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cdeane library [71 articles]

Статьи, недавно добавленные в библиотеку cdeane .
  • A Microtubule Interactome: Complexes with Roles in Cell Cycle and Mitosis
    PLoS Biology, Vol. 6, No. 4. (1 April 2008), e98.
    by Julian R Hughes, Ana M Meireles, Katherine H Fisher, Angel Garcia, Philip R Antrobus, Alan Wainman, Nicole Zitzmann, Charlotte Deane, Hiroyuki Ohkura, James G Wakefield
    posted to networks microtubule interactions by cdeane on 2008-04-23 14:19:22 as ** along with 1 person and 1 group barry Bioinformatics
  • Integrating physical and genetic maps: from genomes to interaction networks
    Nature Reviews Genetics, Vol. 8, No. 9., pp. 699-710.
    by Andreas Beyer, Sourav Bandyopadhyay, Trey Ideker
    posted to networks motifs interactions by cdeane on 2008-04-23 14:15:05 as *** along with 9 people and 3 groups jyuh balicea dchughes sebastien_vigneau grahamc joepickrell zwang shikin lh1 Bioinformatics G4ID Genetics-of-Gambling
  • Modeling cellular machinery through biological network comparison
    Nature Biotechnology, Vol. 24, No. 4. (06 April 2006), pp. 427-433.
    by Roded Sharan, Trey Ideker
    posted to networks motifs interactions by cdeane on 2008-04-23 14:10:54 as *** along with 15 people and 2 groups tmmurali kuhn tuck yas balajis wnpx ma_ko gurkanbebek koller gcalda grahamc massivemayhem karfunkel mingzhi vietanh0 T_lab ParkinsonLab_at_MaRS
  • A model study of protein nascent chain and cotranslational folding using hydrophobic-polar residues.
    Proteins (6 August 2007)
    by Hsiao-Mei M Lu, Jie Liang
    posted to cotranslation folding lattice by cdeane on 2008-04-22 11:38:54 as ** along with 1 person and 1 group saunders OPIG
  • Lattice simulations of cotranslational folding of single domain proteins.
    Proteins (5 September 2007)
    by Peiyu Wang, Dmitri K K Klimov
    posted to cotranslation folding lattice by cdeane on 2008-04-22 11:38:16 as ** along with 1 person saunders
  • Discrimination between Distant Homologs and Structural Analogs: Lessons from Manually Constructed, Reliable Data Sets
    Journal of Molecular Biology, Vol. 377, No. 4. (4 April 2008), pp. 1265-1278.
    by Hua Cheng, Bong-Hyun Kim, Nick V Grishin
    posted to fold folding by cdeane on 2008-04-22 11:34:53 as *** along with 1 person and 1 group barry structural_bioinformatics
  • Estimating the significance of sequence order in protein secondary structure and prediction.
    Bioinformatics, Vol. 16, No. 11. (November 2000), pp. 978-987.
    by J Park, S Dietmann, A Heger, L Holm
    posted to cotranslation modelling secondary structure by cdeane on 2008-04-01 14:57:29 as read
  • Selective Constraints, Amino Acid Composition, and the Rate of Protein Evolution
    Mol Biol Evol, Vol. 17, No. 4. (1 April 2000), pp. 656-664.
    by Nicolas J Tourasse, Wen-Hsiung Li
    posted to folding membrane modelling by cdeane on 2008-03-13 11:37:37 as read along with 3 people and 1 group penka RamuAnandakrishnan sebk Nie
  • Remote homology detection of integral membrane proteins using conserved sequence features
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Andreas Bernsel, Håkan Viklund, Arne Elofsson
    posted to hmm membrane modelling structure by cdeane on 2008-03-13 11:33:56 as read
  • Accurate prediction of protein-protein interactions from sequence alignments using a Bayesian method
    Mol Syst Biol, Vol. 4 (12 February 2008)
    by Lukas Burger, Erik van Nimwegen
    posted to interactions by cdeane on 2008-02-20 06:22:24 as *** along with 9 people kengg grahamc laughcry zwang biomcgary cabbagezs roys gjuggler phoenixzxl
  • Loopholes and missing links in protein modeling.
    Protein Sci, Vol. 16, No. 9. (September 2007), pp. 1999-2012.
    by KA Rossi, CA Weigelt, A Nayeem, SR Krystek
    posted to loop modelling by cdeane on 2008-02-20 06:19:59 as ****
  • Conformations of co-translational folding intermediates.
