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mkurcs library [384 articles]

Nye artikler sendt til mkurcs bibliotek.
  • I-TASSER server for protein 3D structure prediction
    BMC Bioinformatics, Vol. 9 (23 January 2008), 40.
    by Yang Zhang
    posted to tasser by mkurc on 2008-02-05 07:52:30 as ** along with 4 people chad_davis rabio zwang mclarenv
  • TOUCHSTONE II: a new approach to ab initio protein structure prediction.
    Biophys J, Vol. 85, No. 2. (August 2003), pp. 1145-1164.
    by Y Zhang, A Kolinski, J Skolnick
    posted to cabs tasser by mkurc on 2007-12-14 08:10:05 as ** along with 1 person j3xucite
  • Free modeling with Rosetta in CASP6.
    Proteins, Vol. 61 (September 2005), pp. 128-134.
    by Philip Bradley, Lars Malmström, Bin Qian, Jack Schonbrun, Dylan Chivian, David EE Kim, Jens Meiler, Kira MSM Misura, David Baker
    posted to casp by mkurc on 2007-10-08 07:25:18 as **
  • Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models.
    Proteins, Vol. 61, No. Suppl 7. (September 2005), pp. 84-90.
    by Andrzej Kolinski, Janusz M Bujnicki
    posted to casp by mkurc on 2007-10-08 07:25:18 as **
  • Exploring protein energy landscapes with hierarchical clustering.
    Int J Quantum Chem, Vol. 105, No. 6. (2005), pp. 826-830.
    by Dominik Gront, Ulrich HEH Hansmann, Andrzej Kolinski
    posted to clustering my_own by mkurc on 2007-10-08 07:25:18 as **
  • Denatured proteins and early folding intermediates simulated in a reduced conformational space.
    Acta Biochim Pol, Vol. 53, No. 1. (December 2006), pp. 131-143.
    by Sebastian Kmiecik, Mateusz Kurcinski, Aleksandra Rutkowska, Dominik Gront, Andrzej Kolinski
    posted to my_own by mkurc on 2007-10-08 07:25:18 as **
  • How Well Can Simulation Predict Protein Folding Kinetics and Thermodynamics?
    Annu Rev Biophys Biomol Struct (October 2004)
    by Christopher DD Snow, Eric JJ Sorin, Young, Vijay SS Pande
    posted to review by mkurc on 2007-10-08 07:25:18 as **
  • Protein structure by mechanical triangulation
    PNAS, Vol. 103, No. 5. (January 2006), pp. 1244-1247.
    by Hendrik Dietz, Matthias Rief
    posted to experimental by mkurc on 2007-10-08 07:25:18 as **
  • Traditional Biomolecular Structure Determination by NMR Spectroscopy Allows for Major Errors.
    PLoS Comput Biol, Vol. 2, No. 2. (February 2006)
    by Sander BB Nabuurs, Chris AEMA Spronk, Geerten WW Vuister, Gert Vriend
    posted to experimental by mkurc on 2007-10-08 07:25:18 as **
  • A general framework for non-Boltzmann Monte Carlo sampling.
    J Chem Phys, Vol. 124, No. 5. (February 2006)
    by CR Abreu, FA Escobedo
    posted to monte_carlo by mkurc on 2007-10-08 07:25:18 as **
  • Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations
    PNAS, Vol. 101, No. 18. (May 2004), pp. 6946-6951.
    by Alexandre V Morozov, Tanja Kortemme, Kiril Tsemekhman, David Baker
    posted to force_field by mkurc on 2007-10-08 07:25:18 as **
  • Direct measurement of protein binding energetics by isothermal titration calorimetry.
    Curr Opin Struct Biol, Vol. 11, No. 5. (October 2001), pp. 560-566.
    by S Leavitt, E Freire
    posted to calorimetry experimental review by mkurc on 2007-10-08 07:25:18 as **
  • Isothermal titration calorimetry of protein-protein interactions.
    Methods, Vol. 19, No. 2. (October 1999), pp. 213-221.
    by MM Pierce, CS Raman, BT Nall
    posted to experimental by mkurc on 2007-10-08 07:25:18 as **
  • Physical methods for structure, dynamics and binding in immunological research.
    Trends Immunol, Vol. 25, No. 12. (December 2004), pp. 700-707.
    by D Morikis, JD Lambris
    posted to experimental review by mkurc on 2007-10-08 07:25:18 as **
  • Measuring protein-protein interactions.
    Curr Opin Struct Biol, Vol. 8, No. 1. (February 1998), pp. 119-123.
    by JH Lakey, EM Raggett
    posted to experimental review by mkurc on 2007-10-08 07:25:18 as **
  • An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes.
