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apaydins protein [71 articles]

Neue Publikationen in apaydins Bibliothek eingetragen unter dem Bezeichner: protein. You can also see everyone's protein.
  • Sampling protein conformations and pathways
    Journal of Computational Chemistry, Vol. 25, No. 9. (5 April 2004), pp. 1133-1148.
    by Ming Lei, Maria I Zavodszky, Leslie A Kuhn, MF Thorpe
    posted to flexibiliy protein rigidity by apaydin on 2008-07-16 21:31:42 as read along with 6 people aqeel blackbart smenor ruvido nh higueruelo
  • Application of the random coil index to studying protein flexibility.
    Journal of biomolecular NMR, Vol. 40, No. 1. (January 2008), pp. 31-48.
    by MV Berjanskii, DS Wishart
    posted to chemical flexibility protein shifts by apaydin on 2008-07-05 21:54:48 as **
  • The RCI server: rapid and accurate calculation of protein flexibility using chemical shifts.
    Nucleic acids research, Vol. 35, No. Web Server issue. (July 2007)
    by MV Berjanskii, DS Wishart
    posted to chemical flexibility protein shifts webserver by apaydin on 2008-07-05 21:52:02 as **
  • NMR: prediction of protein flexibility.
    Nature protocols, Vol. 1, No. 2. (2006), pp. 683-688.
    by M Berjanskii, DS Wishart
    posted to flexibility nmr protein by apaydin on 2008-07-05 21:44:11 as **
  • From the Cover: Consistent blind protein structure generation from NMR chemical shift data
    Proceedings of the National Academy of Sciences, Vol. 105, No. 12. (25 March 2008), pp. 4685-4690.
    by Yang Shen, Oliver Lange, Frank Delaglio, Paolo Rossi, James M Aramini, Gaohua Liu, Alexander Eletsky, Yibing Wu, Kiran K Singarapu, Alexander Lemak, Alexandr Ignatchenko, Cheryl H Arrowsmith, Thomas Szyperski, Gaetano T Montelione, David Baker, Ad Bax
    posted to chemical nmr prediction protein shifts structure by apaydin on 2008-07-05 20:30:20 as read along with 5 people and 1 group dgront zwang biehl sunhwan skoddet Nielsen group
  • A generative, probabilistic model of local protein structure
    Proceedings of the National Academy of Sciences, Vol. 105, No. 26. (1 July 2008), pp. 8932-8937.
    by Wouter Boomsma, Kanti V Mardia, Charles C Taylor, Jesper Ferkinghoff-Borg, Anders Krogh, Thomas Hamelryck
    posted to prediction protein structure by apaydin on 2008-07-02 17:55:01 as ** along with 5 people j3xucite bertelsen biehl zwang mijam
  • Protein folding: Independent unrelated pathways or predetermined pathway with optional errors
    Proceedings of the National Academy of Sciences, Vol. 105, No. 20. (20 May 2008), pp. 7182-7187.
    by Sabrina Bedard, Mallela M Krishna, Leland Mayne, Walter S Englander
    posted to folding pathways protein by apaydin on 2008-05-21 21:49:48 as ** along with 1 person cactus
  • Prediction of aggregation-prone regions in structured proteins
    Journal of Molecular Biology, Vol. In Press, Accepted Manuscript
    by Gian G Tartaglia, Amol P Pawar, Silvia Campioni, Christopher M Dobson, Fabrizio Chiti, Michele Vendruscolo
    posted to aggregation prediction protein structure by apaydin on 2008-05-14 15:18:38 as **
  • Protein conformational transitions explored by mixed elastic network models.
    Proteins (27 June 2007)
    by Wenjun Zheng, Bernard R R Brooks, Gerhard Hummer
    posted to conformational elastic folding model network protein transition by apaydin on 2008-04-17 13:45:43 as ** along with 2 people aqeel choonpeng
  • Coarse Master Equations for Peptide Folding Dynamics
    J. Phys. Chem. B (31 January 2008)
    by NV Buchete, G Hummer
    posted to dynamics equation folding master molecular protein by apaydin on 2008-04-17 13:16:30 as ** along with 2 people and 1 group ruvido sobolevnrm baker-group
  • High-resolution structure prediction and the crystallographic phase problem
    Nature (14 October 2007)
    by Bin Qian, Srivatsan Raman, Rhiju Das, Philip Bradley, Airlie J Mccoy, Randy J Read, David Baker
    posted to molecular prediction protein replacement structure by apaydin on 2008-02-18 00:04:34 as ** along with 14 people and 2 groups aheilbut jwm eckart_bindewald ffranca dgront massivemayhem cjeans zwang cactus sobolevnrm boris_aguilar Ema chenway ardalby baker-group OPIG
  • Backbone solution structures of proteins using residual dipolar couplings: application to a novel structural genomics target
    Journal of Structural and Functional Genomics, Vol. 5, No. 4. (25 January 2005), pp. 241-254.
    by H Valafar, KL Mayer, CM Bougault, PD Leblond, FE Jenney, PS Brereton, MWW Adams, JH Prestegard
    posted to determination fragment structure based protein rdc backbone by apaydin on 2007-10-30 18:31:59 as **
  • Use of residual dipolar couplings as restraints in ab initio protein structure prediction.
