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de chad_davis library [270 articles]

Articles dernièrement stockés dans la bibliothèque de chad_davis ordered by to_read.
  • Targeting and tinkering with interaction networks.
    Nature chemical biology, Vol. 4, No. 11. (20 October 2008), pp. 666-673.
    by Robert B B Russell, Patrick Aloy
    posted to review proj_assembly ppi networks embl by chad_davis on 2008-10-27 11:58:57 as ***** along with 1 person zwang
  • Homology modelling of protein-protein complexes: a simple method and its possibilities and limitations
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Guillaume Launay, Thomas Simonson
    posted to structure proj_assembly modelling complexes binding algorithm by chad_davis on 2008-10-10 07:36:29 as ***** along with 1 person lptolik
  • Protein Structure Fitting and Refinement Guided by Cryo-EM Density
    Structure, Vol. 16, No. 2. (12 February 2008), pp. 295-307.
    by Maya Topf, Keren Lasker, Ben Webb, Haim Wolfson, Wah Chiu, Andrej Sali
    posted to structure proj_assembly modelling data_integration complexes algorithm by chad_davis on 2008-10-08 16:10:16 as *****
  • Structural characterization of assemblies from overall shape and subcomplex compositions.
    Structure, Vol. 13, No. 3. (March 2005), pp. 435-445.
    by F Alber, MF Kim, A Sali
    posted to structure proj_assembly ppi modelling data_integration complexes binding algorithm by chad_davis on 2008-10-08 15:51:24 as ***** along with 1 person faion
  • notes PRISM: protein interactions by structural matching.
    Nucleic Acids Res, Vol. 33, No. Web Server issue. (1 July 2005)
    by U Ogmen, O Keskin, AS Aytuna, R Nussinov, A Gursoy
    posted to service structure proj_interprets proj_assembly ppi binding algorithm by chad_davis on 2008-10-07 10:15:00 as ***** along with 4 people apaydin bicko j3xucite henschel
  • United we stand: combining structural methods
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Nathan P Cowieson, Bostjan Kobe, Jennifer L Martin
    posted to structure review proj_assembly data_integration complexes by chad_davis on 2008-09-13 10:54:58 as ***** along with 1 person paulschlesinger
  • PPiClust: EFFICIENT CLUSTERING OF 3D PROTEIN-PROTEIN INTERACTION INTERFACES.
    Journal of bioinformatics and computational biology, Vol. 6, No. 3. (June 2008), pp. 415-433.
    by Z Aung, SH Tan, SK Ng, KL Tan
    posted to algorithm clustering ppi proj_assembly proj_interprets structure by chad_davis on 2008-08-26 18:15:46 as ***** along with 1 person bicko
  • notes MotifVoter: a novel ensemble method for fine-grained integration of generic motif finders.
    Bioinformatics (Oxford, England) (12 August 2008)
    by Edward Wijaya, Siu, Ngo, Rajaraman Kanagasabai, Wing
    posted to algorithm classification ensemble gene_regulation proj_credo by chad_davis on 2008-08-26 18:08:44 as ***** along with 3 people nuin maximilianh idonaldson
  • Protein Complex Evolution Does Not Involve Extensive Network Rewiring
    PLoS Comput Biol, Vol. 4, No. 7. (25 July 2008), e1000132.
    by Teunis J van Dam, Berend Snel
    posted to complexes evolution proj_assembly structure by chad_davis on 2008-08-07 15:58:06 as ***** along with 2 people phoenixzxl cabbagesofdoom
  • Taking advantage of local structure descriptors to analyze interresidue contacts in protein structures and protein complexes
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by Juliette Martin, Leslie Regad, Catherine Etchebest, Anne C Camproux
    posted to algorithm complexes feature_selection proj_assembly proj_interprets statistics structure binding by chad_davis on 2008-06-15 13:54:46 as *****
  • Incorporating high-throughput proteomics experiments into structural biology pipelines: Identification of the low-hanging fruits.