    J Mol Biol, Vol. 326, No. 4. (February 2003), pp. 1239-1259.
    by T Kortemme, AV Morozov, D Baker
    posted to force_field by mkurc on 2007-10-08 07:25:18 as **
  • BioShell - a package of tools for structural biology computations
    Bioinformatics, Vol. 22, No. 5. (March 2006), pp. 621-622.
    by Dominik Gront, Andrzej Kolinski
    posted to my_own by mkurc on 2007-10-08 07:25:18 as **
  • A quantum mechanical polarizable force field for biomolecular interactions.
    Proc Natl Acad Sci U S A, Vol. 102, No. 22. (May 2005), pp. 7829-7834.
    by AG Donchev, VD Ozrin, MV Subbotin, OV Tarasov, VI Tarasov
    posted to force_field by mkurc on 2007-10-08 07:25:18 as **
  • Algorithms for Model-Based Gaussian Hierarchical Clustering
    SIAM Journal on Scientific Computing, Vol. 20, No. 1. (1999), pp. 270-281.
    by Chris Fraley
    posted to clustering by mkurc on 2007-10-08 07:25:18 as **
  • 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 secondary_structure tools by mkurc on 2007-10-08 07:25:18 as **
  • Synchrotron crystallography.
    Trends Biochem Sci, Vol. 25, No. 12. (December 2000), pp. 637-643.
    by WA Hendrickson
    posted to experimental review by mkurc on 2007-10-08 07:25:18 as **
  • Extended Ensemble Monte Carlo
    (Jun 2001)
    by Yukito Iba
    posted to monte_carlo review by mkurc on 2007-10-08 07:25:18 as **
  • Structure-derived potentials and protein simulations.
    Curr Opin Struct Biol, Vol. 6, No. 2. (April 1996), pp. 195-209.
    by RL Jernigan, I Bahar
    posted to force_field review by mkurc on 2007-10-08 07:25:18 as **
  • On Design of Optimal Nonlinear Kernel Potential Function for Protein Folding and Protein Design
    (Jan 2003)
    by Changyu Hu, Xiang Li, Jie Liang
    posted to force_field by mkurc on 2007-10-08 07:25:18 as **
  • Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures.
    J Comput Aided Mol Des, Vol. 7, No. 4. (August 1993), pp. 473-501.
    by MJ Sippl
    posted to force_field by mkurc on 2007-10-08 07:25:18 as **
  • Efficient free-energy calculations by the simulation of nonequilibrium processes
    Computing in Science and Engg., Vol. 2, No. 3. (May 2000), pp. 88-96.
    by Maurice de Koning, Wei Cai, Alex Antonelli, Sidney Yip
    posted to free_energy monte_carlo by mkurc on 2007-10-08 07:25:18 as **
  • Progress in Modeling of Protein Structures and Interactions
    Science, Vol. 310, No. 5748. (October 2005), pp. 638-642.
    by Ora S Furman, Chu Wang, Phil Bradley, Kira Misura, David Baker
    posted to review by mkurc on 2007-10-08 07:25:18 as **
  • De novo design of catalytic proteins.
    Proc Natl Acad Sci U S A, Vol. 101, No. 32. (August 2004), pp. 11566-11570.
    by J Kaplan, WF Degrado
    posted to protein_design by mkurc on 2007-10-08 07:25:18 as **
  • Computational design of receptor and sensor proteins with novel functions.
    Nature, Vol. 423, No. 6936. (May 2003), pp. 185-190.
    by LL Looger, MA Dwyer, JJ Smith, HW Hellinga
    posted to experimental protein_design by mkurc on 2007-10-08 07:25:18 as **
  • Simultaneous determination of protein structure and dynamics
    Nature, Vol. 433, No. 7022. (January 2005), pp. 128-132.
    by Kresten L Larsen, Robert B Best, Mark A Depristo, Christopher M Dobson, Michele Vendruscolo
    posted to biomolecular_dynamics by mkurc on 2007-10-08 07:25:18 as **
  • The dead-end elimination theorem and its use in protein side-chain positioning
    Nature, Vol. 356, No. 6369. (April 1992), pp. 539-542.
    by Johan Desmet, Marc D Maeyer, Bart Hazes, Ignace Lasters
    posted to dee rotamers by mkurc on 2007-10-08 07:25:18 as **
  • Efficient rotamer elimination applied to protein side-chains and related spin glasses.
    Biophys J, Vol. 66, No. 5. (May 1994), pp. 1335-1340.
    by RF Goldstein
    posted to dee by mkurc on 2007-10-08 07:25:18 as **
  • Enzyme dynamics during catalysis.
    Science, Vol. 295, No. 5559. (February 2002), pp. 1520-1523.
    by EZ Eisenmesser, DA Bosco, M Akke, D Kern
    posted to biomolecular_dynamics experimental by mkurc on 2007-10-08 07:25:18 as **
  • Veni, vidi, vici - atomic resolution unravelling the mysteries of protein function.
