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gisle's library [74 articles]

Recent papers added to gisle's library.
  • Structural Biology: Analysis of 'downhill' protein folding
    Nature, Vol. 445, No. 7129. (14 February 2007), pp. E14-E15.
    by Neil Ferguson, Timothy D Sharpe, Christopher M Johnson, Pamela J Schartau, Alan R Fersht
    posted to no-tag by gisle on 2008-03-05 10:11:56 as ***
  • Estimating Free-Energy Barrier Heights for an Ultrafast Folding Protein from Calorimetric and Kinetic Data.
    J Phys Chem B (16 February 2008)
    by Raquel Godoy-Ruiz, Eric R Henry, Jan Kubelka, James Hofrichter, Victor Muñoz, Jose M Sanchez-Ruiz, William A Eaton
    posted to no-tag by gisle on 2008-03-05 10:11:40 as ***
  • Experimental identification of downhill protein folding.
    Science, Vol. 298, No. 5601. (13 December 2002), pp. 2191-2195.
    by MM Garcia-Mira, M Sadqi, N Fischer, JM Sanchez-Ruiz, V Muñoz
    posted to proteinstability protein_structure by gisle on 2008-03-05 10:03:49 as ***
  • Native protein sequences are close to optimal for their structures.
    Proc Natl Acad Sci U S A, Vol. 97, No. 19. (12 September 2000), pp. 10383-10388.
    by B Kuhlman, D Baker
    posted to bioinformatics proteinstability protein_structure by gisle on 2008-03-03 10:41:11 as ** along with 2 people jwm analogAI
  • Atom-by-atom analysis of global downhill protein folding
    Nature, Vol. 442, No. 7100. (14 June 2006), pp. 317-321.
    by Mourad Sadqi, David Fushman, Victor Muã±oz
    posted to proteinstability protein_structure by gisle on 2008-02-29 13:17:57 as ** along with 4 people and 2 groups marcius wouterboomsma choonpeng huyun110 BioinfoCIPF SGU-CIPF
  • Reduced global cooperativity is a common feature underlying the amyloidogenicity of pathogenic lysozyme mutations.
    J Mol Biol, Vol. 346, No. 3. (25 February 2005), pp. 773-788.
    by M Dumoulin, D Canet, AM Last, E Pardon, DB Archer, S Muyldermans, L Wyns, A Matagne, CV Robinson, C Redfield, CM Dobson
    posted to proteinstability protein_structure by gisle on 2008-02-29 13:11:23 as ** along with 1 person allmensch
  • Destruction of long-range interactions by a single mutation in lysozyme.
    Proc Natl Acad Sci U S A (26 March 2007)
    by Ruhong Zhou, Maria Eleftheriou, Ajay K Royyuru, Bruce J J Berne
    posted to protein_structure thermodynamics thermostability by gisle on 2008-02-29 13:10:59 as ** along with 3 people and 1 group Einat allmensch choonpeng structural_bioinformatics
  • Impact of local and non-local interactions on thermodynamics and kinetics of protein folding.
    J Mol Biol, Vol. 252, No. 4. (29 September 1995), pp. 460-471.
    by VI Abkevich, AM Gutin, EI Shakhnovich
    posted to protein_structure by gisle on 2008-02-29 12:40:50 as ***
  • Estimation of changes in side chain configurational entropy in binding and folding: General methods and application to helix formation
    Proteins: Structure, Function, and Genetics, Vol. 20, No. 1. (1994), pp. 68-84.
    by Kon H Lee, Dong Xie, Ernesto Freire, Mario L Amzel
    posted to no-tag by gisle on 2008-02-26 08:57:43 as read along with 1 person apaydin
  • Computational Thermostabilization of an Enzyme
    Science, Vol. 308, No. 5723. (6 May 2005), pp. 857-860.
    by Aaron Korkegian, Margaret E Black, David Baker, Barry L Stoddard
    posted to mutatants mutatations thermodynamics thermostability by gisle on 2008-02-21 12:10:54 as read
  • Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.
    Biopolymers, Vol. 22, No. 12. (December 1983), pp. 2577-2637.
    by W Kabsch, C Sander
    posted to protein_structure secondary_structure by gisle on 2008-02-21 12:03:39 as read along with 14 people mschofie kaarsinogen lna chad_davis wouterboomsma penka ffranca dgront choonpeng leelarcombe rabio medic0747 martainn chgjb
  • Increased flexibility as a strategy for cold adaptation: a comparative molecular dynamics study of cold- and warm-active uracil DNA glycosylase.
