Tag proj_assembly [66 articles] Export

Recent papers classified by the tag proj_assembly.

	ProtorP: A Protein-Protein Interaction Analysis Server [My Copy] Bioinformatics (11 November 2008), btn584. by Christopher Reynolds, David Damerell, Susan Jones posted to annotation binding proj_assembly proj_interprets service structure by chad_davis on 2009-01-31 18:25:28 as along with 7 people and 1 group idoerg bicko barry behindtherabbit neils kshameer hugowill structural_bioinformatics
	HADDOCK versus HADDOCK: new features and performance of HADDOCK2.0 on the CAPRI targets. [My Copy] Proteins, Vol. 69, No. 4. (1 December 2007), pp. 726-733. by S. J. de Vries, A. D. van Dijk, M. Krzeminski, et al.M. van Dijk, A. Thureau, V. Hsu, T. Wassenaar, A. M. Bonvin posted to algorithm binding complexes docking download modelling ppi proj_assembly structure by chad_davis on 2009-01-14 13:39:14 as along with 1 person martainn
	HADDOCK: A Protein−Protein Docking Approach Based on Biochemical or Biophysical Information [My Copy] Journal of the American Chemical Society, Vol. 125, No. 7. (1 February 2003), pp. 1731-1737. by Cyril Dominguez, Rolf Boelens, Alexandre M. J. J. Bonvin posted to algorithm binding complexes docking download modelling ppi proj_assembly proj_interprets structure by chad_davis on 2009-01-14 13:34:03 as along with 10 people bmduggan laurabailey A_Coletta_Thesis betainverse dgruiz bicko bluvsh1 gloria ruvido yalexeev
	An evolutionary and structural characterization of mammalian protein complex organization. [My Copy] BMC genomics, Vol. 9, No. 1. (23 December 2008) by Philip Wong, Sonja Althammer, Andrea Hildebrand, et al.Andreas Kirschner, Philipp Pagel, Bernd Geissler, Pawel Smialowski, Florian Blöchl, Matthias Oesterheld, Thorsten Schmidt, Normann Strack, Fabian J. Theis, Andreas Ruepp, Dmitrij Frishman posted to complexes evolution ppi proj_assembly structure by chad_davis on 2008-12-26 21:54:40 as along with 3 people chica zwang phoenixzxl
	Malleable machines in transcription regulation: the mediator complex. [My Copy] PLoS computational biology, Vol. 4, No. 12. (December 2008) by A. Tóth-Petróczy, C. J. Oldfield, I. Simon, et al.Y. Takagi, A. K. Dunker, V. N. Uversky, M. Fuxreiter posted to binding complexes disorder ppi proj_assembly proj_disocons structure by chad_davis on 2008-12-26 21:41:43 as along with 2 people siebert akraemer
	The archaeal exosome core is a hexameric ring structure with three catalytic subunits [My Copy] Nature Structural & Molecular Biology, Vol. 12, No. 7. (12 June 2005), pp. 575-581. by Esben Lorentzen, Pamela Walter, Sebastien Fribourg, Elena Evguenieva-Hackenberg, Gabriele Klug, Elena Conti posted to classic complexes embl evolution experimental proj_assembly structure by chad_davis on 2008-12-22 13:11:34 as
	Age-Dependent Evolution of the Yeast Protein Interaction Network Suggests a Limited Role of Gene Duplication and Divergence [My Copy] PLoS Comput Biol, Vol. 4, No. 11. (28 November 2008), e1000232. by Wan K. Kim, Edward M. Marcotte posted to complexes evolution networks ppi proj_assembly proj_interprets statistics validation by chad_davis on 2008-12-19 09:35:41 as along with 7 people wangbo dakelley biomcgary cabbagesofdoom grahamc bpcusack tmmurali
	A dataset of protein-protein interfaces generated with a sequence-order-independent comparison technique. [My Copy] J Mol Biol, Vol. 260, No. 4. (26 July 1996), pp. 604-620. by C. J. Tsai, S. L. Lin, H. J. Wolfson, R. Nussinov posted to algorithm binding classic complexes database non-redundant ppi proj_assembly proj_interprets statistics structure by chad_davis on 2008-12-18 22:10:13 as along with 1 person bicko