    Protein Pept Lett, Vol. 12, No. 2. (February 2005), pp. 189-195.
    by MS Evans, TF Clarke, PL Clark
    posted to cotranslation folding invivo by cdeane on 2008-02-06 00:39:45 as read
  • Empirical potential function for simplified protein models: Combining contact and local sequence-structure descriptors.
    Proteins (13 February 2006)
    by Jinfeng Zhang, Rong Chen, Jie Liang
    posted to cotranslation folding potential simplemodel by cdeane on 2008-02-06 00:23:05 as read along with 1 person wouterboomsma
  • An assessment of the uses of homologous interactions
    Bioinformatics (27 November 2007), btm576.
    by Ramazan Saeed, Charlotte Deane
    posted to interactions by cdeane on 2008-01-18 18:01:16 as read along with 6 people chad_davis grahamc cjeans laughcry mingzhi Pao-Yang
  • From the Cover: Evolutionary genomics reveals conserved structural determinants of signaling and adaptation in microbial chemoreceptors
    PNAS, Vol. 104, No. 8. (20 February 2007), pp. 2885-2890.
    by Roger P Alexander, Igor B Zhulin
    posted to chemotaxis interactions by cdeane on 2008-01-15 14:23:05 as read along with 2 people chrn RebeccaHamer
  • Bio3d: an R package for the comparative analysis of protein structures.
    Bioinformatics (29 August 2006)
    by Barry J J Grant, Ana P C P Rodrigues, Karim M M Elsawy, J Andrew A McCammon, Leo S D S Caves
    posted to comparison r structure by cdeane on 2008-01-09 15:56:21 as ** along with 6 people and 2 groups ana barry Einat plofje krishnaJCSG insectopalo structural_bioinformatics Bioinformatics
  • Evidence for dynamically organized modularity in the yeast protein-protein interaction network
    Nature, Vol. 430, No. 6995. (01 July 2004), pp. 88-93.
    by Jing-Dong J Han, Nicolas Bertin, Tong Hao, Debra S Goldberg, Gabriel F Berriz, Lan V Zhang, Denis Dupuy, Albertha JM Walhout, Michael E Cusick, Frederick P Roth, Marc Vidal
    posted to date interactions party by cdeane on 2008-01-09 14:15:44 as read along with 17 people and 1 group dragonrez lfriedl balajis yoh j3xucite koller mikaelhuss ruvido gcalda grahamc iris_2001 lpfernandes winterschlaefer Evangelia shung phoenixzxl stefanoallesina kdl
  • Hubs with network motifs organize modularity dynamically in the protein-protein interaction network of yeast.
    PLoS ONE, Vol. 2, No. 11. (2007)
    by G Jin, S Zhang, XS Zhang, L Chen
    posted to date interactions party by cdeane on 2008-01-09 14:15:15 as *** along with 2 people lpfernandes cabbagezs
  • Relating three-dimensional structures to protein networks provides evolutionary insights.
    Science, Vol. 314, No. 5807. (22 December 2006), pp. 1938-1941.
    by PM Kim, LJ Lu, Y Xia, MB Gerstein
    posted to interactions sin structure by cdeane on 2008-01-09 14:14:34 as read along with 14 people and 2 groups bicko lfriedl chad_davis Einat tny choonpeng timflutre grahamc ramensky massivemayhem efge lpfernandes Pao-Yang phoenixzxl structural_bioinformatics kdl
  • Protein stability promotes evolvability
    PNAS, Vol. 103, No. 15. (11 April 2006), pp. 5869-5874.
    by Jesse D Bloom, Sy T Labthavikul, Christopher R Otey, Frances H Arnold
    posted to folding stability by cdeane on 2007-11-22 12:35:59 as *** along with 10 people and 2 groups rklancer Retchless lna Einat penka cmm redelings BioNica Cristiano wilbur structural_bioinformatics FAB-lab
  • Evolution favors protein mutational robustness in sufficiently large populations
    BMC Biology, Vol. 5, No. 1. (2007)
    by Jesse Bloom, Zhongyi Lu, David Chen, Alpan Raval, Ophelia Venturelli, Frances Arnold
    posted to folding stability by cdeane on 2007-11-22 12:34:33 as **** along with 1 person Pao-Yang
  • Rigorous performance evaluation in protein structure modelling and implications for computational biology.