    Proteomics, Vol. 8, No. 10. (19 May 2008), pp. 1959-1964.
    by Roland AA Pache, Patrick Aloy
    posted to complexes embl proj_assembly structure yeast by chad_davis on 2008-05-25 01:26:08 as *****
  • Protein disorder prediction at multiple levels of sensitivity and specificity.
    BMC genomics, Vol. 9 Suppl 1 (2008)
    by J Hecker, JY Yang, J Cheng
    posted to algorithm classification disorder proj_disocons review structure by chad_davis on 2008-04-20 11:16:25 as *****
  • notes Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs.
    Genome Res, Vol. 14, No. 6. (June 2004), pp. 1107-1118.
    by H Yu, NM Luscombe, HX Lu, X Zhu, Y Xia, JD Han, N Bertin, S Chung, M Vidal, M Gerstein
    posted to evolution binding by chad_davis on 2008-02-29 15:09:39 as ***** along with 7 people and 1 group tharris bicko dragonrez balajis koller cjeans cerca C. elegans / WormBase
  • WI-PHI: A weighted yeast interactome enriched for direct physical interactions.
    Proteomics (6 February 2007)
    by Lars Kiemer, Stefano Costa, Marius Ueffing, Gianni Cesareni
    posted to database yeast binding by chad_davis on 2008-01-18 14:57:48 as ***** along with 1 person nicoleq
  • Predicting 3D structures of transient protein-protein complexes by homology.
    Biochim Biophys Acta, Vol. 1764, No. 9. (September 2006), pp. 1498-1511.
    by PJ Kundrotas, E Alexov
    posted to binding by chad_davis on 2008-01-15 09:52:23 as ***** along with 1 person bicko
  • Where Have All the Interactions Gone? Estimating the Coverage of Two-Hybrid Protein Interaction Maps
    PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e214.
    by Hailiang Huang, Bruno M Jedynak, Joel S Bader
    posted to review statistics validation yeast binding by chad_davis on 2008-01-08 09:55:53 as ***** along with 4 people guhjy cjeans zwang Ema
  • Dynamic personalities of proteins
    Nature, Vol. 450, No. 7172. (12 December 2007), pp. 964-972.
    by Katherine H Wildman, Dorothee Kern
    posted to complexes experimental review binding by chad_davis on 2007-12-23 23:01:32 as ***** along with 15 people and 1 group viktor21614 ruvido barry pavanghatty allmensch choonpeng rsantana cjeans sobolevnrm wilbur mijam kjell phoenixzxl higueruelo GeeSharpMinor baker-group
  • Identifying protein complexes directly from high-throughput TAP data with Markov random fields
    BMC Bioinformatics, Vol. 8 (19 December 2007), 482.
    by Wasinee Rungsarityotin, Roland Krause, Arno Schodl, Alexander Schliep
    posted to algorithm clustering complexes networks binding by chad_davis on 2007-12-21 13:42:25 as ***** along with 1 person Yanno
  • Determining the architectures of macromolecular assemblies
    Nature, Vol. 450, No. 7170. (2007), pp. 683-694.
    by Frank Alber, Svetlana Dokudovskaya, Liesbeth M Veenhoff, Wenzhu Zhang, Julia Kipper, Damien Devos, Adisetyantari Suprapto, Orit K Schmidt, Rosemary Williams, Brian T Chait, Michael P Rout, Andrej Sali
    posted to algorithm complexes embl modelling structure by chad_davis on 2007-12-03 12:54:01 as ***** along with 8 people bicko neils cjeans zwang CameronNeylon faion phoenixzxl higueruelo
  • The molecular architecture of the nuclear pore complex
    Nature, Vol. 450, No. 7170. (29 November 2007), pp. 695-701.
    by Frank Alber, Svetlana Dokudovskaya, Liesbeth M Veenhoff, Wenzhu Zhang, Julia Kipper, Damien Devos, Adisetyantari Suprapto, Orit K Schmidt, Rosemary Williams, Brian T Chait, Andrej Sali, Michael P Rout
    posted to complexes disorder embl structure yeast by chad_davis on 2007-12-03 12:50:44 as ***** along with 6 people neils cjeans zwang mkikkawa faion phoenixzxl
  • Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions.