    J Biol Chem, Vol. 280, No. 18. (6 May 2005), pp. 18042-18048.
    by M Olufsen, AO Smalås, E Moe, BO Brandsdal
    posted to extremophiles psychrophiles by gisle on 2008-02-20 14:39:50 as read
  • Cold-adapted enzymes.
    Annu Rev Biochem, Vol. 75 (2006), pp. 403-433.
    by KS Siddiqui, R Cavicchioli
    posted to no-tag by gisle on 2008-02-20 14:18:31 as read along with 1 person bpb
  • Life at low temperatures: is disorder the driving force?
    Extremophiles, Vol. 11, No. 2. (March 2007), pp. 211-216.
    by Feller, Georges
    posted to extremophiles psychrophiles by gisle on 2008-02-18 10:08:53 as **
  • The impact of extremophiles on structural genomics (and vice versa).
    Extremophiles, Vol. 12, No. 1. (January 2008), pp. 39-50.
    by FE Jenney, MW Adams
    posted to extremophiles thermophiles thermostability by gisle on 2008-02-18 10:07:15 as **
  • Implication for buried polar contacts and ion pairs in hyperthermostable enzymes
    FEBS Journal, Vol. 274, No. 16. (August 2007), pp. 4012-4022.
    by Matsui, Ikuo, Harata, Kazuaki
    posted to no-tag by gisle on 2008-02-18 10:06:39 as **
  • Thermodynamic stability and folding of proteins from hyperthermophilic organisms
    FEBS Journal, Vol. 274, No. 16. (2007), pp. 4023-4033.
    by Kathryn A Luke, Catherine L Higgins, Pernilla Wittung-Stafshede
    posted to extremophiles thermophiles thermostability by gisle on 2008-02-18 10:06:01 as **** along with 1 person and 2 groups dchughes G4ID Genetics-of-Gambling
  • Observations of Amino Acid Gain and Loss during Protein Evolution Are Explained by Statistical Bias
    Molecular Biology and Evolution, Vol. 23, No. 7. (July 2006), pp. 1444-1449.
    by Goldstein, A Richard, Pollock, D David
    posted to ancestral_reconstruction by gisle on 2007-11-22 08:24:44 as **
  • Reconstructing large regions of an ancestral mammalian genome in silico
    Genome Res., Vol. 14, No. 12. (1 December 2004), pp. 2412-2423.
    by Mathieu Blanchette, Eric D Green, Webb Miller, David Haussler
    posted to ancestral_reconstruction by gisle on 2007-11-22 07:45:40 as ** along with 3 people Neeperando aprasad balajis
  • Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins
    Nature, Vol. 425, No. 6955. (2003), pp. 285-288.
    by Eric A Gaucher, Michael J Thomson, Michelle F Burgan, Steven A Benner
    posted to ancestral_reconstruction mutations thermophiles by gisle on 2007-11-22 07:41:01 as ** along with 1 person cactus
  • Apparent Trends of Amino Acid Gain and Loss in Protein Evolution Due to Nearly Neutral Variation
    Molecular Biology and Evolution, Vol. 23, No. 2. (20 February 2006), pp. 240-244.
    by John H Mcdonald
    posted to ancestral_reconstruction by gisle on 2007-11-22 07:38:16 as **
  • A universal trend of amino acid gain and loss in protein evolution
    Nature, Vol. aop, No. current. (19 January 2005)
    by King K Jordan, Fyodor A Kondrashov, Ivan A Adzhubei, Yuri I Wolf, Eugene V Koonin, Alexey S Kondrashov, Shamil Sunyaev
    posted to ancestral_reconstruction by gisle on 2007-11-22 07:37:33 as read along with 3 people karbak nagendranow michaelbarton
  • Structure-dependent relationships between growth temperature of prokaryotes and the amino acid frequency in their proteins
    Extremophiles, Vol. 11, No. 4. (July 2007), pp. 585-596.
    by Saelensminde, Gisle, Halskau, Oyvind, Helland, Ronny, Willassen, Nils-Peder, Jonassen, Inge
    posted to bioinformatics extremophiles psychrophiles thermophiles thermostability by gisle on 2007-10-04 09:44:30 as **
  • Electrostatic Contributions to the Stability of a Thermophilic Cold Shock Protein
    Biophys. J., Vol. 84, No. 4. (1 April 2003), pp. 2216-2222.
    by Huan-Xiang Zhou, Feng Dong
    posted to extremophiles saltbridges thermophiles by gisle on 2007-10-04 09:34:07 as **
  • Different packing of external residues can explain differences in the thermostability of proteins from thermophilic and mesophilic organisms.
