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chad_davis's embl [103 articles]

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  • Morphological aspects of oligomeric protein structures.
    Progress in biophysics and molecular biology, Vol. 89, No. 1. (September 2005), pp. 9-35.
    by H Ponstingl, T Kabir, D Gorse, JM Thornton
    posted to structure proj_assembly ppi embl complexes by chad_davis on 2008-08-26 17:56:35 as **** along with 1 person bicko
  • Performance evaluation of image processing algorithms on the GPU.
    Journal of structural biology (24 July 2008)
    by Daniel C Diez, Dominik Moser, Andreas Schoenegger, Sabine Pruggnaller, Achilleas S Frangakis
    posted to validation embl distributed algorithm by chad_davis on 2008-08-12 16:43:25 as ***
  • Understanding the molecular machinery of genetics through 3D structures.
    Nat Rev Genet (27 December 2007)
    by Roman AA Laskowski, Janet MM Thornton
    posted to structure review evolution embl by chad_davis on 2008-08-07 15:13:11 as **** along with 5 people aalibes higueruelo jwm sebastien_vigneau grottenolm
  • Understanding and Predicting Protein Assemblies With 3D Structures.
    Comparative and functional genomics, Vol. 4, No. 4. (2003), pp. 410-415.
    by P Aloy, RB Russell
    posted to binding structure proj_assembly modelling embl data_integration complexes classic algorithm by chad_davis on 2008-08-03 18:17:16 as read
  • Protein-DNA Interactions: The Story so Far and a New Method for Prediction.
    Comparative and functional genomics, Vol. 4, No. 4. (2003), pp. 428-431.
    by S Jones, JM Thornton
    posted to binding structure review embl annotation algorithm by chad_davis on 2008-08-03 18:14:04 as **
  • MSDmotif: exploring protein sites and motifs
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Adel Golovin, Kim Henrick
    posted to binding web_service structure embl drug data_integration database complexes algorithm by chad_davis on 2008-07-17 16:18:19 as read along with 3 people Evangelia massivemayhem reyez
  • Peptide-mediated interactions in biological systems: new discoveries and applications.
    Current opinion in biotechnology (1 July 2008)
    by Evangelia Petsalaki, Robert BB Russell
    posted to binding structure review embl by chad_davis on 2008-07-14 12:54:41 as read
  • notes Inference of macromolecular assemblies from crystalline state.
    J Mol Biol, Vol. 372, No. 3. (21 September 2007), pp. 774-797.
    by E Krissinel, K Henrick
    posted to binding web_service validation structure proj_assembly embl database complexes annotation algorithm by chad_davis on 2008-07-13 16:28:44 as **** along with 1 person bicko
  • The social network of a cell: Recent advances in interactome mapping.
    Biotechnology annual review, Vol. 14 (2008), pp. 1-28.
    by S Charbonnier, O Gallego, AC Gavin
    posted to review proj_assembly networks embl data_integration by chad_davis on 2008-07-09 19:38:51 as ****
  • Evolvability and hierarchy in rewired bacterial gene networks
    Nature, Vol. 452, No. 7189. (17 April 2008), pp. 840-845.
    by Mark Isalan, Caroline Lemerle, Konstantinos Michalodimitrakis, Carsten Horn, Pedro Beltrao, Emanuele Raineri, Mireia G Canut, Luis Serrano
    posted to proj_mol_evo networks gene_regulation evolution embl by chad_davis on 2008-07-07 12:11:29 as read along with 18 people and 4 groups zwang michaelbarton aheilbut austin AbnerCYH hryk margaritis cactus dbikard Garamonfok caseybrown biehl aalibes tmmurali dullhunk neils cmzmasek josedavid BergmanLab SynBioSys Centre de Recherches Interdisciplinaires GEB
  • Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames.
    Nucleic acids research, Vol. 28, No. 17. (1 September 2000), pp. 3278-3288.
    by T Dandekar, M Huynen, JT Regula, B Ueberle, CU Zimmermann, MA Andrade, T Doerks, Sánchez L Pulido, B Snel, M Suyama, YP Yuan, R Herrmann, P Bork
    posted to mycoplasma embl classic annotation by chad_davis on 2008-07-04 11:09:46 as ** along with 2 people shana operon
  • Simple fold composition and modular architecture of the nuclear pore complex.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 103, No. 7. (14 February 2006), pp. 2172-2177.
    by D Devos, S Dokudovskaya, R Williams, F Alber, N Eswar, BT Chait, MP Rout, A Sali
    posted to structure modelling evolution embl complexes by chad_davis on 2008-06-27 14:31:05 as read
  • Systematic discovery of in vivo phosphorylation networks.