    Biopolymers, Vol. 70, No. 4. (December 2003), pp. 548-562.
    by T Haliloglu, A Kolinski, J Skolnick
    posted to lattice model prediction protein rdc structure by apaydin on 2007-10-30 18:08:24 as ** along with 1 person j3xucite
  • De novo determination of protein backbone structure from residual dipolar couplings using Rosetta.
    J Am Chem Soc, Vol. 124, No. 11. (20 March 2002), pp. 2723-2729.
    by CA Rohl, D Baker
    posted to denovo determination protein rdc rosetta structure by apaydin on 2007-10-30 18:02:03 as ** along with 1 person j3xucite
  • Determination of protein backbone structures from residual dipolar couplings.
    Methods Enzymol, Vol. 394 (2005), pp. 175-209.
    by JH Prestegard, KL Mayer, H Valafar, GC Benison
    posted to backbone determination protein rdc structure by apaydin on 2007-10-30 17:56:17 as **
  • Automated NMR structure calculation with CYANA.
    Methods Mol Biol, Vol. 278 (2004), pp. 353-378.
    by P Güntert
    posted to cyana determination nmr noe protein protein_structure_determination structure by apaydin on 2007-09-17 16:14:40 as **
  • Automated analysis of NMR assignments and structures for proteins
    Current Opinion in Structural Biology, Vol. 9, No. 5. (1 October 1999), pp. 635-642.
    by Hunter NB Moseley, Gaetano T Montelione
    posted to determination protein review structure by apaydin on 2007-09-07 16:31:57 as **
  • Protein Structural Change Upon Ligand Binding: Linear Response Theory
    Physical Review Letters, Vol. 94, No. 7. (2005)
    by Mitsunori Ikeguchi, Jiro Ueno, Miwa Sato, Akinori Kidera
    posted to binding dynamics ligand protein by apaydin on 2007-08-27 17:08:20 as ** along with 2 people boris_aguilar aqeel
  • Large Amplitude Conformational Change in Proteins Explored with a Plastic Network Model: Adenylate Kinase
    Journal of Molecular Biology, Vol. 352, No. 4. (30 September 2005), pp. 807-822.
    by Paul Maragakis, Martin Karplus
    posted to dynamics enm normal_mode_analysis protein by apaydin on 2007-08-27 17:02:45 as ** along with 2 people aqeel choonpeng
  • A fast method to sample real protein conformational space
    Proteins: Structure, Function, and Genetics, Vol. 39, No. 2. (2000), pp. 112-131.
    by Howard J Feldman, Christopher WV Hogue
    posted to conformational foldtraj protein sampling space by apaydin on 2007-07-06 16:03:27 as ** along with 2 people j3xucite yxue
  • Dynamics and entropy of a calmodulin-peptide complex studied by NMR and molecular dynamics.
    Biochemistry, Vol. 42, No. 2. (21 January 2003), pp. 562-570.
    by NV Prabhu, AL Lee, AJ Wand, KA Sharp
    posted to dynamics molecular nmr order parameter protein by apaydin on 2007-06-20 22:30:17 as ** along with 1 person allmensch
  • Can Conformational Change Be Described by Only a Few Normal Modes?
    by Pande, Petrone
    posted to dynamics nma protein by apaydin on 2007-06-11 16:01:56 as **
  • Anisotropy of fluctuation dynamics of proteins with an elastic network model.
    Biophys J, Vol. 80, No. 1. (January 2001), pp. 505-515.
    by AR Atilgan, SR Durell, RL Jernigan, MC Demirel, O Keskin, I Bahar
    posted to anm dynamics nma protein by apaydin on 2007-06-10 21:32:52 as ** along with 5 people lna aqeel simone insectopalo choonpeng
  • Amplitudes of protein backbone dynamics and correlated motions in a small alpha/beta protein: correspondence of dipolar coupling and heteronuclear relaxation measurements.
