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mijam's library [60 articles]

最近录入 mijam's 文献库.
  • Sampling Realistic Protein Conformations Using Local Structural Bias
    PLoS Computational Biology, Vol. 2, No. 9. (1 September 2006), e131.
    by Thomas Hamelryck, John T Kent, Anders Krogh
    posted to no-tag by mijam on 2008-07-05 10:13:30 as ** along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
  • A generative, probabilistic model of local protein structure
    Proceedings of the National Academy of Sciences, Vol. 105, No. 26. (1 July 2008), pp. 8932-8937.
    by Wouter Boomsma, Kanti V Mardia, Charles C Taylor, Jesper Ferkinghoff-Borg, Anders Krogh, Thomas Hamelryck
    posted to no-tag by mijam on 2008-07-05 09:51:48 as ** along with 3 people apaydin zwang biehl
  • Mechanisms of membrane fusion: disparate players and common principles
    Nature Reviews Molecular Cell Biology, Vol. 9, No. 7. (21 May 2008), pp. 543-556.
    by Sascha Martens, Harvey T Mcmahon
    posted to no-tag by mijam on 2008-06-29 19:21:59 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 thesis by mijam on 2008-05-08 09:48:44 as ** along with 5 people mcbla vavi dgront rabio sekmi
  • Distance Geometry and Molecular Conformation (Chemometrics Series)
    by GM Crippen, TF Havel
    posted to thesis by mijam on 2008-03-25 13:18:40 as **
  • Cluster Computing for Determining Three-Dimensional Protein Structure
    The Journal of Supercomputing, Vol. 34, No. 3. (December 2005), pp. 243-271.
    by Paulius Micikevicius, Narsingh Deo
    posted to thesis by mijam on 2008-03-21 10:59:22 as **
  • Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
    Nucleic Acids Res, Vol. 25, No. 17. (1 September 1997), pp. 3389-3402.
    by SF Altschul, TL Madden, AA Schäffer, J Zhang, Z Zhang, W Miller, DJ Lipman
    posted to thesis by mijam on 2008-03-20 17:45:22 as ** along with 44 people and 4 groups CharlesM marti granujilla newton1234 david_parsons edvin bandrewfox mariakmejia knaseanka setar iakes miguel kaarsinogen bjorns bicko jmeppley chad_davis balajis nuke2005 eweaver indigoviolet dullhunk robert dgront happy_manatee caporaso treangen kengg manzanita leelarcombe CitoJam jdelcampo aengisch rabio massivemayhem mirzazadeh azazello sujaikumar beatrizfernandez GustavoLacerda siebertm adijr viktor21614 grottenolm EisenLab biomedical-nlp Microbial-Ecology Plantandetc
  • The theory and practice of distance geometry
    Bulletin of Mathematical Biology, Vol. 45, No. 5. (1983), pp. 665-720.
    by Timothy Havel, Irwin Kuntz, Gordon Crippen
    posted to thesis by mijam on 2008-03-20 16:56:30 as ** along with 1 person jlh64
  • 3D-Jury: a simple approach to improve protein structure predictions.
    Bioinformatics, Vol. 19, No. 8. (22 May 2003), pp. 1015-1018.
    by K Ginalski, A Elofsson, D Fischer, L Rychlewski
    posted to thesis by mijam on 2008-03-02 13:50:25 as ** along with 3 people karbak dgront schuylrp
  • 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 rosetta by mijam on 2008-02-23 23:44:32 as ** along with 7 people and 2 groups joule ana jwm vavi wouterboomsma j3xucite hmk structural_bioinformatics Bioinformatics
  • De novo prediction of three-dimensional structures for major protein families.
    J Mol Biol, Vol. 322, No. 1. (6 September 2002), pp. 65-78.
    by R Bonneau, CE Strauss, CA Rohl, D Chivian, P Bradley, L Malmström, T Robertson, D Baker
    posted to rosetta by mijam on 2008-02-23 23:44:15 as ** along with 1 person jwm
  • Fast procedure for reconstruction of full-atom protein models from reduced representations
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA.
    by Piotr Rotkiewicz, Jeffrey Skolnick
    posted to thesis by mijam on 2008-02-22 15:17:03 as read along with 1 person middledomain
  • A composite score for predicting errors in protein structure models.