    Nucleic Acids Res, Vol. 35, No. Web Server issue. (1 July 2007)
    by T Okumura, H Makiguchi, Y Makita, R Yamashita, K Nakai
    posted to service ensemble gene_regulation proj_credo by chad_davis on 2007-11-16 13:36:52 as ***** along with 1 person guhjy
  • Structural disorder promotes assembly of protein complexes
    BMC Structural Biology, Vol. 7 (08 October 2007), 65.
    by Hedi Hegyi, Eva Schad, Peter Tompa
    posted to proj_disocons complexes disorder structure yeast binding by chad_davis on 2007-10-15 09:07:57 as *****
  • notes The Many Faces of Protein-Protein Interactions: A Compendium of Interface Geometry
    PLoS Computational Biology, Vol. 2, No. 9. (1 September 2006), e124.
    by Wan K Kim, Andreas Henschel, Christof Winter, Michael Schroeder
    posted to evolution structure binding by chad_davis on 2007-09-27 10:54:45 as ***** along with 9 people and 2 groups zdai raik bicko marcius choonpeng Evangelia wilbur allmensch marck BioinfoCIPF SGU-CIPF
  • A new, structurally nonredundant, diverse data set of protein-protein interfaces and its implications.
    Protein Sci, Vol. 13, No. 4. (April 2004), pp. 1043-1055.
    by O Keskin, CJ Tsai, H Wolfson, R Nussinov
    posted to non-redundant structure binding by chad_davis on 2007-09-26 14:06:27 as ***** along with 6 people thomaskelder baaden bicko nickolay henschel ladab
  • Reconstitution, activities, and structure of the eukaryotic RNA exosome.
    Cell, Vol. 127, No. 6. (15 December 2006), pp. 1223-1237.
    by Q Liu, JC Greimann, CD Lima
    posted to classic complexes experimental structure by chad_davis on 2007-09-18 09:28:38 as ***** along with 1 person jrweir82
  • POODLE-L: a two-level SVM prediction system for reliably predicting long disordered regions
    Bioinformatics, Vol. 23, No. 16. (15 August 2007), pp. 2046-2053.
    by Shuichi Hirose, Kana Shimizu, Satoru Kanai, Yutaka Kuroda, Tamotsu Noguchi
    posted to proj_disocons classification disorder feature_selection by chad_davis on 2007-09-13 16:08:33 as *****
  • Cataloging the relationships between proteins: a review of interaction databases.
    Mol Biotechnol, Vol. 34, No. 1. (September 2006), pp. 69-93.
    by C Rohl, Y Price, TB Fischer, M Paczkowski, MF Zettel, J Tsai
    posted to database review structure binding by chad_davis on 2007-09-04 10:55:50 as ***** along with 1 person bicko
  • Benchmarking of dimeric threading and structure refinement.
    Proteins, Vol. 63, No. 3. (15 May 2006), pp. 457-465.
    by V Grimm, Y Zhang, J Skolnick
    posted to algorithm structure validation binding by chad_davis on 2007-08-30 08:36:39 as *****
  • Development of unified statistical potentials describing protein-protein interactions.
    Biophys J, Vol. 84, No. 3. (March 2003), pp. 1895-1901.
    by H Lu, L Lu, J Skolnick
    posted to statistics binding by chad_davis on 2007-08-29 13:32:42 as ***** along with 7 people bicko mdimmic cjeans selrac iris_2001 wilbur kgutwin
  • How optimal are the binding energetics of barnase and barstar?