    Cell, Vol. 129, No. 7. (29 June 2007), pp. 1415-1426.
    by R Linding, LJ Jensen, GJ Ostheimer, MA van Vugt, C Jørgensen, IM Miron, F Diella, K Colwill, L Taylor, K Elder, P Metalnikov, V Nguyen, A Pasculescu, J Jin, JG Park, LD Samson, JR Woodgett, RB Russell, P Bork, MB Yaffe, T Pawson
    posted to binding networks embl data_integration algorithm by chad_davis on 2008-06-20 11:13:19 as **** along with 15 people and 2 groups bouncingbudha carlk daed Evangelia renatomilani jyuh skhadar julius zwang cdppublications lp2 psique robrussell snowcrash larsjuhljensen SysbioMPI-TCells Durbin group
  • Phylogeny-Aware Gap Placement Prevents Errors in Sequence Alignment and Evolutionary Analysis
    Science, Vol. 320, No. 5883. (20 June 2008), pp. 1632-1635.
    by Ari Loytynoja, Nick Goldman
    posted to validation evolution embl classic alignment algorithm by chad_davis on 2008-06-20 11:03:06 as *** along with 22 people and 3 groups marti nuin emptyhb michaelbarton jlgreen AbnerCYH bpcusack bmaust gulsacan Schmidtc bpb zwang aprasad imtechnology marck ArtemPankin djkt gjuggler hpaces dinnes jago phoenixzxl iSEEM Green Lab Khavkin's lab
  • MedEvi: Retrieving textual evidence of relations between biomedical concepts from Medline.
    Bioinformatics (Oxford, England) (9 April 2008)
    by Jung, Piotr Pezik, Dietrich R Schuhmann
    posted to web_service text_mining embl algorithm by chad_davis on 2008-06-15 13:11:16 as ** along with 3 people jyuh dullhunk Gaetan
  • Understanding eukaryotic linear motifs and their role in cell signaling and regulation.
    Frontiers in bioscience : a journal and virtual library, Vol. 13 (2008), pp. 6580-6603.
    by F Diella, N Haslam, C Chica, A Budd, S Michael, NP Brown, G Trave, TJ Gibson
    posted to binding review embl disorder by chad_davis on 2008-06-01 12:04:07 as read along with 1 person cabbagesofdoom
  • 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 yeast structure proj_assembly embl complexes by chad_davis on 2008-05-25 01:26:08 as *****
  • An analysis of conformational changes on protein-protein association: implications for predictive docking.
    Protein Eng, Vol. 12, No. 4. (April 1999), pp. 271-283.
    by MJ Betts, MJ Sternberg
    posted to binding structure embl docking complexes by chad_davis on 2008-05-04 15:32:44 as **** along with 2 people bicko ffranca
  • A new protein linear motif benchmark for multiple sequence alignment software
    BMC Bioinformatics, Vol. 9 (25 April 2008), 213.
    by Emmanuel Perrodou, Claudia Chica, Olivier Poch, Toby J Gibson, Julie D Thompson
    posted to validation review embl disorder alignment by chad_davis on 2008-05-04 10:10:39 as *** along with 2 people biehl niallhaslam
  • Rintact: enabling computational analysis of molecular interaction data from the IntAct repository.
    Bioinformatics (7 November 2007)
    by Tony Chiang, Nianhua Li, Sandra Orchard, Samuel Kerrien, Henning Hermjakob, Robert Gentleman, Wolfgang Huber
    posted to data_integration embl microarray toolkit by chad_davis on 2008-04-11 17:30:56 as ** along with 1 person jyuh
  • Subunit Architecture of Intact Protein Complexes from Mass Spectrometry and Homology Modeling
    Acc. Chem. Res. (4 March 2008)
    by Thomas Taverner, Helena Hernandez, Michal Sharon, Brandon T Ruotolo, Dijana M Vinkovic, Damien Devos, Robert B Russell, Carol V Robinson
    posted to binding algorithm complexes embl experimental modelling networks proj_assembly structure yeast by chad_davis on 2008-03-10 08:53:48 as read along with 1 person faion
  • Interaction networks for systems biology.
    FEBS Lett (15 February 2008)
    by Samuel Bader, Sebastian Kühner, Anne
    posted to embl networks review by chad_davis on 2008-02-25 10:42:22 as *** along with 3 people adacier ruvido zwang
  • A careful disorderliness in the proteome: Sites for interaction and targets for future therapies.