    Philos Trans R Soc Lond B Biol Sci, Vol. 361, No. 1467. (29 March 2006), pp. 453-458.
    by J Moult
    posted to casp modelling by cdeane on 2007-11-22 09:47:29 as ** along with 2 people chad_davis wouterboomsma
  • A topologically related singularity suggests a maximum preferred size for protein domains
    Proteins: Structure, Function, and Bioinformatics, Vol. 66, No. 3. (2007), pp. 621-629.
    by Joseph P Zbilut, Gek H Chua, Arun Krishnan, Cecilia Bossa, Kristian Rother, Charles L Webber, Alessandro Giuliani
    posted to folding modelling by cdeane on 2007-11-22 09:45:41 as *** along with 2 people choonpeng Pao-Yang
  • The protein folding problem: when will it be solved?
    Curr Opin Struct Biol (13 June 2007)
    by Ken A A Dill, S Banu B Ozkan, Thomas R R Weikl, John D D Chodera, Vincent A A Voelz
    posted to folding by cdeane on 2007-11-22 09:40:23 as ***** along with 6 people wouterboomsma cat_worth cactus Jporci kalicuta sebk
  • Assessing model accuracy using the homology modeling automatically software.
    Proteins (19 July 2007)
    by Aneerban Bhattacharya, Zeba Wunderlich, Daniel Monleon, Roberto Tejero, Gaetano T T Montelione
    posted to model modelling potential by cdeane on 2007-11-22 09:34:30 as *** along with 1 person choonpeng
  • Protein folding by zipping and assembly.
    Proc Natl Acad Sci U S A, Vol. 104, No. 29. (17 July 2007), pp. 11987-11992.
    by SB Ozkan, GA Wu, JD Chodera, KA Dill
    posted to folding md time by cdeane on 2007-11-21 15:54:16 as *** along with 2 people aqeel wouterboomsma
  • Folding time predictions from all-atom replica exchange simulations.
    J Mol Biol, Vol. 372, No. 3. (21 September 2007), pp. 756-763.
    by S Yang, JN Onuchic, AE García, H Levine
    posted to folding time by cdeane on 2007-11-21 15:53:23 as **
  • QMEAN: A comprehensive scoring function for model quality assessment.
    Proteins (11 October 2007)
    by Pascal Benkert, Silvio C E C Tosatto, Dietmar Schomburg
    posted to model potential by cdeane on 2007-11-21 15:52:28 as ***
  • An efficient conformational sampling method for homology modeling.
    Proteins (11 October 2007)
    by Rongsheng Han, Alejandra Leo-Macias, Daniel Zerbino, Ugo Bastolla, Bruno Contreras-Moreira, Angel R R Ortiz
    posted to md montecarlo teaching by cdeane on 2007-11-21 15:51:49 as ** along with 4 people dimka choonpeng insectopalo sebk
  • Protein stability imposes limits on organism complexity and speed of molecular evolution
    Proceedings of the National Academy of Sciences, Vol. 104, No. 41. (9 October 2007), pp. 16152-16157.
    by Konstantin B Zeldovich, Peiqiu Chen, Eugene I Shakhnovich
    posted to evolution stability by cdeane on 2007-11-21 15:27:38 as ** along with 4 people operon penka cjeans cactus
  • An introduction to ROC analysis
    Pattern Recognition Letters, Vol. 27, No. 8. (June 2006), pp. 861-874.
    by Tom Fawcett
    posted to roc by cdeane on 2007-11-21 15:26:24 as ** along with 19 people and 7 groups AbnerCYH ldietz vavi dquest sdvillal xiaoyan2006 dwf camu schlauchi vmoa drivard nklee imrchen kmdaily gsiwo tgyork idonaldson napvasconcelos haiyeong Skill-Inference Bioinformatics Crypto VT_DLRL Randomness LIVIA BergmanLab
  • Saturating representation of loop conformational fragments in structure databanks
    BMC Structural Biology, Vol. 6 (04 July 2006), 15.
    by Narcis Fernandez-Fuentes, Andras Fiser
    posted to loop model modelling by cdeane on 2007-11-21 15:19:45 as *** along with 2 people iakes vavi
  • ArchPRED: a template based loop structure prediction server.
    Nucleic Acids Res, Vol. 34, No. Web Server issue. (1 July 2006)
    by N Fernandez-Fuentes, J Zhai, A Fiser
    posted to loop model modelling by cdeane on 2007-11-21 15:19:25 as *** along with 2 people vavi eckart_bindewald
  • Long loop prediction using the protein local optimization program.
    Proteins (22 August 2006)
    by Kai Zhu, David L L Pincus, Suwen Zhao, Richard A A Friesner
    posted to loop model modelling by cdeane on 2007-11-21 15:18:56 as *** along with 1 person vavi
  • Statistical potential for assessment and prediction of protein structures.
