of loop geometries using a generalized born model of solvation effects.
    Proteins, Vol. 35, No. 2. (1 May 1999), pp. 173-183.
    by CS Rapp, RA Friesner
    posted to loop by yongzhao on 2006-04-03 23:26:05 as **** along with 1 group TSRI_MGL
  • Modeling structurally variable regions in homologous proteins with rosetta.
    Proteins, Vol. 55, No. 3. (15 May 2004), pp. 656-677.
    by CA Rohl, CE Strauss, D Chivian, D Baker
    posted to loop by yongzhao on 2006-02-19 07:15:20 as ** along with 5 people and 1 group jwm vavi thamelry Alan hmk TSRI_MGL
  • Working memory and language: an overview
    Journal of Communication Disorders, Vol. 36, No. 3. ( 2003), pp. 189-208.
    by Alan Baddeley
    posted to language loop memory phonological working by wenhsin on 2005-10-29 07:50:09 as ** along with 3 people and 4 groups garyfeng aufrank njincho ReadingLab ur-cls Neuroscience LanguageAndBrain
  • Conformation of [beta]-hairpins in protein structures : A systematic classification with applications to modelling by homology, electron density fitting and protein engineering
    Journal of Molecular Biology, Vol. 206, No. 4. (20 April 1989), pp. 759-777.
    by Bancinyane Sibanda, Tom L Blundell, Janet M Thornton
    posted to loop structure by warlock6x3 on 2005-06-25 18:57:26 as ***
  • Prediction of the conformation and geometry of loops in globular proteins: Testing ArchDB, a structural classification of loops
    Proteins: Structure, Function, and Genetics (14 July 2005)
    by Narcis Fernandez-Fuentes, Enrique Querol, Francesc X Aviles, Michael JE Sternberg, Baldomero Oliva
    posted to loop prediction by vavi on 2005-07-25 09:33:18 as read along with 2 people baldo Alan
  • Improved protein loop prediction from sequence alone.
    Protein Eng, Vol. 14, No. 7. (July 2001), pp. 473-478.
    by DF Burke, CM Deane
    posted to loop prediction sequence by vavi on 2005-07-25 17:11:54 as ** along with 3 people Alan j3xucite cdeane
  • Modeling of loops in protein structures.
    Protein Sci, Vol. 9, No. 9. (September 2000), pp. 1753-1773.
    by A Fiser, RK Do, A Sali
    posted to loop modeling prediction by vavi on 2005-07-25 09:47:12 as ** along with 4 people warlock6x3 ttjoseph mirzazadeh tji
  • Protein loop structure prediction with flexible stem geometries.
    Proteins (12 October 2005)
    by M Mönnigmann, C A A Floudas
    posted to loop protein structure_prediction by vavi on 2005-10-20 13:19:50 as *** along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
  • PDB-based protein loop prediction: parameters for selection and methods for optimization
    Journal of Molecular Biology, Vol. 267, No. 4. (11 April 1997), pp. 975-1001.
    by Herman W van Vlijmen, Martin Karplus
    posted to fragments library loop prediction by vavi on 2005-10-06 10:22:31 as ****
  • ArchDB: automated protein loop classification as a tool for structural genomics.
    Nucleic Acids Res, Vol. 32, No. Database issue. (1 January 2004)
    by J Espadaler, N Fernandez-Fuentes, A Hermoso, E Querol, FX Aviles, MJ Sternberg, B Oliva
    posted to classification loop protein by vavi on 2006-08-06 09:06:23 as ** along with 1 person baldo
  • Loops In Proteins (LIP)--a comprehensive loop database for homology modelling.
    Protein Eng, Vol. 16, No. 12. (December 2003), pp. 979-985.
    by E Michalsky, A Goede, R Preissner
    posted to fragments library loop prediction by vavi on 2005-07-25 09:43:05 as read
  • Sector Decomposition
    (16 May 2008)
    by Gudrun Heinrich
    posted to loop by terning on 2008-09-04 23:11:30 as **
  • An architectural approach to autonomic computing
    Autonomic Computing, 2004. Proceedings. International Conference on (2004), pp. 2-9.
    by SR White, JE Hanson, I Whalley, DM Chess, JO Kephart
    posted to autonomic ibm loop by slatre on 2007-11-29 10:29:03 as ***** along with 13 people and 4 groups broussea fzou ddahlem marcia pverstra franco dabhishe mzygmunt greatgator cybrpunk ingstrup japarejo thiagomanel Rigi P2P-SeC macc dopsy
  • Cohesin Smc1 determines meiotic chromatin axis loop organization.
