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gisle's library [107 articles]

Recent papers added to gisle's library ordered by importance.
  • 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
  • Physics and evolution of thermophilic adaptation.
    Proc Natl Acad Sci U S A, Vol. 102, No. 36. (6 September 2005), pp. 12742-12747.
    by IN Berezovsky, EI Shakhnovich
    posted to extremophiles thermophiles by gisle on 2007-03-16 14:05:02 as ****
  • 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 ***
  • 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 ***
  • 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
  • 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
  • MUSCLE: a multiple sequence alignment method with reduced time and space complexity.
    BMC Bioinformatics, Vol. 5, No. 1. (19 August 2004)
    by RC Edgar
    posted to alignment bioinformatics by gisle on 2007-03-16 14:13:21 as *** along with 13 people and 3 groups wallacei knaseanka chrn jwm balajis gbart caporaso sriram_s cdallett sanchezbuelna timflutre urgi Ema Radiation_Damage Stressosome biomedical-nlp
  • I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure.
    Nucleic Acids Res, Vol. 33, No. Web Server issue. (1 July 2005)
    by E Capriotti, P Fariselli, R Casadio
    posted to webapp thermodynamics prediction mutatants by gisle on 2007-01-21 12:50:20 as ***
  • From Levinthal to pathways to funnels
    Nat Struct Mol Biol, Vol. 4, No. 1. (January 1997), pp. 10-19.
    by Ken A Dill, Hue S Chan
    posted to proteinstability protein_structure by gisle on 2008-09-02 08:46:06 as **
  • The Ultimate Speed Limit to Protein Folding Is Conformational Searching
    J. Am. Chem. Soc. (7 September 2007)
    by K Ghosh, SB Ozkan, KA Dill
    posted to protein_structure by gisle on 2008-09-02 08:43:15 as ** along with 1 person karmarae
  • A View of the Hydrophobic Effect
    J. Phys. Chem. B, Vol. 106, No. 3. (24 January 2002), pp. 521-533.
    by NT Southall, KA Dill, ADJ Haymet
    posted to no-tag by gisle on 2008-09-02 08:36:49 as **
  • Evolutionary conservation of protein vibrational dynamics.
    Gene, Vol. 422, No. 1-2. (1 October 2008), pp. 7-13.
    by S Maguid, S Fernandez-Alberti, J Echave
    posted to protein_structure dynamics by gisle on 2008-09-02 08:02:39 as **
  • Evolutionary Conservation of Protein Backbone Flexibility
    Journal of Molecular Evolution, Vol. 63, No. 4. (14 October 2006), pp. 448-457.
    by Sandra Maguid, Sebastián Fernández-Alberti, Gustavo Parisi, Julián Echave
    posted to no-tag by gisle on 2008-09-02 08:01:15 as ** along with 4 people and 2 groups barry jlh64 edvin tny structural_bioinformatics Bioinformatics
  • Exploring the common dynamics of homologous proteins. Application to the globin family.
    Biophys J, Vol. 89, No. 1. (July 2005), pp. 3-13.
    by S Maguid, S Fernandez-Alberti, L Ferrelli, J Echave
    posted to protein_structure dynamics by gisle on 2008-09-02 07:59:58 as ** along with 4 people and 2 groups barry Einat jlh64 edvin structural_bioinformatics Bioinformatics
  • Macromolecular modeling with rosetta.
    Annual review of biochemistry, Vol. 77 (2008), pp. 363-382.
    by R Das, D Baker
    posted to no-tag by gisle on 2008-09-01 17:37:58 as **
  • Transproteomic evidence of a loop-deletion mechanism for enhancing protein thermostability
    Journal of Molecular Biology, Vol. 290, No. 2. (9 July 1999), pp. 595-604.
    by Michael J Thompson, David Eisenberg
    posted to thermostability thermophiles proteinstability protein_structure extremophiles by gisle on 2008-09-01 14:02:33 as **
  • Structural comparison of psychrophilic and mesophilic trypsins
    European Journal of Biochemistry, Vol. 267, No. 4. (2000), pp. 1039-1049.
    by Hanna-Kirsti S Leiros, Nils P Willassen, Arne O Smalås
    posted to extremophiles psychrophiles by gisle on 2008-08-29 15:08:13 as **
  • Residue determinants and sequence analysis of cold-adapted trypsins
    Extremophiles, Vol. 3, No. 3. (1999), pp. 205-219.
    by Schrøder, Nils P Willassen, AO Smalås
    posted to extremophiles psychrophiles by gisle on 2008-08-29 15:04:47 as **
  • Amino acid difference formula to help explain protein evolution.
    Science, Vol. 185, No. 4154. (6 September 1974), pp. 862-864.
    by R Grantham
    posted to evolution mutations by gisle on 2008-08-29 14:05:32 as ** along with 1 person Iden-J_GluR
  • A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach
    Mol Biol Evol, Vol. 18, No. 5. (1 May 2001), pp. 691-699.
    by Simon Whelan, Nick Goldman
    posted to ancestral_reconstruction bioinformatics evolution by gisle on 2008-08-29 14:00:02 as ** along with 4 people bpb chrn ssgong gjuggler
  • A solution for the best rotation to relate two sets of vectors
    Acta Crystallographica Section A, Vol. 32, No. 5. (September 1976), pp. 922-923.
    by W Kabsch
    posted to protein_structure by gisle on 2008-08-29 09:39:49 as ** along with 1 person rabio
  • Atlas of protein sequence and structure
    Vol. 5
    by MO Dayhoff
    posted to alignment mutations by gisle on 2008-08-29 08:58:16 as **
  • Amino acid substitution matrices from protein blocks.