    Biochemistry, Vol. 43, No. 33. (24 August 2004), pp. 10678-10691.
    by GM Clore, CD Schwieters
    posted to dynamics nmr protein rdc by apaydin on 2007-06-08 14:33:00 as **
  • How much backbone motion in ubiquitin is required to account for dipolar coupling data measured in multiple alignment media as assessed by independent cross-validation?
    J Am Chem Soc, Vol. 126, No. 9. (10 March 2004), pp. 2923-2938.
    by GM Clore, CD Schwieters
    posted to backbone dynamics motion protein rdc by apaydin on 2007-06-08 14:31:56 as read
  • A methodology for efficiently sampling the conformation space of molecular structures.
    Phys Biol, Vol. 2, No. 4. (November 2005)
    by A Lee, I Streinu, O Brock
    posted to closure loop protein robotics structure by apaydin on 2007-06-05 14:53:14 as ** along with 1 person aqeel
  • NMR studies of protein structure and dynamics
    Journal of Magnetic Resonance, Vol. 173, No. 2. (April 2005), pp. 193-207.
    by Lewis E Kay
    posted to dynamics nmr protein review structure by apaydin on 2007-06-05 14:40:28 as ****
  • Comparing atomistic simulation data with the NMR experiment: How much can NOEs actually tell us?
    Proteins: Structure, Function, and Bioinformatics, Vol. 63, No. 1. (2006), pp. 210-218.
    by Bojan Zagrovic, Wilfred F van Gunsteren
    posted to folding nmr noe protein unfolded by apaydin on 2007-06-04 18:50:33 as * along with 1 person allmensch
  • Direct use of unassigned resonances in NMR structure calculations with proxy residues.
    J Am Chem Soc, Vol. 128, No. 23. (14 June 2006), pp. 7566-7571.
    by E AB, DJ Pugh, R Kaptein, R Boelens, AM Bonvin
    posted to calculation nmr prediction protein structure by apaydin on 2007-06-02 16:38:50 as **
  • Dynamics of ribonuclease H: temperature dependence of motions on multiple time scales.
    Biochemistry, Vol. 35, No. 50. (17 December 1996), pp. 16009-16023.
    by AM Mandel, M Akke, AG Palmer
    posted to dynamics nmr protein by apaydin on 2007-05-09 00:37:23 as *
  • Atomic-level characterization of disordered protein ensembles
    Current Opinion in Structural Biology, Vol. 17, No. 1. (February 2007), pp. 3-14.
    by Tanja Mittag, Julie D Forman-Kay
    posted to denatured disordered ensembles protein by apaydin on 2007-03-27 16:13:38 as ** along with 4 people and 1 group xdeupi cactus biehl allmensch LabCompMed
  • A general method for the unbiased improvement of solution NMR structures by the use of related X-Ray data, the AUREMOL-ISIC algorithm
    BMC Structural Biology, Vol. 6 (26 June 2006), 14.
    by Konrad Brunner, Wolfram Gronwald, Jochen M Trenner, Klaus-Peter Neidig, Hans R Kalbitzer
    posted to determination nmr nvr protein structure by apaydin on 2007-03-27 16:00:29 as **
  • protein molecular fragment replacement
    by Ad Bax
    posted to fragment molecular protein replacement by apaydin on 2007-03-23 16:57:24 as **
  • Chemical Theory and Computation Special Feature: Protein folding pathways from replica exchange simulations and a kinetic network model
    PNAS, Vol. 102, No. 19. (10 May 2005), pp. 6801-6806.
    by Michael Andrec, Anthony K Felts, Emilio Gallicchio, Ronald M Levy
    posted to exchange folding kinetic model network protein replica simulations by apaydin on 2007-03-09 22:58:30 as ** along with 1 person allmensch
  • mastereqn-alanine-long-times.pdf (application/pdf Object)
    by Chodera, Dill
    posted to dynamics folding molecular protein srs by apaydin on 2007-03-08 19:01:57 as **
  • Side-chain and Backbone Flexibility in Protein Core Design
    pp. 305-318.
    by JR Desjarlais
    posted to backbone design flexibility protein sidechain by apaydin on 2007-03-06 23:22:26 as **
  • RefDB: A database of uniformly referenced protein chemical shifts
    Journal of Biomolecular NMR, Vol. V25, No. 3. (1 March 2003), pp. 173-195.
    by Haiyan Zhang, Stephen Neal, David S Wishart
    posted to assignment chemical database determination nmr protein shifts structure by apaydin on 2007-03-06 15:38:14 as **
  • Molecular Replacement
    by Rossman, Blow
    posted to xray structure protein mr determination by apaydin on 2007-01-29 17:32:48 as **
  • Constrained geometric simulation of diffusive motion in proteins.