    Curr Opin Struct Biol, Vol. 12, No. 6. (December 2002), pp. 698-703.
    by A Schmidt, VS Lamzin
    posted to experimental review by mkurc on 2007-10-08 07:25:18 as **
  • Protein modeling and structure prediction with a reduced representation.
    Acta Biochim Pol, Vol. 51, No. 2. (2004), pp. 349-371.
    by A Kolinski
    posted to lattice_model tools by mkurc on 2007-10-08 07:25:18 as **
  • Comparison of three Monte Carlo conformational search strategies for a proteinlike homopolymer model: Folding thermodynamics and identification of low-energy structures
    The Journal of Chemical Physics, Vol. 113, No. 12. (2000), pp. 5065-5071.
    by Dominik Gront, Andrzej Kolinski, Jeffrey Skolnick
    posted to monte_carlo my_own replica_method by mkurc on 2007-10-08 07:25:18 as **
  • HCPM--program for hierarchical clustering of protein models.
    Bioinformatics, Vol. 21, No. 14. (July 2005), pp. 3179-3180.
    by D Gront, A Kolinski
    posted to clustering my_own tools by mkurc on 2007-10-08 07:25:18 as **
  • Data clustering: a review
    ACM Comput. Surv., Vol. 31, No. 3. (September 1999), pp. 264-323.
    by AK Jain, MN Murty, PJ Flynn
    posted to clustering review by mkurc on 2007-10-08 07:25:18 as **
  • Markov chain Monte Carlo maximum likelihood.
    (1991), pp. 156-163.
    by CJ Geyer
    posted to monte_carlo replica_method by mkurc on 2007-10-08 07:25:18 as **
  • Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation.
    Proc Natl Acad Sci U S A, Vol. 101, No. 43. (October 2004), pp. 15346-15351.
    by B Qian, AR Ortiz, D Baker
    posted to comparative_modeling by mkurc on 2007-10-08 07:25:18 as **
  • Wurst: a protein threading server with a structural scoring function, sequence profiles and optimized substitution matrices.
    Nucleic Acids Res, Vol. 32, No. Web Server issue. (July 2004)
    by AE Torda, JB Procter, T Huber
    posted to threading by mkurc on 2007-10-08 07:25:18 as **
  • Perspectives in protein-fold recognition.
    Curr Opin Struct Biol, Vol. 7, No. 2. (April 1997), pp. 200-205.
    by AE Torda
    posted to review threading by mkurc on 2007-10-08 07:25:18 as **
  • Protein structure prediction and structural genomics.
    Science, Vol. 294, No. 5540. (October 2001), pp. 93-96.
    by D Baker, A Sali
    posted to comparative_modeling review by mkurc on 2007-10-08 07:25:18 as **
  • Basic local alignment search tool.
    J Mol Biol, Vol. 215, No. 3. (October 1990), pp. 403-410.
    by SF Altschul, W Gish, W Miller, EW Myers, DJ Lipman
    posted to sequence_alignment by mkurc on 2007-10-08 07:25:18 as **
  • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
    Nucleic Acids Res, Vol. 25, No. 17. (September 1997), pp. 3389-3402.
    by SF Altschul, TL Madden, AA Schäffer, J Zhang, Z Zhang, W Miller, DJ Lipman
    posted to sequence_alignment by mkurc on 2007-10-08 07:25:18 as **
  • ClusPro: a fully automated algorithm for protein-protein docking.
    Nucleic Acids Res, Vol. 32, No. Web Server issue. (July 2004), pp. 96-99.
    by SR Comeau, DW Gatchell, S Vajda, CJ Camacho
    posted to clustering docking by mkurc on 2007-10-08 07:25:18 as **
  • Free energy landscapes of encounter complexes in protein-protein association.
    Biophys J, Vol. 76, No. 3. (March 1999), pp. 1166-1178.
    by CJ Camacho, Z Weng, S Vajda, C Delisi
    posted to docking free_energy by mkurc on 2007-10-08 07:25:18 as **
  • Integrative database analysis in structural genomics.
    Nat Struct Biol, Vol. 7 Suppl (November 2000), pp. 960-963.
    by M Gerstein
    posted to databases review by mkurc on 2007-10-08 07:25:18 as **
  • Correlated mutations and residue contacts in proteins.
    Proteins, Vol. 18, No. 4. (April 1994), pp. 309-317.
    by U Göbel, C Sander, R Schneider, A Valencia
    posted to comparative_modeling contact_map sequence_alignment by mkurc on 2007-10-08 07:25:18 as **
  • Tech.Sight. Industrializing structural biology.
    Science, Vol. 293, No. 5529. (July 2001), pp. 519-520.
    by RC Stevens, IA Wilson
    posted to experimental review structural_genomics by mkurc on 2007-10-08 07:25:18 as **
    • NB: Du kan sitere denne siden som: http://www.citeulike.org/user/mkurc

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