    Protein Sci, Vol. 15, No. 7. (July 2006), pp. 1653-1666.
    by D Eramian, MY Shen, D Devos, F Melo, A Sali, MA Marti-Renom
    posted to no-tag by mijam on 2008-01-30 20:46:32 as ** along with 4 people j3xucite dimka vavi wouterboomsma
  • Universal model for [alpha]-helix and [beta]-sheet structures in protein
    Physica A: Statistical Mechanics and its Applications, Vol. 321, No. 1-2. (1 April 2003), pp. 181-188.
    by Jeff Z Chen, Hideo Imamura
    posted to h-bond by mijam on 2008-01-27 15:35:22 as **
  • Hydrogen Bonds, Hydrophobicity Forces and the Character of the Collapse Transition
    Journal of Biological Physics, Vol. 27, No. 2. (1 June 2001), pp. 169-179.
    by A Irbäck, F Sjunnesson, S Wallin
    posted to h-bond by mijam on 2008-01-27 14:31:01 as **
  • Cyclic coordinate descent: A robotics algorithm for protein loop closure.
    Protein Sci, Vol. 12, No. 5. (May 2003), pp. 963-972.
    by AA Canutescu, RL Dunbrack
    posted to no-tag by mijam on 2008-01-27 12:39:31 as ** along with 4 people and 1 group vavi yongzhao j3xucite dgront TSRI_MGL
  • Nonparametric relevance-shifted multiple testing procedures for the analysis of high-dimensional multivariate data with small sample sizes
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Cornelia Froemke, Ludwig Hothorn, Siegfried Kropf
    posted to no-tag by mijam on 2008-01-27 12:35:37 as **** along with 2 people jyuh shigepong
  • Protein Stucture and Function (Primers in Biology)
    by Gregory A Petsko, Dagmar Ringe
    posted to no-tag by mijam on 2008-01-25 16:19:26 as **
  • Scaling Concepts in Polymer Physics
    (31 January 1980)
    by Pierre-Giles De Gennes
    posted to no-tag by mijam on 2008-01-25 16:10:32 as ** along with 3 people dherkova kaz229 sjanusz
  • Large-amplitude nonlinear motions in proteins
    Physical Review Letters, Vol. 68, No. 17. (27 April 1992), 2696.
    by Angel E García
    posted to no-tag by mijam on 2008-01-18 23:26:13 as *** along with 1 person pgasper
  • Web Development with Java: Using Hibernate, JSPs and Servlets
    (01 October 2007)
    by Tim Downey
    posted to no-tag by mijam on 2008-01-18 17:22:43 as **
  • Dynamic personalities of proteins
    Nature, Vol. 450, No. 7172. (12 December 2007), pp. 964-972.
    by Katherine Henzler-Wildman, Dorothee Kern
    posted to no-tag by mijam on 2008-01-14 19:16:21 as ** along with 11 people and 1 group GeeSharpMinor higueruelo chad_davis allmensch choonpeng rsantana cjeans sobolevnrm wilbur kjell phoenixzxl baker-group
  • Differentiable, multi-dimensional, knowledge-based energy terms for torsion angle probabilities and propensities
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by El-Ad D Amir, Nir Kalisman, Chen Keasar
    posted to no-tag by mijam on 2008-01-11 09:23:40 as read along with 1 person dgront
  • A contact map matching approach to protein structure similarity analysis.
    Genet Mol Res, Vol. 5, No. 2. (2006), pp. 284-308.
    by RC de Melo, CE Lopes, FA Fernandes, CH da Silveira, MM Santoro, RL Carceroni, W Meira, Ade A Araújo
    posted to contact map by mijam on 2008-01-09 12:46:03 as ** along with 2 people vavi dgront
  • Recovery of protein structure from contact maps.
