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allmensch's library [366 articles]

Recent papers added to allmensch's ordered by to_read.
  • Improved Efficiency of Replica Exchange Simulations through Use of a Hybrid Explicit/Implicit Solvation Model
    J. Chem. Theory Comput., Vol. 2, No. 2. (14 March 2006), pp. 420-433.
    by A Okur, L Wickstrom, M Layten, R Geney, K Song, V Hornak, C Simmerling
    posted to hybrid remd by allmensch on 2008-01-07 10:03:51 as ***** along with 2 people and 1 group ruvido sobolevnrm baker-group
  • How consistent are molecular dynamics simulations? Comparing structure and dynamics in reduced and oxidized Escherichia coli thioredoxin.
    J Mol Biol, Vol. 233, No. 4. (20 October 1993), pp. 766-780.
    by A Elofsson, L Nilsson
    posted to md startingstructuredependence by allmensch on 2007-12-06 16:04:24 as *****
  • Locally accessible conformations of proteins: multiple molecular dynamics simulations of crambin.
    Protein Sci, Vol. 7, No. 3. (March 1998), pp. 649-666.
    by LS Caves, JD Evanseck, M Karplus
    posted to no-tag by allmensch on 2007-12-06 11:55:16 as ***** along with 2 people lillekatt toerst
  • Comparison of MD simulations and NMR experiments for hen lysozyme. Analysis of local fluctuations, cooperative motions, and global changes.
    Biochemistry, Vol. 34, No. 34. (29 August 1995), pp. 10918-10931.
    by LJ Smith, AE Mark, CM Dobson, WF van Gunsteren
    posted to nmr md lysozym by allmensch on 2007-01-19 13:49:12 as *****
  • Characterization of conformational preferences in a partly folded protein by heteronuclear NMR spectroscopy: assignment and secondary structure analysis of hen egg-white lysozyme in trifluoroethanol.
    Biochemistry, Vol. 34, No. 40. (10 October 1995), pp. 13219-13232.
    by M Buck, H Schwalbe, CM Dobson
    posted to nmr lysozym by allmensch on 2007-01-19 12:41:39 as *****
  • Structural determinants of protein dynamics: analysis of 15N NMR relaxation measurements for main-chain and side-chain nuclei of hen egg white lysozyme.
    Biochemistry, Vol. 34, No. 12. (28 March 1995), pp. 4041-4055.
    by M Buck, J Boyd, C Redfield, DA MacKenzie, DJ Jeenes, DB Archer, CM Dobson
    posted to nmr lysozym by allmensch on 2007-01-19 12:36:34 as ***** along with 1 person lna
  • Dynamic and structural analysis of isotropically distributed molecular ensembles.
    Proteins, Vol. 46, No. 2. (1 February 2002), pp. 177-189.
    by JJ Prompers, R Brüschweiler
    posted to ide by allmensch on 2006-08-02 10:13:44 as *****
  • New approaches to the dynamic interpretation and prediction of NMR relaxation data from proteins.
    Curr Opin Struct Biol, Vol. 13, No. 2. (April 2003), pp. 175-183.
    by R Brüschweiler
    posted to no-tag by allmensch on 2006-07-31 15:25:12 as *****
  • Protein aggregation and amyloidosis: confusion of the kinds?
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Frederic Rousseau, Joost Schymkowitz, Luis Serrano
    posted to no-tag by allmensch on 2006-07-31 13:35:46 as ***** along with 3 people and 1 group aalibes thamelry caporaso biomedical-nlp
  • Molecular dimensions and their distributions in early folding intermediates.
    Curr Opin Struct Biol, Vol. 16, No. 1. (February 2006), pp. 86-93.
    by O Bilsel, CR Matthews
    posted to no-tag by allmensch on 2006-07-31 13:30:50 as ***** along with 1 person dgront
  • Protein misfolding, functional amyloid, and human disease.
    Annu Rev Biochem, Vol. 75 (2006), pp. 333-366.
    by F Chiti, CM Dobson
    posted to alzheimer parkinson prion proteinaggregation by allmensch on 2006-07-06 14:05:32 as ***** along with 2 people inbetweener jennifermbui
  • The effect of motional averaging on the calculation of NMR-derived structural properties.
    Proteins, Vol. 36, No. 4. (1 September 1999), pp. 542-555.
    by X Daura, I Antes, WF van Gunsteren, W Thiel, AE Mark
    posted to statisticalerror nmr by allmensch on 2007-01-30 15:52:25 as ****
  • Influence of internal dynamics on accuracy of protein NMR structures: derivation of realistic model distance data from a long molecular dynamics trajectory.