    Phys Biol, Vol. 2, No. 4. (November 2005)
    by S Wells, S Menor, B Hespenheide, MF Thorpe
    posted to rigidity protein froda flexibility by apaydin on 2007-01-25 23:15:53 as ** along with 3 people lna aqeel smenor
  • Folding rates and low-entropy-loss routes of two-state proteins.
    J Mol Biol, Vol. 329, No. 3. (6 June 2003), pp. 585-598.
    by TR Weikl, KA Dill
    posted to srs rate protein prediction folding entropy by apaydin on 2007-01-19 21:39:58 as ****
  • Single-step determination of protein substructures using dipolar couplings: aid to structural genomics.
    J Am Chem Soc, Vol. 123, No. 38. (26 September 2001), pp. 9490-9491.
    by M Zweckstetter, A Bax
    posted to structure rdc protein nmr dipolar determination couplings by apaydin on 2007-01-19 16:32:09 as **
  • PACES: Protein sequential assignment by computer-assisted exhaustive search
    Journal of Biomolecular NMR, Vol. V26, No. 2. (1 June 2003), pp. 93-111.
    by Brian E Coggins, Pei Zhou
    posted to sequential protein nmr assignment by apaydin on 2007-01-19 16:00:01 as **
  • The magnitude of the backbone conformational entropy change in protein folding.
    Proteins, Vol. 25, No. 2. (June 1996), pp. 143-156.
    by JA D'Aquino, J Gómez, VJ Hilser, KH Lee, LM Amzel, E Freire
    posted to protein folding entropy conformational backbone by apaydin on 2007-01-17 22:29:56 as **** along with 1 person rsantana
  • Local conformational fluctuations can modulate the coupling between proton binding and global structural transitions in proteins.
    Proc Natl Acad Sci U S A, Vol. 102, No. 12. (22 March 2005), pp. 4282-4287.
    by ST Whitten, B García-Moreno E, VJ Hilser
    posted to srs protein folding corex by apaydin on 2007-01-12 23:00:30 as ** along with 1 person lna
  • protein flexibility analysis
    by David Hsu, Nigham
    posted to protein flexibility analysis by apaydin on 2007-01-11 22:55:26 as **
  • A statistical thermodynamic model of the protein ensemble.
    Chem Rev, Vol. 106, No. 5. (May 2006), pp. 1545-1558.
    by VJ Hilser, B García-Moreno E, TG Oas, G Kapp, ST Whitten
    posted to simplified protein model go folding finkelstein ensemble denatured by apaydin on 2007-01-10 21:10:38 as read
  • Fast High-Resolution Protein Structure Determination by Using Unassigned NMR Data.
    Angew Chem Int Ed Engl (5 January 2007)
    by Jegannath Korukottu, Monika Bayrhuber, Pierre Montaville, Vinesh Vijayan, Young-Sang S Jung, Stefan Becker, Markus Zweckstetter
    posted to determination nmr protein structure by apaydin on 2007-01-08 21:37:24 as **
  • Construction of Modified Ribosomes for Incorporation of <font size="-1">D</font>-Amino Acids into Proteins
    Biochemistry (1 December 2006)
    by LM Dedkova, NE Fahmi, SY Golovine, SM Hecht
    posted to d-amino-acid protein ribosome synthesis by apaydin on 2006-12-06 15:45:19 as **
  • Predicting the reactivity of proteins from their sequence alone: Kazal family of protein inhibitors of serine proteinases
    PNAS, Vol. 98, No. 4. (13 February 2001), pp. 1410-1415.
    by Stephen M Lu, Wuyuan Lu, MA Qasim, Stephen Anderson, Izydor Apostol, Wojciech Ardelt, Theresa Bigler, Yi W Chiang, James Cook, Michael N James, Ikunoshin Kato, Clyde Kelly, William Kohr, Tomoko Komiyama, Tiao-Yin Lin, Michio Ogawa, Jacek Otlewski, Soon-Jae Park, Sabiha Qasim, Michael Ranjbar, Misao Tashiro, Nicholas Warne, Harry Whatley, Anna Wieczorek, Maciej Wieczorek, Tadeusz Wilusz, Richard Wynn, Wenlei Zhang, Michael Laskowski
    posted to constant ddg design equilibrium kstar protein by apaydin on 2006-12-05 22:56:17 as ** along with 2 people hmk softsimu
  • Structural parameterization of the binding enthalpy of small ligands.
    Proteins, Vol. 49, No. 2. (1 November 2002), pp. 181-190.
    by I Luque, E Freire
    posted to binding energy function ligand protein structural by apaydin on 2006-11-30 15:30:43 as ** along with 2 people lillekatt carlescorbi
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