    Fold Des, Vol. 2, No. 5. (1997), pp. 295-306.
    by M Vendruscolo, E Kussell, E Domany
    posted to thesis by mijam on 2008-01-09 12:45:19 as ***** along with 3 people vavi dgront babakap
  • Introduction To Monte Carlo Algorithms
    (14 Nov 1998)
    by Werner Krauth
    edited by J Kertesz, Kondor
    posted to no-tag by mijam on 2008-01-09 12:36:42 as ** along with 10 people tertel tharris ansobol stephensalomons penka dgront gane5h rabio ujarmatokyaniv softsimu
  • The penultimate rotamer library
    Proteins: Structure, Function, and Genetics, Vol. 40, No. 3. (2000), pp. 389-408.
    by Simon C Lovell, Michael J Word, Jane S Richardson, David C Richardson
    posted to rotamer by mijam on 2008-01-08 13:23:02 as ** along with 2 people dgront kazemi
  • Rotamer libraries in the 21st century.
    Curr Opin Struct Biol, Vol. 12, No. 4. (August 2002), pp. 431-440.
    by RL Dunbrack
    posted to rotamer by mijam on 2008-01-08 12:46:45 as read along with 8 people and 1 group jwm yongzhao dgront blackbart kazemi rsantana medic0747 LamBras TSRI_MGL
  • Folding a protein in the computer: reality or hope?
    Structure (Camb), Vol. 13, No. 4. (April 2005), pp. 497-498.
    by AE Garcia, JN Onuchic
    posted to no-tag by mijam on 2008-01-07 17:42:42 as **** along with 2 people fjc1 owarburg
  • Protein folding mediated by solvation: Water expulsion and formation of the hydrophobic core occur after the structural collapse
    Proceedings of the National Academy of Sciences, Vol. 99, No. 2. (22 January 2002), pp. 685-690.
    by Margaret S Cheung, Angel E Garcia, Jose N Onuchic
    posted to no-tag by mijam on 2008-01-07 17:40:42 as **
  • Folding a protein in a computer: an atomic description of the folding/unfolding of protein A.
    Proc Natl Acad Sci U S A, Vol. 100, No. 24. (25 November 2003), pp. 13898-13903.
    by AE García, JN Onuchic
    posted to no-tag by mijam on 2008-01-07 17:35:17 as **** along with 1 person balicea
  • Radical performance enhancements for combinatorial optimization algorithms based on the dead-end elimination theorem
    Journal of Computational Chemistry, Vol. 19, No. 13. (1998), pp. 1505-1514.
    by Benjamin D Gordon, Stephen L Mayo
    posted to dee by mijam on 2008-01-07 10:29:46 as ****
  • Protein Design is NP-hard
    Protein Eng., Vol. 15, No. 10. (1 October 2002), pp. 779-782.
    by Niles A Pierce, Erik Winfree
    posted to dee by mijam on 2008-01-06 22:53:21 as ** along with 6 people ansobol ima gane5h bluvsh1 kray iantunbridge
  • 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 mijam on 2008-01-06 14:00:36 as ** along with 5 people carlk dgront bluvsh1 kazemi rsantana
  • 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 by mijam on 2008-01-06 13:02:07 as ** along with 2 people dgront bluvsh1
  • From coarse-grain to all-atom: Toward multiscale analysis of protein landscapes
    Proteins: Structure, Function, and Bioinformatics, Vol. 68, No. 3. (2007), pp. 646-661.
    by Allison P Heath, Lydia E Kavraki, Cecilia Clementi
    posted to no-tag by mijam on 2008-01-04 08:18:02 as ** along with 1 person aqeel
  • Accurate reconstruction of all-atom protein representations from side-chain-based low-resolution models
    Proteins: Structure, Function, and Genetics, Vol. 41, No. 1. (2000), pp. 86-97.
    by Michael Feig, Piotr Rotkiewicz, Andrzej Kolinski, Jeffrey Skolnick, Charles L Brooks
    posted to thesis by mijam on 2008-01-04 08:16:51 as **
  • Structure validation by Calpha geometry: phi,psi and Cbeta deviation.