    J Mol Biol, Vol. 285, No. 2. (15 January 1999), pp. 727-740.
    by TR Schneider, AT Brünger, M Nilges
    posted to nmr md by allmensch on 2007-01-26 13:10:30 as **** along with 1 person lna
  • Computational methods for generating models of denatured and partially folded proteins
    Methods, Vol. 34, No. 1. (September 2004), pp. 144-150.
    by Lorna J Smith
    posted to no-tag by allmensch on 2007-01-04 15:03:04 as **** along with 1 person karbak
  • Protein folding and unfolding at atomic resolution.
    Cell, Vol. 108, No. 4. (22 February 2002), pp. 573-582.
    by AR Fersht, V Daggett
    posted to proteinfolding unfoldedproteins by allmensch on 2006-11-28 10:55:21 as ****
  • Isotropic reorientational eigenmode dynamics complements NMR relaxation measurements for RNA.
    Methods Enzymol, Vol. 394 (2005), pp. 465-480.
    by SA Showalter, KB Hall
    posted to ired rna by allmensch on 2006-11-23 14:46:13 as ****
  • Fundamental processes of protein folding: measuring the energetic balance between helix formation and hydrophobic interactions.
    Protein Sci, Vol. 15, No. 9. (September 2006), pp. 2062-2070.
    by W Xian, PJ Connolly, M Oslin, AC Hausrath, JJ Osterhout
    posted to proteinfolding by allmensch on 2006-09-28 16:16:50 as ****
  • Molecular dynamics and NMR spin relaxation in proteins.
    Acc Chem Res, Vol. 35, No. 6. (June 2002), pp. 325-331.
    by DA Case
    posted to md nmr by allmensch on 2006-08-17 10:23:36 as ****
  • Unfolded proteins and protein folding studied by NMR.
    Chem Rev, Vol. 104, No. 8. (August 2004), pp. 3607-3622.
    by HJ Dyson, PE Wright
    posted to nmr proteinfolding unfoldedproteins by allmensch on 2006-08-16 11:04:53 as **** along with 2 people ruvido yxue
  • Studies of folding and misfolding using simplified models
    Current Opinion in Structural Biology, Vol. 16, No. 1. (February 2006), pp. 79-85.
    by Nikolay V Dokholyan
    posted to proteinfolding by allmensch on 2006-08-15 15:41:19 as **** along with 3 people apaydin choonpeng mtw
  • Intrinsically disordered protein.
    J Mol Graph Model, Vol. 19, No. 1. (2001), pp. 26-59.
    by AK Dunker, JD Lawson, CJ Brown, RM Williams, P Romero, JS Oh, CJ Oldfield, AM Campen, CM Ratliff, KW Hipps, J Ausio, MS Nissen, R Reeves, C Kang, CR Kissinger, RW Bailey, MD Griswold, W Chiu, EC Garner, Z Obradovic
    posted to unfoldedproteins by allmensch on 2006-08-01 13:32:51 as **** along with 1 person carlosjavierna
  • Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm.
    J Mol Biol, Vol. 293, No. 2. (22 October 1999), pp. 321-331.
    by PE Wright, HJ Dyson
    posted to nmr unfoldedproteins by allmensch on 2006-08-01 13:20:27 as **** along with 2 people chad_davis ARobson
  • Global mapping of pharmacological space
    Nature Biotechnology, Vol. 24, No. 7. (13 July 2006), pp. 805-815.
    by Gaia V Paolini, Richard HB Shapland, Willem P van Hoorn, Jonathan S Mason, Andrew L Hopkins
    posted to drugdesign by allmensch on 2006-07-26 14:59:56 as **** along with 7 people and 1 group Yanno BragilMassoud jyuh kuhn bicko caporaso jerome_ucsf_slb biomedical-nlp
  • Replica exchange molecular dynamics simulations of amyloid peptide aggregation.
    J Chem Phys, Vol. 121, No. 21. (1 December 2004), pp. 10748-10756.
    by M Cecchini, F Rao, M Seeber, A Caflisch
    posted to md proteinfolding replicaexchange by allmensch on 2006-07-06 14:12:28 as ****
  • Structure and disorder in the ribonuclease S-peptide probed by NMR residual dipolar couplings.
    Protein Sci, Vol. 12, No. 10. (October 2003), pp. 2132-2140.
    by AT Alexandrescu, RA Kammerer
    posted to nmr by allmensch on 2006-07-03 15:51:49 as ****
  • Is there a unifying mechanism for protein folding?
