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hmks protein_structure [50 articles]

Artikler nylig sendt til hmks bibliotek klassifisert med nøkkelordet protein_structure. You can also see everyone's protein_structure.
  • Protein Side-Chain Placement Through MAP Estimation and Problem-Size Reduction,
    pp. 219-230.
    posted to side_chain_prediction protein_structure protein_design inference graphical_models by hmk on 2008-07-20 15:54:09 as **
  • Thermodynamic basis of resistance to HIV-1 protease inhibition: calorimetric analysis of the V82F/I84V active site resistant mutant.
    Biochemistry, Vol. 39, No. 39. (3 October 2000), pp. 11876-11883.
    by MJ Todd, I Luque, A Velázquez-Campoy, E Freire
    posted to protein_structure hivpr drug_design data alternatives by hmk on 2008-07-08 15:27:35 as **
  • Kinetic characterization and cross-resistance patterns of HIV-1 protease mutants selected under drug pressure.
    Biochemistry, Vol. 34, No. 29. (25 July 1995), pp. 9282-9287.
    by SV Gulnik, LI Suvorov, B Liu, B Yu, B Anderson, H Mitsuya, JW Erickson
    posted to protein_structure hivpr drug_design data by hmk on 2008-07-08 15:25:51 as **
  • Extraction of configurational entropy from molecular simulations via an expansion approximation
    The Journal of Chemical Physics, Vol. 127, No. 2. (2007)
    by Benjamin J Killian, Joslyn Y Kravitz, Michael K Gilson
    posted to free_energy protein_structure by hmk on 2008-04-03 20:46:55 as **
  • The statistical-thermodynamic basis for computation of binding affinities: a critical review.
    Biophys J, Vol. 72, No. 3. (March 1997), pp. 1047-1069.
    by MK Gilson, JA Given, BL Bush, JA McCammon
    posted to entropy free_energy molecular_dynamics physics protein_structure review by hmk on 2008-04-03 20:07:07 as ** along with 2 people and 2 groups cchang ssomani group structure-bii
  • Calculation of the Entropy and Free Energy from Monte Carlo Simulations of a Peptide Stretched by an External Force
    J. Phys. Chem. B, Vol. 109, No. 46. (24 November 2005), pp. 21963-21970.
    by S Cheluvaraja, H Meirovitch
    posted to data entropy free_energy molecular_dynamics protein_structure by hmk on 2008-04-03 19:54:33 as **
  • On Design of Optimal Nonlinear Kernel Potential Function for Protein Folding and Protein Design
    by Changyu Hu, Xiang Li, Jie Liang
    posted to data decoy decoy_detection molecular_mechanics protein_design protein_structure by hmk on 2008-01-06 00:26:29 as **
  • Framework for kernel regularization with application to protein clustering
    Proceedings of the National Academy of Sciences, Vol. 102, No. 35. (30 August 2005), pp. 12332-12337.
    by Fan Lu, Sunduz Keles, Stephen J Wright, Grace Wahba
    posted to alternatives data dynamics molecular_dynamics protein_structure by hmk on 2007-12-25 01:10:04 as **
  • A consensus view of fold space: combining SCOP, CATH, and the Dali Domain Dictionary.
    Protein Sci, Vol. 12, No. 10. (October 2003), pp. 2150-2160.
    by R Day, DA Beck, RS Armen, V Daggett
    posted to data protein_fold protein_structure by hmk on 2007-12-09 05:38:39 as ** along with 4 people and 2 groups ana barry tjimenez dimka structural_bioinformatics Bioinformatics
  • High-throughput modeling and analysis of protein structural dynamics
    Brief Bioinform, Vol. 8, No. 6. (1 November 2007), pp. 432-445.
    by Xiong Liu, Hassan A Karimi
    posted to alternatives data molecular_dynamics protein_structure by hmk on 2007-12-09 02:50:59 as ** along with 1 person aqeel
  • Construction of effective free energy landscape from single-molecule time series
    Proceedings of the National Academy of Sciences, Vol. 104, No. 49. (4 December 2007), pp. 19297-19302.
    by Akinori Baba, Tamiki Komatsuzaki
    posted to free_energy graphical_models protein_folding protein_structure by hmk on 2007-12-07 03:49:47 as ** along with 6 people and 1 group hsekiguc zwang cactus sobolevnrm Diego_Prada arnaudriegert baker-group
  • Protein Free Energy Landscapes Remodeled by Ligand Binding
    Biophys. J., Vol. 93, No. 2. (15 July 2007), pp. 579-585.
    by Troy C Messina, David S Talaga
    posted to free_energy graphical_models protein_folding protein_structure by hmk on 2007-12-07 03:46:10 as **
  • Large-scale characteristics of the energy landscape in protein-protein interactions.