    Biophys J, Vol. 87, No. 3. (September 2004), pp. 1618-1630.
    by T Wang, S Tomic, RR Gabdoulline, RC Wade
    posted to chemistry experimental structure binding by chad_davis on 2007-08-19 12:50:35 as ***** along with 1 person ras
  • SCOPPI: a structural classification of protein-protein interfaces.
    Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006)
    by C Winter, A Henschel, WK Kim, M Schroeder
    posted to annotation classification clustering complexes database binding by chad_davis on 2007-08-15 12:12:11 as ***** along with 8 people and 4 groups sjcockell ana kuhn bicko marcius choonpeng Evangelia kintoki structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
  • Empirical potentials and functions for protein folding and binding.
    Curr Opin Struct Biol, Vol. 7, No. 2. (April 1997), pp. 222-228.
    by S Vajda, M Sippl, J Novotny
    posted to algorithm feature_selection modelling review statistics structure binding by chad_davis on 2007-07-25 12:35:46 as ***** along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
  • Protein-Protein Interactions More Conserved within Species than across Species
    PLoS Computational Biology, Vol. 2, No. 7. (1 July 2006), e79.
    by Sven Mika, Burkhard Rost
    posted to algorithm annotation chemistry evolution modelling statistics structure validation yeast binding by chad_davis on 2007-07-24 17:12:50 as ***** along with 4 people and 2 groups jeremymiller marcius skhadar dquest BioinfoCIPF SGU-CIPF
  • PIPER: an FFT-based protein docking program with pairwise potentials.
    Proteins, Vol. 65, No. 2. (1 November 2006), pp. 392-406.
    by D Kozakov, R Brenke, SR Comeau, S Vajda
    posted to algorithm chemistry download structure binding by chad_davis on 2007-07-24 16:22:43 as ***** along with 1 person selrac
  • Receptor Specificity of the Fibroblast Growth Factor Family
    J. Biol. Chem., Vol. 271, No. 25. (21 June 1996), pp. 15292-15297.
    by David M Ornitz, Jingsong Xu, Jennifer S Colvin, Donald G Mcewen, Craig A Macarthur, Francois Coulier, Guangxia Gao, Mitchell Goldfarb
    posted to binding by chad_davis on 2007-05-16 16:59:38 as ***** along with 2 people Alan lisa1
  • notes Stability of macromolecular complexes.
    Proteins, Vol. 48, No. 4. (1 September 2002), pp. 645-653.
    by N Brooijmans, KA Sharp, ID Kuntz
    posted to chemistry evolution structure drug binding by chad_davis on 2007-04-27 15:02:07 as *****
  • DisProt: the Database of Disordered Proteins.
    Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007)
    by M Sickmeier, JA Hamilton, T Legall, V Vacic, MS Cortese, A Tantos, B Szabo, P Tompa, J Chen, VN Uversky, Z Obradovic, AK Dunker
    posted to disorder structure database proj_disocons by chad_davis on 2007-04-23 15:04:21 as ***** along with 4 people carlosjavierna higueruelo choonpeng allmensch
  • Diversity of protein-protein interactions.
    EMBO J, Vol. 22, No. 14. (15 July 2003), pp. 3486-3492.
    by IM Nooren, JM Thornton
    posted to embl evolution review structure binding by chad_davis on 2007-04-02 16:21:42 as ***** along with 4 people bicko drastic Evangelia higueruelo
  • 3D complex: a structural classification of protein complexes.
    PLoS Comput Biol, Vol. 2, No. 11. (17 November 2006)
    by ED Levy, Pereira JB Leal, C Chothia, SA Teichmann
    posted to classification non-redundant structure database binding by chad_davis on 2007-03-21 12:46:03 as ***** along with 2 people and 1 group bicko Einat structural_bioinformatics
  • Identification of distant homologues of fibroblast growth factors suggests a common ancestor for all beta-trefoil proteins.