    Trends Biochem Sci, Vol. 28, No. 1. (January 2003), pp. 18-25.
    by V Daggett, AR Fersht
    posted to proteinfolding by allmensch on 2006-07-03 15:42:18 as **** along with 4 people and 1 group Einat dgront rabio mirzazadeh structural_bioinformatics
  • From Levinthal to pathways to funnels.
    Nat Struct Biol, Vol. 4, No. 1. (January 1997), pp. 10-19.
    by KA Dill, HS Chan
    posted to proteinfolding by allmensch on 2006-07-03 15:10:18 as **** along with 1 person dgront
  • Modulation of Compactness and Long-Range Interactions of Unfolded Lysozyme by Single Point Mutations
    Angewandte Chemie International Edition, Vol. 43, No. 43. (2004), pp. 5780-5785.
    by Julia Wirmer, Christian Schlörb, Judith Klein-Seetharaman, Ryoma Hirano, Tadashi Ueda, Taiji Imoto, Harald Schwalbe
    posted to lysozym nmr unfoldedproteins by allmensch on 2006-06-22 09:09:17 as ****
  • Characterization of the unfolded state of bovine alpha-lactalbumin and comparison with unfolded states of homologous proteins
    Protein Sci, Vol. 15, No. 6. (1 June 2006), pp. 1397-1407.
    by Julia Wirmer, Holger Berk, Raffaella Ugolini, Christina Redfield, Harald Schwalbe
    posted to lysozym nmr unfoldedproteins by allmensch on 2006-06-22 09:04:24 as ****
  • Long-range interactions within a nonnative protein.
    Science, Vol. 295, No. 5560. (1 March 2002), pp. 1719-1722.
    by J Klein-Seetharaman, M Oikawa, SB Grimshaw, J Wirmer, E Duchardt, T Ueda, T Imoto, LJ Smith, CM Dobson, H Schwalbe
    posted to nmr unfoldedproteins by allmensch on 2006-06-22 08:30:40 as **** along with 2 people dgront yxue
  • Dynamic Distance Disorder in Proteins Is Caused by Trapping
    J. Phys. Chem. B, Vol. 110, No. 19. (18 May 2006), pp. 9363-9367.
    by G Luo, I Andricioaei, XS Xie, M Karplus
    posted to no-tag by allmensch on 2006-06-14 14:52:49 as **** along with 1 person ruvido
  • Transition State Contact Orders Correlate with Protein Folding Rates
    Journal of Molecular Biology, Vol. 352, No. 3. (23 September 2005), pp. 495-500.
    by Emanuele Paci, Kresten Lindorff-Larsen, Christopher M Dobson, Martin Karplus, Michele Vendruscolo
    posted to proteinfolding by allmensch on 2006-06-13 08:55:27 as **** along with 2 people and 2 groups ana RamuAnandakrishnan structural_bioinformatics Bioinformatics
  • A molecular dynamics approach to the structural characterization of amyloid aggregation.
    J Mol Biol, Vol. 357, No. 4. (7 April 2006), pp. 1306-1321.
    by M Cecchini, R Curcio, M Pappalardo, R Melki, A Caflisch
    posted to amyloidaggregation md replicaexchange by allmensch on 2006-06-13 08:52:31 as **** along with 1 person yalexeev
  • 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 proteinfolding replicaexchange by allmensch on 2006-06-13 08:49:57 as **** along with 1 person apaydin
  • Universal Results from an Alternate Random-Matrix Model for QCD with a Baryon Chemical Potential
    Physical Review Letters, Vol. 93, No. 22. (2004)
    by James C Osborn
    posted to no-tag by allmensch on 2006-06-07 13:43:12 as **** along with 1 person RMT
  • Multiplexed-Replica Exchange Molecular Dynamics Method for Protein Folding Simulation
    Biophys. J., Vol. 84, No. 2. (1 February 2003), pp. 775-786.
    by Young M Rhee, Vijay S Pande
    posted to no-tag by allmensch on 2006-06-07 13:42:46 as **** along with 1 person dgront
  • Replica-exchange molecular dynamics method for protein folding
    Chemical Physics Letters, Vol. 314, No. 1-2. (26 November 1999), pp. 141-151.
    by Yuji Sugita, Yuko Okamoto
    posted to replicaexchange by allmensch on 2006-06-07 13:40:28 as **** along with 3 people andreasauerwein dgront rulix
  • Conformational constraints for amyloid fibrillation: the importance of being unfolded.