    Bioinformatics, Vol. 23, No. 17. (1 September 2007), pp. 2231-2238.
    by AV Glyakina, SO Garbuzynskiy, MY Lobanov, OV Galzitskaya
    posted to extrmophiles thermophiles thermostability by gisle on 2007-10-04 09:18:51 as ** along with 1 person aalibes
  • Molecular simulations suggest protein salt bridges are uniquely suited to life at high temperatures.
    J Am Chem Soc, Vol. 126, No. 7. (25 February 2004), pp. 2208-2214.
    by AS Thomas, AH Elcock
    posted to extrmophiles saltbridges thermophiles thermostability by gisle on 2007-10-04 09:05:37 as **
  • The stability of salt bridges at high temperatures: implications for hyperthermophilic proteins.
    J Mol Biol, Vol. 284, No. 2. (27 November 1998), pp. 489-502.
    by AH Elcock
    posted to extremophiles saltbridges thermophiles by gisle on 2007-10-04 08:49:17 as **
  • Protein thermal stability, hydrogen bonds, and ion pairs.
    J Mol Biol, Vol. 269, No. 4. (20 June 1997), pp. 631-643.
    by G Vogt, S Woell, P Argos
    posted to extrmophiles thermophiles thermostability by gisle on 2007-10-03 13:45:49 as *** along with 1 person Cristiano
  • Binding of small organic molecules to macromolecular targets: evaluation of conformational entropy changes.
    Proteins, Vol. Suppl 4 (2000), pp. 93-107.
    by JA D'Aquino, E Freire, LM Amzel
    posted to no-tag by gisle on 2007-10-03 13:23:07 as read
  • Amino-acid interactions in psychrophiles, mesophiles, thermophiles, and hyperthermophiles: Insights from the quasi-chemical approximation.
    Protein Sci, Vol. 16, No. 9. (September 2007), pp. 1887-1895.
    by RA Goldstein
    posted to contacts extremophiles thermophiles by gisle on 2007-10-03 13:13:59 as read along with 2 people choonpeng cdeane
  • Positive and Negative Design in Stability and Thermal Adaptation of Natural Proteins
    PLoS Computational Biology, Vol. 3, No. 3. (1 March 2007), e52.
    by Igor N Berezovsky, Konstantin B Zeldovich, Eugene I Shakhnovich
    posted to no-tag by gisle on 2007-06-07 15:09:18 as read along with 2 people bpb cjeans
  • Compositional changes in RNA, DNA and proteins for bacterial adaptation to higher and lower temperatures.
    J Biochem (Tokyo), Vol. 133, No. 4. (April 2003), pp. 507-513.
    by H Nakashima, S Fukuchi, K Nishikawa
    posted to no-tag by gisle on 2007-06-07 13:06:30 as read
  • The stability of thermophilic proteins: a study based on comprehensive genome comparison
    Functional & Integrative Genomics, Vol. 1, No. 1. (May 2000), pp. 76-88.
    by Rajdeep Das, Mark Gerstein
    posted to no-tag by gisle on 2007-06-07 12:24:39 as read
  • Water's Hydrogen Bonds in the Hydrophobic Effect: A Simple Model
    J. Phys. Chem. B, Vol. 109, No. 49. (15 December 2005), pp. 23611-23617.
    by H Xu, KA Dill
    posted to protein_structure proteinstability by gisle on 2007-06-07 12:23:18 as read
  • Can a biologist fix a radio?--Or, what I learned while studying apoptosis.
    Cancer Cell, Vol. 2, No. 3. (September 2002), pp. 179-182.
    by Y Lazebnik
    posted to systems-biology by gisle on 2007-06-07 10:23:57 as read along with 14 people and 6 groups leilaperie Tominator dbikard balicea mattjb tvdbulck quianominorleo rklancer dbk irenas manduca monod chihchun_chen massivemayhem SynBioSys Centre de Recherches Interdisciplinaires DSTO-CAS ComplexAdaptiveSystems streptomyces dbk-lab
  • Prediction of protein stability changes for single-site mutations using support vector machines.
    Proteins, Vol. 62, No. 4. (21 December 2005), pp. 1125-1132.
    by Jianlin Cheng, Arlo Randall, Pierre Baldi
    posted to mutatations prediction thermodynamics by gisle on 2007-06-07 08:26:37 as *** along with 2 people bicko massivemayhem
  • Introduction to Protein Structure
    (1999)
    by Carl Branden, John Tooze
    posted to protein_structure by gisle on 2007-06-04 14:49:08 as read
  • The Genomics of Disulfide Bonding and Protein Stabilization in Thermophiles.