    FEBS Lett (16 February 2008)
    by Robert BB Russell, Toby JJ Gibson
    posted to binding disorder drug embl by chad_davis on 2008-02-25 10:34:04 as read along with 5 people higueruelo kluck jyuh Evangelia robrussell
  • Evolution of function in protein superfamilies, from a structural perspective
    Journal of Molecular Biology, Vol. 307, No. 4. (6 April 2001), pp. 1113-1143.
    by Annabel E Todd, Christine A Orengo, Janet M Thornton
    posted to embl evolution structure by chad_davis on 2008-02-25 10:09:40 as *** along with 8 people and 2 groups sim82 ana kuhn tny sriram_s choonpeng cdallett uz_labu_laimi structural_bioinformatics Bioinformatics
  • Components of Coated Vesicles and Nuclear Pore Complexes Share a Common Molecular Architecture
    PLoS Biology, Vol. 2, No. 12. (1 December 2004), e380.
    by Damien Devos, Svetlana Dokudovskaya, Frank Alber, Rosemary Williams, Brian T Chait, Andrej Sali, Michael P Rout
    posted to complexes embl evolution structure by chad_davis on 2008-02-21 12:32:21 as **
  • 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 7 people higueruelo neils cjeans zwang CameronNeylon faion phoenixzxl
  • 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
  • SuperTarget and Matador: resources for exploring drug-target relationships.
    Nucleic Acids Res (16 October 2007)
    by Stefan Guenther, Michael Kuhn, Mathias Dunkel, Monica Campillos, Christian Senger, Evangelia Petsalaki, Jessica Ahmed, Eduardo G Urdiales, Andreas Gewiess, Lars J Jensen, Reinhard Schneider, Roman Skoblo, Robert B Russell, Philip E Bourne, Peer Bork, Robert Preissner
    posted to drug embl by chad_davis on 2007-10-21 01:28:30 as *** along with 6 people jyuh mdimmic daevans massivemayhem Evangelia larsjuhljensen
  • 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 binding algorithm classic complexes embl structure web_service by chad_davis on 2007-09-28 13:07:21 as **** along with 4 people apaydin aalibes hmk carlescorbi
  • Coverage and error models of protein-protein interaction data by directed graph analysis
    Genome Biology, Vol. 8 (10 September 2007), R186.
    by Tony Chiang, Denise Scholtens, Deepayan Sarkar, Robert Gentleman, Wolfgang Huber
    posted to clustering embl networks review statistics validation yeast by chad_davis on 2007-09-27 16:28:59 as **** along with 5 people Yanno jfr grahamc winterschlaefer Pao-Yang
  • Protein-protein interfaces: analysis of amino acid conservation in homodimers.
    Proteins, Vol. 42, No. 1. (1 January 2001), pp. 108-124.
    by WS Valdar, JM Thornton
    posted to binding embl evolution by chad_davis on 2007-09-27 11:10:18 as **** along with 1 person kintoki
  • Prediction of Ras-effector interactions using position energy matrices.
    Bioinformatics, Vol. 23, No. 17. (1 September 2007), pp. 2226-2230.
    by C Kiel, L Serrano
    posted to binding algorithm embl modelling networks structure by chad_davis on 2007-09-16 11:44:33 as ****
  • Database of homology-derived protein structures and the structural meaning of sequence alignment.
    Proteins, Vol. 9, No. 1. (1991), pp. 56-68.
    by C Sander, R Schneider
    posted to classic embl modelling structure by chad_davis on 2007-09-05 19:54:00 as * along with 2 people Lombardo_7 ca3295
  • Mass spectrometry of macromolecular assemblies: preservation and dissociation.
    Curr Opin Struct Biol, Vol. 16, No. 2. (April 2006), pp. 245-251.
    by JL Benesch, CV Robinson
    posted to complexes embl experimental by chad_davis on 2007-09-04 12:13:31 as ***
  • The hard cell: From proteomics to a whole cell model
    FEBS Letters, Vol. 581, No. 15. (19 June 2007), pp. 2870-2876.
    by Matthew J Betts, Robert B Russell
    posted to complexes embl modelling review by chad_davis on 2007-09-04 12:02:13 as read along with 2 people higueruelo ruvido
  • Multiple protein sequence alignment from tertiary structure comparison: assignment of global and residue confidence levels.
    Proteins, Vol. 14, No. 2. (October 1992), pp. 309-323.
    by RB Russell, GJ Barton
    posted to algorithm embl structure by chad_davis on 2007-08-22 12:34:13 as read along with 2 people analogAI jefferlyemerson
  • Prediction of water and metal binding sites and their affinities by using the Fold-X force field.
    Proc Natl Acad Sci U S A, Vol. 102, No. 29. (19 July 2005), pp. 10147-10152.
    by JW Schymkowitz, F Rousseau, IC Martins, Ferkinghoff J Borg, F Stricher, L Serrano
    posted to binding algorithm chemistry embl modelling structure by chad_davis on 2007-08-19 12:37:25 as ****
  • CATH--a hierarchic classification of protein domain structures.