    Biochim Biophys Acta, Vol. 1698, No. 2. (6 May 2004), pp. 131-153.
    by VN Uversky, AL Fink
    posted to no-tag by allmensch on 2006-06-06 16:19:50 as **** along with 1 person dougjoemartin
  • Computer simulation of protein motion
    Computer Physics Communications, Vol. 91, No. 1-3. (2 September 1995), pp. 305-319.
    by WF van Gunsteren, PH Hunenberger, AE Mark, PE Smith, IG Tironi
    posted to md by allmensch on 2007-10-11 14:56:17 as ***
  • Reorientational Contact-Weighted Elastic Network Model for the Prediction of Protein Dynamics: Comparison with NMR Relaxation.
    Biophys J (24 February 2006)
    by Dengming Ming, Rafael Brüschweiler
    posted to relaxation elasticnetworkmodel by allmensch on 2007-03-13 09:46:52 as *** along with 2 people apaydin aqeel
  • Main-chain dynamics of a partially folded protein: 15N NMR relaxation measurements of hen egg white lysozyme denatured in trifluoroethanol.
    J Mol Biol, Vol. 257, No. 3. (5 April 1996), pp. 669-683.
    by M Buck, H Schwalbe, CM Dobson
    posted to lysozyme nmr relaxation by allmensch on 2007-02-14 11:28:14 as ***
  • Iron Responsive Element RNA Flexibility Described by NMR and Isotropic Reorientational Eigenmode Dynamics
    Journal of Biomolecular NMR, Vol. 32, No. 3. (July 2005), pp. 179-193.
    by Scott Showalter, Nathan Baker, Changguo Tang, Kathleen Hall
    posted to ired md rna by allmensch on 2006-12-08 13:23:13 as ***
  • Characterizing semilocal motions in proteins by NMR relaxation studies.
    Proc Natl Acad Sci U S A, Vol. 95, No. 14. (7 July 1998), pp. 8016-8019.
    by MW Fischer, L Zeng, A Majumdar, ER Zuiderweg
    posted to nmr by allmensch on 2006-07-20 09:49:13 as ***
  • Guanosine binding required for cyclization of the self-splicing intervening sequence ribonucleic acid from Tetrahymena thermophila.
    Biochemistry, Vol. 26, No. 12. (16 June 1987), pp. 3330-3340.
    by NK Tanner, TR Cech
    posted to fluorobases by allmensch on 2008-10-13 17:44:14 as **
  • Destabilization of the Escherichia coli RNase H kinetic intermediate: switching between a two-state and three-state folding mechanism.
    Journal of molecular biology, Vol. 335, No. 2. (9 January 2004), pp. 609-618.
    by GM Spudich, EJ Miller, S Marqusee
    posted to trpzip by allmensch on 2008-10-13 16:53:44 as **
  • Direct observation of the three-state folding of a single protein molecule.
    Science, Vol. 309, No. 5743. (23 September 2005), pp. 2057-2060.
    by C Cecconi, EA Shank, C Bustamante, S Marqusee
    posted to trpzip by allmensch on 2008-10-13 16:51:59 as ** along with 3 people nigham FBerkemeier ruudvanleeuwen
  • Energetics of Base Pairs in B-DNA in Solution: An Appraisal of Potential Functions and Dielectric Treatments
    J. Phys. Chem. B, Vol. 102, No. 31. (30 July 1998), pp. 6139-6144.
    by N Arora, B Jayaram
    posted to fluorobases fl by allmensch on 2008-10-13 16:44:23 as **
  • Molecular dynamics simulation of nucleic acids.
    Annual review of physical chemistry, Vol. 51 (2000), pp. 435-471.
    by TE Cheatham, PA Kollman
    posted to fluorobases by allmensch on 2008-10-13 16:36:29 as **
  • Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes
    Journal of Computational Physics, Vol. 23 (March 1977), 327.
    by JP Ryckaert, G Ciccotti, HJC Berendsen
    posted to fluorobases by allmensch on 2008-09-24 10:10:00 as **
  • Crystal structure of acceptor stem of tRNA(Ala) from Escherichia coli shows unique G.U wobble base pair at 1.16 A resolution.
    RNA (New York, N.Y.), Vol. 5, No. 5. (May 1999), pp. 670-677.
    by U Mueller, H Schübel, M Sprinzl, U Heinemann
    posted to fluorobases by allmensch on 2008-09-24 09:51:59 as **
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