    Proc Natl Acad Sci U S A, Vol. 89, No. 22. (15 November 1992), pp. 10915-10919.
    by S Henikoff, JG Henikoff
    posted to alignment mutations by gisle on 2008-08-29 08:44:21 as **
  • Automatic generation of primary sequence patterns from sets of related protein sequences.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 87, No. 1. (January 1990), pp. 118-122.
    by RF Smith, TF Smith
    posted to alignment bioinformatics by gisle on 2008-08-29 08:38:10 as **
  • Protein contacts, inter-residue interactions and side-chain modelling
    Biochimie, Vol. 90, No. 4. (April 2008), pp. 626-639.
    by Guilhem Faure, Aurélie Bornot, Alexandre G de Brevern
    posted to no-tag by gisle on 2008-08-29 08:16:34 as **
  • GROMACS: A message-passing parallel molecular dynamics implementation
    Computer Physics Communications, Vol. 91, No. 1-3. (2 September 1995), pp. 43-56.
    by HJC Berendsen, D van der Spoel, R van Drunen
    posted to molecular_dynamics by gisle on 2008-08-28 12:28:09 as ** along with 3 people ffranca tji robertvacha
  • The Amber biomolecular simulation programs.
    J Comput Chem, Vol. 26, No. 16. (December 2005), pp. 1668-1688.
    by DA Case, TE Cheatham, T Darden, H Gohlke, R Luo, KM Merz, A Onufriev, C Simmerling, B Wang, RJ Woods
    posted to molecular_dynamics by gisle on 2008-08-28 12:27:20 as ** along with 11 people and 3 groups lna jwm simone ttjoseph xdeupi tovrstra bilab RamuAnandakrishnan IrinaMoreira adilson_mohr mikaellund Radiation_Damage Stressosome LabCompMed
  • CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
    Journal of Computational Chemistry, Vol. 4, No. 2. (1983), pp. 187-217.
    by Bernard R Brooks, Robert E Bruccoleri, Barry D Olafson, David J States, S Swaminathan, Martin Karplus
    posted to molecular_dynamics by gisle on 2008-08-28 12:26:17 as ** along with 4 people dgront mmuecke rabio saravan
  • GenBank.
    Nucleic acids research, Vol. 30, No. 1. (1 January 2002), pp. 17-20.
    by DA Benson, I Karsch-Mizrachi, DJ Lipman, J Ostell, BA Rapp, DL Wheeler
    posted to database by gisle on 2008-08-28 12:12:13 as **
  • Psychrophilic microorganisms: challenges for life.
    EMBO Rep, Vol. 7, No. 4. (April 2006), pp. 385-389.
    by S D'Amico, T Collins, JC Marx, G Feller, C Gerday
    posted to enzyme_efficiency extremophiles psychrophiles by gisle on 2008-08-28 11:59:23 as ** along with 1 person gilda
  • Psychrophilic enzymes: revisiting the thermodynamic parameters of activation may explain local flexibility.
    Biochimica et biophysica acta, Vol. 1543, No. 1. (30 November 2000), pp. 1-10.
    by T Lonhienne, C Gerday, G Feller
    posted to extremophiles psychrophiles by gisle on 2008-08-28 11:57:01 as **
  • Ion pairs and their role in modulating stability of cold- and warm-active uracil DNA glycosylase
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Magne Olufsen, Elena Papaleo, Arne O Smalås, Bjørn O Brandsdal
    posted to no-tag by gisle on 2008-08-28 09:46:05 as ** along with 2 people camster RamuAnandakrishnan
  • Protein flexibility in psychrophilic and mesophilic trypsins. Evidence of evolutionary conservation of protein dynamics in trypsin-like serine-proteases.
    FEBS letters, Vol. 582, No. 6. (19 March 2008), pp. 1008-1018.
    by E Papaleo, M Pasi, L Riccardi, I Sambi, P Fantucci, L De Gioia
    posted to extremophiles molecular_dynamics by gisle on 2008-08-28 09:45:02 as **
  • Comparative structural analysis of psychrophilic and meso- and thermophilic enzymes.
    Proteins, Vol. 47, No. 2. (1 May 2002), pp. 236-249.
    by G Gianese, F Bossa, S Pascarella
    posted to extremophiles prediction psychrophiles by gisle on 2008-08-28 09:37:21 as ** along with 1 person neils
  • Cold adaptation of proteins. Purification, characterization, and sequence of the heat-labile subtilisin from the antarctic psychrophile Bacillus TA41.
    The Journal of biological chemistry, Vol. 269, No. 26. (1 July 1994), pp. 17448-17453.
    by S Davail, G Feller, E Narinx, C Gerday
    posted to extremophiles protein_structure by gisle on 2008-08-28 09:35:30 as **
  • Cold-adapted beta-galactosidase from the Antarctic psychrophile Pseudoalteromonas haloplanktis.
    Applied and environmental microbiology, Vol. 67, No. 4. (April 2001), pp. 1529-1535.
    by A Hoyoux, I Jennes, P Dubois, S Genicot, F Dubail, JM François, E Baise, G Feller, C Gerday
    posted to enzyme_efficiency extrmophiles psychrophiles by gisle on 2008-08-28 09:28:13 as **
  • Reversible thermal unfolding of thermostable phosphoglycerate kinase. Thermostability associated with mean zero enthalpy change.
    Journal of molecular biology, Vol. 116, No. 3. (5 November 1977), pp. 429-442.
    by H Nojima, A Ikai, T Oshima, H Noda
    posted to proteinstability thermophiles thermostability by gisle on 2008-08-28 09:08:54 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
  • 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 **
  • 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 aprasad balajis Neeperando
  • 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 **
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