    Proteins (11 October 2007)
    by Nicholas O'toole, Ilya A A Vakser
    posted to free_energy protein_folding protein_protein_interactions protein_structure by hmk on 2007-12-06 07:18:22 as ** along with 2 people bicko paulschlesinger
  • Sampling Realistic Protein Conformations Using Local Structural Bias.
    PLoS Comput Biol, Vol. 2, No. 9. (22 September 2006)
    by Thomas Hamelryck, John T T Kent, Anders Krogh
    posted to free_energy graphical_models protein_fold protein_structure statistics by hmk on 2007-10-31 17:54:26 as ***** along with 2 people wouterboomsma j3xucite
  • Computational design of antibody-affinity improvement beyond in vivo maturation.
    Nat Biotechnol (23 September 2007)
    by Shaun M M Lippow, K Dane D Wittrup, Bruce Tidor
    posted to data free_energy graphical_models protein_design protein_fold protein_structure by hmk on 2007-10-31 14:06:33 as ***** along with 1 person and 1 group zwang group
  • Toward high-resolution prediction and design of transmembrane helical protein structures
    Proceedings of the National Academy of Sciences, Vol. 104, No. 40. (2 October 2007), pp. 15682-15687.
    by P Barth, J Schonbrun, D Baker
    posted to data decoy_detection molecular_mechanics physics protein_structure by hmk on 2007-10-02 22:57:07 as ** along with 3 people zwang biehl Ema
  • All are not equal: A benchmark of different homology modeling programs
    Protein Sci, Vol. 14, No. 5. (1 May 2005), pp. 1315-1327.
    by Bjorn Wallner, Arne Elofsson
    posted to protein_structure side_chain_prediction by hmk on 2007-04-10 21:39:25 as ** along with 5 people and 2 groups karbak marcius eweaver BioNica rsantana BioinfoCIPF SGU-CIPF
  • 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 free_energy loops protein_structure by hmk on 2007-03-23 01:39:24 as ** along with 6 people and 2 groups apaydin nigham aqeel yongzhao elham sobolevnrm TSRI_MGL baker-group
  • An Orientation-dependent Hydrogen Bonding Potential Improves Prediction of Specificity and Structure for Proteins and Protein-Protein Complexes
    Journal of Molecular Biology, Vol. 326, No. 4. (28 February 2003), pp. 1239-1259.
    by Tanja Kortemme, Alexandre V Morozov, David Baker
    posted to molecular_mechanics physics protein_structure side_chain_prediction by hmk on 2007-03-15 20:47:05 as ** along with 1 person mirzazadeh
  • Design of a novel globular protein fold with atomic-level accuracy.
    Science, Vol. 302, No. 5649. (21 November 2003), pp. 1364-1368.
    by B Kuhlman, G Dantas, GC Ireton, G Varani, BL Stoddard, D Baker
    posted to graphical_models molecular_mechanics physics protein_structure by hmk on 2007-03-14 01:23:38 as ** along with 5 people ca3295 jwm chad_davis heymiki kevinchannon
  • Effective energy function for proteins in solution.
    Proteins, Vol. 35, No. 2. (1 May 1999), pp. 133-152.
    by T Lazaridis, M Karplus
    posted to molecular_mechanics physics protein_structure by hmk on 2007-03-13 18:18:43 as ** along with 4 people and 2 groups kgutwin marcius bluvsh1 choonpeng BioinfoCIPF SGU-CIPF
  • Structural stability of oligomeric proteins: A mean-field theoretical approach
    Journal of Computer-Aided Materials Design, Vol. V4, No. 1. (1 April 1997), pp. 1-8.
    by Armin R Vã¶lkel, Jaan Noolandi
    posted to free_energy inference protein_structure by hmk on 2007-03-09 00:04:55 as **
  • Streptavidin Tetramerization and 2D Crystallization: A Mean-Field Approach
    Biophys. J., Vol. 80, No. 4. (1 April 2001), pp. 2004-2010.
    by T Coussaert, AR Volkel, J Noolandi, AP Gast
    posted to free_energy graphical_models inference protein_structure by hmk on 2007-03-09 00:01:52 as **
  • Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions.