    Structure, Vol. 5, No. 8. (15 August 1997), pp. 1093-1108.
    by CA Orengo, AD Michie, S Jones, DT Jones, MB Swindells, JM Thornton
    posted to algorithm annotation classic classification embl evolution structure by chad_davis on 2007-08-07 12:41:10 as ** along with 9 people and 4 groups gulkur jteyra sim82 massivemayhem tjimenez dimka jwm Einat caporaso structural_bioinformatics Radiation_Damage Stressosome biomedical-nlp
  • Analysis of protein-protein interaction sites using surface patches.
    J Mol Biol, Vol. 272, No. 1. (12 September 1997), pp. 121-132.
    by S Jones, JM Thornton
    posted to binding chemistry classification embl structure by chad_davis on 2007-07-25 11:51:17 as **** along with 1 person cjeans
  • A more complete, complexed and structured interactome.
    Curr Opin Struct Biol (14 June 2007)
    by Damien Devos, Robert B Russell
    posted to binding embl networks review structure by chad_davis on 2007-07-24 17:42:04 as read along with 4 people balicea skhadar choonpeng ruvido
  • Supersites within superfolds. Binding site similarity in the absence of homology
    Journal of Molecular Biology, Vol. 282, No. 4. (2 October 1998), pp. 903-918.
    by Robert B Russell, Peter D Sasieni, Michael J Sternberg
    posted to embl evolution structure by chad_davis on 2007-07-16 11:42:54 as read along with 1 person nickolay
  • The CATH protein family database: a resource for structural and functional annotation of genomes.
    Proteomics, Vol. 2, No. 1. (January 2002), pp. 11-21.
    by CA Orengo, JE Bray, DW Buchan, A Harrison, D Lee, FM Pearl, I Sillitoe, AE Todd, JM Thornton
    posted to annotation classification embl evolution review structure database by chad_davis on 2007-05-18 14:35:23 as ***
  • E-MSD: an integrated data resource for bioinformatics.
    Nucleic Acids Res, Vol. 33, No. Database issue. (1 January 2005)
    by S Velankar, P Mcneil, Mittard V Runte, A Suarez, D Barrell, R Apweiler, K Henrick
    posted to annotation database data_integration embl by chad_davis on 2007-05-11 10:15:47 as read along with 2 people bicko massivemayhem
  • Structural features can be unconserved in proteins with similar folds. An analysis of side-chain to side-chain contacts secondary structure and accessibility.
    J Mol Biol, Vol. 244, No. 3. (2 December 1994), pp. 332-350.
    by RB Russell, GJ Barton
    posted to embl evolution structure by chad_davis on 2007-04-30 15:46:12 as **** along with 2 people and 2 groups ana barry structural_bioinformatics Bioinformatics
  • EMBOSS: the European Molecular Biology Open Software Suite.
    Trends Genet, Vol. 16, No. 6. (June 2000), pp. 276-277.
    by P Rice, I Longden, A Bleasby
    posted to classic download embl toolkit by chad_davis on 2007-04-19 14:46:41 as read along with 4 people dna dullhunk mtagaya dgront
  • Multiple sequence alignment with the Clustal series of programs.
    Nucleic Acids Res, Vol. 31, No. 13. (1 July 2003), pp. 3497-3500.
    by R Chenna, H Sugawara, T Koike, R Lopez, TJ Gibson, DG Higgins, JD Thompson
    posted to algorithm classic clustering download embl evolution web_service by chad_davis on 2007-04-18 09:17:52 as *** along with 5 people and 1 group marck miguel beatrizfernandez raylim xingxu Microbial-Ecology
  • Twilight zone of protein sequence alignments.
    Protein Eng, Vol. 12, No. 2. (February 1999), pp. 85-94.
    by B Rost
    posted to classic embl evolution statistics by chad_davis on 2007-04-16 16:36:07 as * along with 3 people bicko sgoetz ffranca
  • PQS: a protein quaternary structure file server.
    Trends Biochem Sci, Vol. 23, No. 9. (September 1998), pp. 358-361.
    by K Henrick, JM Thornton
    posted to binding embl structure database by chad_davis on 2007-04-10 11:19:11 as read along with 1 person bicko
  • notes SMART 5: domains in the context of genomes and networks.
    Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006)
    by I Letunic, RR Copley, B Pils, S Pinkert, J Schultz, P Bork
    posted to classic classification disorder embl web_service proj_disocons by chad_davis on 2007-04-02 19:40:37 as *** along with 1 person siebertm
  • Protein families and their evolution-a structural perspective.
    Annu Rev Biochem, Vol. 74 (2005), pp. 867-900.
    by CA Orengo, JM Thornton
    posted to embl evolution review structure by chad_davis on 2007-04-02 16:36:36 as *** along with 13 people and 6 groups sim82 nigham ana barry tjimenez jwm Einat Schmidtc marcius sriram_s ezotenko redelings medic0747 structural_bioinformatics Radiation_Damage Stressosome Bioinformatics BioinfoCIPF SGU-CIPF
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