    J Cell Biol (7 January 2008)
    by Ivana Novak, Hong Wang, Ekaterina Revenkova, Rolf Jessberger, Harry Scherthan, Christer Höög
    posted to chromatin cohesin loop meiosis smc1 by sebastien_vigneau on 2008-01-14 09:16:43 as read
  • Knots, operads and double loop spaces
    (21 Aug 2006)
    by Paolo Salvatore
    posted to knots loop operads by scis0000001 on 2006-09-13 14:23:34 as **
  • Self-duality, Helicity and Higher-loop Euler-Heisenberg Effective Actions
    (11 Dec 2003)
    by Gerald V Dunne, Christian Schubert
    posted to duality helicity loop self-duality by scis0000001 on 2006-09-19 16:58:59 as **
  • Saturating representation of loop conformational fragments in structure databanks
    BMC Structural Biology, Vol. 6 (04 July 2006), 15.
    by Narcis Fernandez-Fuentes, Andras Fiser
    posted to angstrom cut-off fragments loop rmsd by saunders on 2008-07-14 14:01:37 as read along with 3 people iakes vavi cdeane
  • Full cyclic coordinate descent: solving the protein loop closure problem in Calpha space.
    BMC Bioinformatics, Vol. 6 (28 June 2005)
    by W Boomsma, T Hamelryck
    posted to loop modelling protein structure by pansapiens on 2006-09-22 06:17:22 as ** along with 3 people vavi wouterboomsma Alan
  • Structure of the Human Protein Kinase MPSK1 Reveals an Atypical Activation Loop Architecture.
    Structure, Vol. 16, No. 1. (January 2008), pp. 115-124.
    by J Eswaran, A Bernad, JM Ligos, B Guinea, JE Debreczeni, F Sobott, SA Parker, R Najmanovich, BE Turk, S Knapp
    posted to activation activity kinase loop mpsk1 specificity structure by neils on 2008-01-12 01:37:14 as **
  • Characterization of dermatoglyphics in PHOX2B-confirmed congenital central hypoventilation syndrome.
    Pediatrics, Vol. 118, No. 2. (August 2006)
    by ES Todd, NM Scott, DE Weese-Mayer, SM Weinberg, EM Berry-Kravis, JM Silvestri, AS Kenny, SA Hauptman, L Zhou, ML Marazita
    posted to arch dermatoglyphics disease loop ulnar by naturecure on 2006-08-22 18:09:19 as ** along with 2 groups Boydian_Society Nutritional_Polymorphisms
  • Dermatoglyphic patterns in schizophrenic patients.
    Acta Psychiatr Scand, Vol. 91, No. 3. (March 1995), pp. 213-215.
    by SL Varma, TV Chary, S Singh, MZ Azhar, AS Dharap
    posted to dermatoglyphics fingerprints loop by naturecure on 2006-07-07 19:24:28 as ** along with 2 groups Boydian_Society Nutritional_Polymorphisms
  • Analysis, clustering and prediction of the conformation of short and medium size loops connecting regular secondary structures.
    Pac Symp Biocomput (1996), pp. 570-589.
    by SD Rufino, LE Donate, L Canard, TL Blundell
    posted to loop protein protein_modelling tlb by medic0747 on 2007-02-21 11:20:20 as ** along with 2 people vavi Alan
  • Conformational analysis and clustering of short and medium size loops connecting regular secondary structures: a database for modeling and prediction.
    Protein Sci, Vol. 5, No. 12. (December 1996), pp. 2600-2616.
    by LE Donate, SD Rufino, LH Canard, TL Blundell
    posted to loop protein protein_modelling tlb by medic0747 on 2007-02-21 11:17:29 as ** along with 1 person Alan
  • Predicting the conformational class of short and medium size loops connecting regular secondary structures: application to comparative modelling.
    J Mol Biol, Vol. 267, No. 2. (28 March 1997), pp. 352-367.
    by SD Rufino, LE Donate, LH Canard, TL Blundell
    posted to loop tlb by medic0747 on 2007-02-21 11:22:59 as ** along with 1 person Alan
  • Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all-atom statistical potential and the AMBER force field with the Generalized Born solvation model.
    Proteins, Vol. 51, No. 1. (1 April 2003), pp. 21-40.
    by PI de Bakker, MA DePristo, DF Burke, TL Blundell
    posted to all-stom_statistical_potential loop tlb by medic0747 on 2007-02-21 12:16:38 as **
  • Browsing the SLoop database of structurally classified loops connecting elements of protein secondary structure.
    Bioinformatics, Vol. 16, No. 6. (June 2000), pp. 513-519.
    by DF Burke, CM Deane, TL Blundell
    posted to loop tlb by medic0747 on 2007-02-21 12:03:35 as ** along with 2 people Alan cdeane
  • Loop analysis of causal feedback in epidemiology: An illustration relating to urban neighborhoods and resident depressive experiences
    Social Science & Medicine, Vol. 65, No. 10. (November 2007), pp. 2043-2057.
    by Alexis Dinno
    posted to complexity epidemiology feedback loop urban by mdebbink on 2007-10-23 05:55:12 as **
  • Summing up the noise in gene networks.