    PLoS Biol, Vol. 3, No. 9. (September 2005)
    by Morgan Beeby, Brian D D Oʼconnor, Carsten Ryttersgaard, Daniel R R Boutz, L Jeanne J Perry, Todd O O Yeates
    posted to proteinstability thermophiles by gisle on 2007-06-04 14:26:31 as ** along with 1 person matzke
  • Elucidation of factors responsible for enhanced thermal stability of proteins: a structural genomics based study.
    Biochemistry, Vol. 41, No. 25. (25 June 2002), pp. 8152-8161.
    by S Chakravarty, R Varadarajan
    posted to proteinstability thermophiles by gisle on 2007-06-04 13:15:39 as ** along with 1 person bpb
  • Exceptionally stable salt bridges in cytochrome P450cam have functional roles.
    Biochemistry, Vol. 36, No. 18. (6 May 1997), pp. 5402-5417.
    by V Lounnas, RC Wade
    posted to no-tag by gisle on 2007-06-04 12:16:16 as **
  • Contributions of a hydrogen bond/salt bridge network to the stability of secondary and tertiary structure in lambda repressor.
    Protein Sci, Vol. 3, No. 12. (December 1994), pp. 2217-2225.
    by S Marqusee, RT Sauer
    posted to no-tag by gisle on 2007-06-04 12:08:21 as **
  • 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 extremophiles psychrophiles thermodynamics thermophiles by gisle on 2007-06-04 12:01:33 as ** along with 2 people bicko chad_davis
  • Electrostatic strengths of salt bridges in thermophilic and mesophilic glutamate dehydrogenase monomers.
    Proteins, Vol. 38, No. 4. (1 March 2000), pp. 368-383.
    by S Kumar, B Ma, CJ Tsai, R Nussinov
    posted to extremophiles proteinstability thermophiles by gisle on 2007-06-04 11:42:22 as **
  • Thermophilic prokaryotes have characteristic patterns of codon usage, amino acid composition and nucleotide content.
    Gene, Vol. 317, No. 1-2. (23 October 2003), pp. 39-47.
    by GA Singer, DA Hickey
    posted to extremophiles thermophiles by gisle on 2007-03-18 20:30:14 as ** along with 1 person nagendraproj
  • Entropic stabilization of proteins and its proteomic consequences.
    PLoS Comput Biol, Vol. 1, No. 4. (September 2005)
    by IN Berezovsky, WW Chen, PJ Choi, EI Shakhnovich
    posted to extremophiles thermophiles by gisle on 2007-03-18 20:29:00 as read along with 1 person bpb
  • Protein and DNA Sequence Determinants of Thermophilic Adaptation
    PLoS Computational Biology, Vol. 3, No. 1. (1 January 2007), e5.
    by Konstantin B Zeldovich, Igor N Berezovsky, Eugene I Shakhnovich
    posted to extremophiles thermophiles by gisle on 2007-03-18 20:28:14 as ** along with 2 people aalibes bpb
  • The classification of amino acid conservation.
    J Theor Biol, Vol. 119, No. 2. (21 March 1986), pp. 205-218.
    by WR Taylor
    posted to bioinformatics by gisle on 2007-03-18 15:56:18 as ** along with 1 person siebertm
  • GenBank.
    Nucleic Acids Res, Vol. 28, No. 1. (1 January 2000), pp. 15-18.
    by DA Benson, I Karsch-Mizrachi, DJ Lipman, J Ostell, BA Rapp, DL Wheeler
    posted to bioinformatics database by gisle on 2007-03-16 15:27:32 as ** along with 2 people CitoJam roland
  • Database resources of the National Center for Biotechnology Information.
    Nucleic Acids Res, Vol. 28, No. 1. (1 January 2000), pp. 10-14.
    by DL Wheeler, C Chappey, AE Lash, DD Leipe, TL Madden, GD Schuler, TA Tatusova, BA Rapp
    posted to bioinformatics database by gisle on 2007-03-16 15:26:45 as **
  • Role of cation-pi interactions to the stability of thermophilic proteins.
    Prep Biochem Biotechnol, Vol. 32, No. 4. (November 2002), pp. 355-362.
    by MM Gromiha, S Thomas, C Santhosh
    posted to extremophiles thermophiles by gisle on 2007-03-16 15:16:44 as **
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