    Proteins, Vol. 50, No. 3. (15 February 2003), pp. 437-450.
    by SC Lovell, IW Davis, WB Arendall, PI de Bakker, JM Word, MG Prisant, JS Richardson, DC Richardson
    posted to thesis by mijam on 2008-01-04 08:07:30 as read along with 7 people and 2 groups pavanghatty aqeel jwm robert dgront xiaobeizhao martainn Radiation_Damage Stressosome
  • Evaluation of coarse grained models for hydrogen bonds in proteins.
    J Comput Chem, Vol. 28, No. 7. (13 May 2007), pp. 1187-1199.
    by David De Sancho, Antonio Rey
    posted to no-tag by mijam on 2008-01-04 08:04:52 as ** along with 2 people dgront choonpeng
  • Prediction of protein conformational freedom from distance constraints
    Proteins: Structure, Function, and Genetics, Vol. 29, No. 2. (7 December 1998), pp. 240-251.
    by BL de Groot, DMF van Aalten, RM Scheek, A Amadei, G Vriend, HJC Berendsen
    posted to thesis by mijam on 2008-01-03 20:15:21 as read along with 5 people and 2 groups aqeel yhu dgront rabio superpyrin TSRI_MGL Conformational_disease
  • HCPM-program for hierarchical clustering of protein models
    Bioinformatics, Vol. 21, No. 14. (15 July 2005), pp. 3179-3180.
    by Dominik Gront, Andrzej Kolinski
    posted to thesis by mijam on 2008-01-03 20:05:20 as **
  • BioShella package of tools for structural biology computations
    Bioinformatics, Vol. 22, No. 5. (1 March 2006), pp. 621-622.
    by Dominik Gront, Andrzej Kolinski
    posted to thesis by mijam on 2008-01-03 20:05:11 as read along with 5 people dimka bicko chad_davis dgront rabio
  • Backbone building from quadrilaterals: A fast and accurate algorithm for protein backbone reconstruction from alpha carbon coordinates.
    J Comput Chem, Vol. 28, No. 9. (15 July 2007), pp. 1593-1597.
    by D Gront, S Kmiecik, A Kolinski
    posted to thesis by mijam on 2008-01-03 20:02:54 as read along with 4 people wouterboomsma j3xucite dgront sekmi
  • Protein Threading
    by Andrew E Torda
    posted to no-tag by mijam on 2008-01-03 19:56:49 as ** along with 1 person rabio
  • Conformational splitting: A more powerful criterion for dead-end elimination
    Journal of Computational Chemistry, Vol. 21, No. 11. (2000), pp. 999-1009.
    by NA Pierce, JA Spriet, J Desmet, SL Mayo
    posted to dee by mijam on 2008-01-03 19:31:04 as *****
  • On updating torsion angles of molecular conformations.
    J Chem Inf Model, Vol. 46, No. 1. (b 2006), pp. 438-444.
    by V Choi
    posted to no-tag by mijam on 2008-01-03 09:18:38 as **** along with 2 people BragilMassoud apaydin
  • A distance geometry heuristic for expanding the range of geometries sampled during conformational search.
    J Comput Chem (10 October 2006)
    by Sergei Izrailev, Fangqiang Zhu, Dimitris K K Agrafiotis
    posted to no-tag by mijam on 2008-01-03 09:18:31 as **** along with 2 people BragilMassoud superpyrin
  • Distance geometry and related methods for protein structure determination from NMR data.
    Q Rev Biophys, Vol. 19, No. 3-4. (May 1987), pp. 115-157.
    by W Braun
    posted to no-tag by mijam on 2008-01-03 09:18:23 as **** along with 1 person and 2 groups barry structural_bioinformatics Bioinformatics
  • Bioinformatics: Sequence and Genome Analysis
    (30 September 2004)
    by David W Mount
    posted to no-tag by mijam on 2008-01-02 16:37:57 as read along with 4 people and 2 groups ep161302 ana aalibes jofiel structural_bioinformatics Bioinformatics
  • Python Scripting for Computational Science (Texts in Computational Science and Engineering)
    (21 December 2005)
    by Hans P Langtangen
    posted to no-tag by mijam on 2008-01-02 15:39:21 as ** along with 1 person winschel
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