    J Mol Biol, Vol. 302, No. 5. (6 October 2000), pp. 1041-1047.
    by CP Ponting, RB Russell
    posted to embl evolution structure by chad_davis on 2007-03-19 11:03:15 as *****
  • notes Correlated sequence-signatures as markers of protein-protein interaction.
    J Mol Biol, Vol. 311, No. 4. (24 August 2001), pp. 681-692.
    by E Sprinzak, H Margalit
    posted to structure binding by chad_davis on 2007-01-22 10:46:05 as ***** along with 10 people behindtherabbit bicko maryee dyermd grahamc cjeans lilith wilbur Rhys phoenixzxl
  • Showing your ID: intrinsic disorder as an ID for recognition, regulation and cell signaling.
    J Mol Recognit, Vol. 18, No. 5. (t 2005), pp. 343-384.
    by VN Uversky, CJ Oldfield, AK Dunker
    posted to disorder gene_regulation proj_disocons review by chad_davis on 2006-07-22 17:38:44 as ***** along with 1 person Evangelia
  • Sequence patterns associated with disordered regions in proteins.
    Proteins, Vol. 58, No. 1. (1 January 2005), pp. 144-150.
    by S Lise, DT Jones
    posted to disorder embl proj_disocons by chad_davis on 2006-07-21 16:59:01 as ***** along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
  • Intrinsic disorder in transcription factors.
    Biochemistry, Vol. 45, No. 22. (6 June 2006), pp. 6873-6888.
    by J Liu, NB Perumal, CJ Oldfield, EW Su, VN Uversky, AK Dunker
    posted to disorder gene_regulation proj_disocons by chad_davis on 2006-07-21 13:22:46 as *****
  • notes Fast fitting of atomic structures to low-resolution electron density maps by surface overlap maximization.
    J Mol Biol, Vol. 338, No. 4. (7 May 2004), pp. 783-793.
    by H Ceulemans, RB Russell
    posted to structure embl algorithm by chad_davis on 2006-06-23 09:46:03 as *****
  • notes 3did Update: domain-domain and peptide-mediated interactions of known 3D structure.
    Nucleic acids research (25 October 2008)
    by Amelie Stein, Alejandro Panjkovich, Patrick Aloy
    posted to proj_interprets proj_assembly ppi embl database classic binding by chad_davis on 2008-10-29 16:29:48 as ****
  • notes Modifying the DPClus algorithm for identifying protein complexes based on new topological structures
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Min Li, Jianer Chen, Jianxin Wang, Bin Hu, Gang Chen
    posted to proj_assembly networks download complexes clustering algorithm by chad_davis on 2008-10-09 15:22:18 as **** along with 1 person neils
  • R/parallel - speeding up bioinformatics analysis with R
    BMC Bioinformatics, Vol. 9 (22 September 2008), 390.
    by Gonzalo Vera, Ritsert C Jansen, Remo L Suppi
    posted to toolkit proj_stabperf download distributed algorithm by chad_davis on 2008-10-09 15:13:43 as **** along with 19 people and 1 group siebert operon talponer dipenps guhjy dakelley ptrobajo pengchy shikin robertlischke chrisamiller cisevol druvus renatomilani rdiaz nuin GeeSharpMinor neils jandot BergmanLab
  • GraphCrunch: a tool for large network analyses
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Tijana Milenkovic, Jason Lai, Natasa Przulj
    posted to service proj_assembly networks download distributed clustering algorithm by chad_davis on 2008-10-06 16:41:38 as **** along with 7 people grahamc laughcry barriot guhjy maralena dullhunk ptrobajo
  • Identifying Cognate Binding Pairs among a Large Set of Paralogs: The Case of PE/PPE Proteins of Mycobacterium tuberculosis
    PLoS Comput Biol, Vol. 4, No. 9. (2008), e1000174.
    by Robert Riley, Matteo Pellegrini, David Eisenberg
    posted to proj_interprets ppi evolution algorithm by chad_davis on 2008-10-06 13:56:25 as **** along with 1 person Ema
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