    Nature, Vol. 427, No. 6973. (29 January 2004), pp. 415-418.
    by J Paulsson
    posted to feedback gene loop negative networks by marcio on 2008-07-05 03:00:50 as ** along with 7 people bayesian balabu jiyu mhucka timflutre margaritis dylanwalker
  • Comparison of classical and autogenous systems of regulation in inducible operons
    Nature, Vol. 252, No. 5484. (13 December 1974), pp. 546-549.
    by Michael A Savageau
    posted to feedback gene loop negative networks noise by marcio on 2008-07-05 02:56:58 as ** along with 1 person jjray
  • microRNA miR-14 acts to modulate a positive autoregulatory loop controlling steroid hormone signaling in Drosophila
    Genes Dev., Vol. 21, No. 18. (15 September 2007), pp. 2277-2282.
    by Jishy Varghese, Stephen M Cohen
    posted to autoregulation drosophila loop microrna mir-14 by maralena on 2008-05-14 16:52:38 as **
  • Coherent Coupling of Feedback Loops: A Design Principle of Cell Signaling Networks.
    Bioinformatics (Oxford, England) (2 July 2008)
    by Yung-Keun K Kwon, Kwang-Hyun H Cho
    posted to feedback loop network principle signaling by maralena on 2008-07-09 08:04:36 as ** along with 4 people bootsy jjray lemke reyez
  • Transcriptional feedback control of insulin receptor by dFOXO/FOXO1.
    Genes Dev, Vol. 19, No. 20. (15 October 2005), pp. 2435-2446.
    by O Puig, R Tjian
    posted to feedback foxo inr loop negative by johncumbers on 2006-08-23 19:52:54 as read
  • Noise in transcription negative feedback loops: simulation and experimental analysis
    Mol Syst Biol, Vol. 2 (2006)
    by Yann Dublanche, Konstantinos Michalodimitrakis, Nico Kummerer, Mathilde Foglierini, Luis Serrano
    posted to feedback loop loops negative by johncumbers on 2006-08-21 02:46:51 as ***** along with 4 people aalibes balabu cjeans marcio
  • Control of cell number by Drosophila FOXO: downstream and feedback regulation of the insulin receptor pathway.
    Genes Dev, Vol. 17, No. 16. (15 August 2003), pp. 2006-2020.
    by O Puig, MT Marr, ML Ruhf, R Tjian
    posted to feedback foxo loop negative oscar by johncumbers on 2006-08-23 19:53:38 as read
  • Structure and function of the feed-forward loop network motif.
    Proc Natl Acad Sci U S A, Vol. 100, No. 21. (14 October 2003), pp. 11980-11985.
    by S Mangan, U Alon
    posted to feedback loop motif network by hannahrajasingh on 2008-07-11 09:33:35 as *** along with 12 people and 3 groups camster rklancer korakot zqshen jstajic jjray alexg balicea ddahlem jtaylor gcalda marck Philosophy_of_Information dbk-lab Blog_and_Wiki_Research
  • Network motifs in the transcriptional regulation network of Escherichia coli
    Nat Genet, Vol. 31, No. 1. (May 2002), pp. 64-68.
    by Shai S Shen-Orr, Ron Milo, Shmoolik Mangan, Uri Alon
    posted to feeback loop motif network by hannahrajasingh on 2008-07-11 09:30:28 as *** along with 13 people and 1 group jstajic jjray ssb nickluscombe gurkanbebek jtaylor jayster4 karfunkel blobbybirdman zibuyu maralena Borelli ethkim EBI-regulation
  • The anatomy of a loop: a story of scope and control
    (2005), pp. 2-14.
    by Olin Shivers
    posted to functionalprogramming lisp loop loopmacro macros scheme by hamish on 2006-05-14 19:33:19 as ***** along with 5 people JeffreyPalmer voigt pintman robennals ryanc
  • An Iterative Loop Matching Approach to the Prediction of RNA Secondary Structures with Pseudoknots
    (2003)
    by Jianhua Ruan, Gary D Stormo, Weixiong Zhang
    posted to iterative loop matching prediction rna by guxiyou on 2008-03-26 20:53:29 as **
  • Closed loops of nearly standard size: common basic element of protein structure.
    FEBS Lett, Vol. 466, No. 2-3. (28 January 2000), pp. 283-286.
    by IN Berezovsky, AY Grosberg, EN Trifonov
    posted to indels loop protein_structure by ana to the group Bioinformatics on 2006-08-15 20:13:47 as ***** along with 1 group structural_bioinformatics
  • Long loops in proteins.
    Protein Eng, Vol. 8, No. 11. (November 1995), pp. 1093-1101.
    by AC Martin, K Toda, HJ Stirk, JM Thornton
    posted to indels loop by ana to the group Bioinformatics on 2006-08-15 20:17:35 as ***** along with 1 person and 1 group cdallett structural_bioinformatics
  • Open FRW model in Loop Quantum Cosmology
    (12 Jul 2007)
    by Lukasz Szulc
    posted to quantum loop cosmology by A_Olympia to the group Blog_and_Wiki_Research on 2007-07-13 13:37:19 as ** along with 1 person and 1 group proportional Philosophy_of_Information
  • Loop modeling: sampling, filtering, and scoring.
    Proteins (29 August 2007)
    by Cinque S S Soto, Marc Fasnacht, Jiang Zhu, Lucy Forrest, Barry Honig
    posted to loop model by cdeane to the group OPIG on 2007-11-23 16:37:56 as **
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