    J Mol Biol, Vol. 268, No. 1. (25 April 1997), pp. 209-225.
    by KT Simons, C Kooperberg, E Huang, D Baker
    posted to decoy_detection protein_structure by hmk on 2007-03-03 20:47:53 as ** along with 7 people and 2 groups joule ana jwm vavi wouterboomsma j3xucite mijam structural_bioinformatics Bioinformatics
  • Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins
    Proteins: Structure, Function, and Genetics, Vol. 34, No. 1., pp. 82-95.
    by Kim T Simons, Ingo Ruczinski, Charles Kooperberg, Brian A Fox, Chris Bystroff, David Baker
    posted to decoy_detection protein_structure by hmk on 2007-03-03 20:45:55 as ** along with 1 person bpb
  • Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations.
    J Mol Biol, Vol. 331, No. 1. (1 August 2003), pp. 281-299.
    by JJ Gray, S Moughon, C Wang, O Schueler-Furman, B Kuhlman, CA Rohl, D Baker
    posted to data decoy_detection docking protein_structure by hmk on 2007-03-02 22:35:12 as ** along with 1 person jwm
  • Improved side-chain modeling for protein-protein docking.
    Protein Sci, Vol. 14, No. 5. (May 2005), pp. 1328-1339.
    by C Wang, O Schueler-Furman, D Baker
    posted to decoy_detection docking protein_structure by hmk on 2007-03-02 22:33:34 as ** along with 9 people and 3 groups barry aqeel jwm bicko yongzhao blackbart bluvsh1 selrac Evangelia structural_bioinformatics Bioinformatics TSRI_MGL
  • Influence of protein structure databases on the predictive power of statistical pair potentials
    Proteins: Structure, Function, and Genetics, Vol. 31, No. 2. (1998), pp. 139-149.
    by Emiko Furuichi, Patrice Koehl
    posted to decoy_detection protein_structure by hmk on 2007-02-27 22:16:10 as **
  • Near-native structure refinement using in vacuo energy minimization
    PNAS, Vol. 104, No. 9. (27 February 2007), pp. 3177-3182.
    by Christopher M Summa, Michael Levitt
    posted to decoy_detection protein_structure by hmk on 2007-02-27 18:54:39 as ** along with 1 person thaliana
  • Flexibility and packing in proteins
    PNAS, Vol. 99, No. 3. (5 February 2002), pp. 1274-1279.
    by Bertil Halle
    posted to free_energy protein_structure by hmk on 2007-02-23 23:57:08 as ** along with 3 people and 2 groups ana aqeel allmensch structural_bioinformatics Bioinformatics
  • Decomposition of the Free Energy of a System in Terms of Specific Interactions : Implications for Theoretical and Experimental Studies
    Journal of Molecular Biology, Vol. 240, No. 2. (7 July 1994), pp. 167-176.
    by Alan E Mark, Wilfred F van Gunsteren
    posted to docking free_energy protein_structure by hmk on 2007-02-23 16:39:50 as **
  • Thermodynamics of the interaction of barnase and barstar: changes in free energy versus changes in enthalpy on mutation
    Journal of Molecular Biology, Vol. 267, No. 3. (4 April 1997), pp. 696-706.
    by Christian Frisch, Gideon Schreiber, Christopher M Johnson, Alan R Fersht
    posted to docking free_energy protein_structure by hmk on 2007-02-23 16:26:49 as **
  • The molecular architecture of protein-protein binding sites
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Dana Reichmann, Ofer Rahat, Mati Cohen, Hani Neuvirth, Gideon Schreiber
    posted to docking protein_structure by hmk on 2007-02-23 14:55:48 as ** along with 5 people higueruelo marti bicko chad_davis choonpeng
  • Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations.
    J Mol Biol, Vol. 320, No. 2. (5 July 2002), pp. 369-387.
    by R Guerois, JE Nielsen, L Serrano
    posted to protein_structure free_energy by hmk on 2007-02-23 14:53:30 as ** along with 4 people apaydin aalibes chad_davis carlescorbi
  • Bayesian statistical analysis of protein side-chain rotamer preferences.