    Protein Sci, Vol. 15, No. 11. (November 2006), pp. 2507-2524.
    by MY Shen, A Sali
    posted to model potential by cdeane on 2007-11-21 15:18:29 as ** along with 3 people dimka wouterboomsma j3xucite
  • Scoring function accuracy for membrane protein structure prediction.
    Proteins, Vol. 68, No. 1. (1 July 2007), pp. 67-75.
    by C Gao, HA Stern
    posted to membrane model by cdeane on 2007-11-21 15:17:20 as *** along with 1 person sebk
  • Prediction of protein loop geometries in solution.
    Proteins, Vol. 69, No. 1. (1 October 2007), pp. 69-74.
    by CS Rapp, T Strauss, A Nederveen, G Fuentes
    posted to loop model by cdeane on 2007-11-21 15:16:44 as **
  • Loop modeling: sampling, filtering, and scoring.
    Proteins (29 August 2007)
    by Cinque S S Soto, Marc Fasnacht, Jiang Zhu, Lucy Forrest, Barry Honig
    posted to loop model by cdeane on 2007-11-21 15:16:03 as ***** along with 1 group OPIG
  • Modeling protein loops with knowledge-based prediction of sequence-structure alignment.
    Bioinformatics, Vol. 23, No. 21. (1 November 2007), pp. 2836-2842.
    by HP Peng, AS Yang
    posted to loop model by cdeane on 2007-11-21 15:15:32 as **
  • Exploring the extremes of sequence/structure space with ensemble fold recognition in the program Phyre.
    Proteins (17 September 2007)
    by Riccardo M M Bennett-Lovsey, Alex D D Herbert, Michael J E J Sternberg, Lawrence A A Kelley
    posted to loop modelling by cdeane on 2007-11-21 15:14:15 as *** along with 1 person j3xucite
  • A molecular model for the origin of protein translation in an RNA world.
    J Theor Biol, Vol. 243, No. 3. (7 December 2006), pp. 393-406.
    by WR Taylor
    posted to fold rna by cdeane on 2007-11-21 15:12:53 as ** along with 1 group OPIG
  • Topological accessibility shows a distinct asymmetry in the folds of betaalpha proteins.
    FEBS Lett, Vol. 580, No. 22. (2 October 2006), pp. 5263-5267.
    by WR Taylor
    posted to cotranslation fold by cdeane on 2007-11-21 15:12:20 as ***
  • Protein knots and fold complexity: some new twists.
    Comput Biol Chem, Vol. 31, No. 3. (June 2007), pp. 151-162.
    by WR Taylor
    posted to fold knots by cdeane on 2007-11-21 15:10:52 as **
  • Evolutionary transitions in protein fold space
    Current Opinion in Structural Biology, Vol. 17, No. 3. (June 2007), pp. 354-361.
    by William R Taylor
    posted to evolution fold by cdeane on 2007-11-21 15:10:22 as **** along with 3 people cat_worth cactus Jporci
  • Using scores derived from statistical coupling analysis to distinguish correct and incorrect folds in de-novo protein structure prediction
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Gail J Bartlett, William R Taylor
    posted to decoys by cdeane on 2007-11-21 15:09:50 as ** along with 1 person RamuAnandakrishnan
  • Evolution of functionality in lattice proteins.
    J Mol Graph Model, Vol. 19, No. 1. (2001), pp. 150-156.
    by PD Williams, DD Pollock, RA Goldstein
    posted to lattice model by cdeane on 2007-11-21 15:08:30 as **
  • Why are proteins marginally stable?
    Proteins, Vol. 46, No. 1. (1 January 2002), pp. 105-109.
    by DM Taverna, RA Goldstein
    posted to stability by cdeane on 2007-11-21 15:07:43 as **
  • Why are proteins so robust to site mutations?
    J Mol Biol, Vol. 315, No. 3. (18 January 2002), pp. 479-484.
    by DM Taverna, RA Goldstein
    posted to lattice model stability by cdeane on 2007-11-21 15:07:11 as ** along with 2 people kaarsinogen eckart_bindewald
  • 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 stability by cdeane on 2007-11-21 15:05:03 as ** along with 2 people choonpeng gisle
  • Protein three-dimensional structural databases: domains, structurally aligned homologues and superfamilies.
    Acta Crystallogr D Biol Crystallogr, Vol. 54, No. Pt 6 Pt 1. (1 November 1998), pp. 1168-1177.
    by R Sowdhamini, DF Burke, C Deane, JF Huang, K Mizuguchi, HA Nagarajaram, JP Overington, N Srinivasan, RE Steward, TL Blundell
    posted to no-tag by cdeane on 2007-11-21 15:04:13 as read along with 1 person sebk
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