    Protein Sci, Vol. 6, No. 8. (August 1997), pp. 1661-1681.
    by RL Dunbrack, FE Cohen
    posted to protein_structure side_chain_prediction by hmk on 2007-02-12 18:29:57 as ** along with 10 people and 1 group jwm karbak nknii j3xucite dgront blackbart kazemi rsantana LamBras mijam TCR_Signaling
  • SMoS: a database of structural motifs of protein superfamilies
    Protein Eng., Vol. 16, No. 11. (1 November 2003), pp. 791-793.
    by Saikat Chakrabarti, K Venkatramanan, R Sowdhamini
    posted to protein_structure protein_fold by hmk on 2007-02-09 15:39:59 as **
  • Ab initio protein structure prediction of CASP III targets using ROSETTA
    Proteins: Structure, Function, and Genetics, Vol. 37, No. S3. (1999), pp. 171-176.
    by Kim T Simons, Rich Bonneau, Ingo Ruczinski, David Baker
    posted to protein_structure decoy_detection by hmk on 2007-02-08 23:26:18 as **
  • 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 protein_structure molecular_mechanics by hmk on 2007-02-08 23:25:10 as ** along with 5 people and 1 group jwm vavi yongzhao thamelry Alan TSRI_MGL
  • Force fields for protein simulations.
    Adv Protein Chem, Vol. 66 (2003), pp. 27-85.
    by JW Ponder, DA Case
    posted to protein_structure molecular_mechanics by hmk on 2007-02-08 22:26:46 as ** along with 3 people and 2 groups karbak marcius papatonyhill BioinfoCIPF SGU-CIPF
  • Structural biology: Molecular machinery in action
    Nature (21 January 2007)
    by Ad Bax, Dennis A Torchia
    posted to protein_structure nmr by hmk on 2007-02-07 23:03:24 as **
  • An atomic environment potential for use in protein structure prediction.
    J Mol Biol, Vol. 352, No. 4. (30 September 2005), pp. 986-1001.
    by CM Summa, M Levitt, WF Degrado
    posted to protein_structure decoy by hmk on 2007-01-30 23:11:31 as **
  • Meanfield approach to the thermodynamics of protein-solvent systems with application to p53.
    Biophysics, Vol. 80 (March 2001), pp. 1524-1537.
    by Volkel R Armin, Noolandi Jaan
    posted to protein_structure graphical_models by hmk on 2007-01-29 19:24:03 as **
  • Graphical models of residue coupling in protein families
    (2005), pp. 12-20.
    by John Thomas, Naren Ramakrishnan, Chris Bailey-Kellogg
    posted to protein_structure graphical_models by hmk on 2007-01-26 16:03:43 as ** along with 1 group Dartmouth Computer Science
  • Rapid and accurate calculation of protein 1H, 13C and 15N chemical shifts.
    J Biomol NMR, Vol. 26, No. 3. (July 2003), pp. 215-240.
    by S Neal, AM Nip, H Zhang, DS Wishart
    posted to protein_structure nmr by hmk on 2007-01-25 18:55:47 as ** along with 3 people betainverse karbak netterpaladin
  • An automated assignment-free Bayesian approach for accurately identifying proton contacts from NOESY data
    Journal of Biomolecular NMR, Vol. 36, No. 3. (November 2006), pp. 189-198.
    by Hung, Ling-Hong, Samudrala, Ram
    posted to statistics protein_structure by hmk on 2007-01-23 00:23:39 as **
  • A knowledge-based scoring function based on residue triplets for protein structure prediction
    Protein Engineering, Design and Selection, Vol. 19, No. 5. (May 2006), pp. 187-193.
    by Ngan, Shing-Chung, Inouye, T Michael, Samudrala, Ram
    posted to protein_structure decoy_detection by hmk on 2007-01-22 23:43:06 as **
  • The dominant role of side-chain backbone interactions in structural realization of amino acid code. ChiRotor: A side-chain prediction algorithm based on side-chain backbone interactions
    Protein Science
    by Velin
    posted to side_chain_prediction protein_structure by hmk on 2007-01-22 23:19:57 as **
  • The shape of things
    Nature Methods, Vol. 4, No. 1., pp. 95-102.
    by Michael Eisenstein
    posted to protein_structure by hmk on 2007-01-22 16:05:59 as **
  • From cryo-EM, multiple protein structures in one shot
    Nature Methods, Vol. 4, No. 1., pp. 20-21.
    by Fred J Sigworth
    posted to statistics protein_structure by hmk on 2007-01-22 15:58:28 as **
  • Disentangling conformational states of macromolecules in 3D-EM through likelihood optimization
    Nature Methods, Vol. 4, No. 1. (10 December 2006), pp. 27-29.
    by Sjors HW Scheres, Haixiao Gao, Mikel Valle, Gabor T Herman, Paul PB Eggermont, Joachim Frank, Jose-Maria Carazo
    posted to statistics protein_structure by hmk on 2007-01-22 15:57:40 as **
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