	Integrating Expression Data with Domain Interaction Networks [My Copy] Bioinformatics (19 August 2008), btn437. by Dorothea Emig, Melissa S. Cline, Thomas Lengauer, Mario Albrecht posted to data_integration download evolution microarray networks ppi proj_assembly proj_stabperf by chad_davis on 2008-12-18 20:35:43 as along with 7 people jfr guhjy zwang barriot druvus zimbo1 grahamc
	The self-assembly and evolution of homomeric protein complexes [My Copy] (22 Nov 2008) by Gabriel Villar, Alex W. Wilber, Alex J. Williamson, et al.Parvinder Thiara, Jonathan P. K. Doye, Ard A. Louis, Mara N. Jochum, Anna C. F. Lewis, Emmanuel D. Levy posted to binding complexes evolution modelling ppi proj_assembly structure by chad_davis on 2008-12-18 20:23:39 as
	3did Update: domain-domain and peptide-mediated interactions of known 3D structure. [My Copy] Nucleic acids research (25 October 2008) by Amelie Stein, Alejandro Panjkovich, Patrick Aloy posted to binding classic database embl ppi proj_assembly proj_interprets by chad_davis on 2008-10-29 16:29:48 as
	MODBASE, a database of annotated comparative protein structure models and associated resources. [My Copy] Nucleic acids research, Vol. 37, No. Database issue. (23 January 2009) by Ursula Pieper, Narayanan Eswar, Ben M. Webb, et al.David Eramian, Libusha Kelly, David T. Barkan, Hannah Carter, Parminder Mankoo, Rachel Karchin, Marc A. Marti-Renom, Fred P. Davis, Andrej Sali posted to classic complexes database modelling ppi proj_assembly service structure by chad_davis on 2008-10-27 12:47:02 as along with 3 people tjimenez noraziz medic0747
	Organization of Physical Interactomes as Uncovered by Network Schemas [My Copy] PLoS Comput Biol, Vol. 4, No. 10. (24 October 2008), e1000203. by Eric Banks, Elena Nabieva, Bernard Chazelle, Mona Singh posted to algorithm data_mining networks ppi proj_assembly by chad_davis on 2008-10-27 12:38:59 as along with 4 people sivaramanb roys marck grahamc
	Targeting and tinkering with interaction networks [My Copy] Nature Chemical Biology, Vol. 4, No. 11. (20 October 2008), pp. 666-673. by Robert B. B. Russell, Patrick Aloy posted to embl networks ppi proj_assembly review by chad_davis on 2008-10-27 11:58:57 as along with 3 people and 1 group lees jperkins zwang Orengo Group Journal Picks
	CORUM: the comprehensive resource of mammalian protein complexes. [My Copy] Nucleic acids research, Vol. 36, No. Database issue. (11 January 2008), pp. D646-650. by Andreas Ruepp, Barbara Brauner, Irmtraud Dunger-Kaltenbach, et al.Goar Frishman, Corinna Montrone, Michael Stransky, Brigitte Waegele, Thorsten Schmidt, Octave Noubibou N. Doudieu, Volker Stümpflen, H. Werner Mewes posted to annotation complexes database ppi proj_assembly by chad_davis on 2008-10-20 13:57:58 as along with 6 people dragonrez poirel carlk tmmurali guhjy shung
	Inferring protein domain interactions from databases of interacting proteins. [My Copy] Genome Biol, Vol. 6, No. 10. (2005) by R. Riley, C. Lee, C. Sabatti, D. Eisenberg posted to algorithm binding ppi proj_assembly proj_interprets statistics structure validation by chad_davis on 2008-10-20 12:49:20 as along with 4 people maryee j3xucite iris_2001 phoenixzxl
	A comparison of MSA tools. [My Copy] Bioinformation, Vol. 2, No. 10. (2008), pp. 452-455. by N. Essoussi, K. Boujenfa, M. Limam posted to algorithm alignment proj_assembly proj_interprets review validation by chad_davis on 2008-10-20 11:14:46 as along with 1 person jwm
	An integrative approach for predicting interactions of protein regions. [My Copy] Bioinformatics (Oxford, England), Vol. 24, No. 16. (15 August 2008) by Sven-Eric E. Schelhorn, Thomas Lengauer, Mario Albrecht posted to algorithm binding complexes ppi proj_assembly proj_interprets structure by chad_davis on 2008-10-16 13:59:56 as along with 1 person kgutwin
	Improved network-based identification of protein orthologs. [My Copy] Bioinformatics (Oxford, England), Vol. 24, No. 16. (15 August 2008) by N. Yosef, R. Sharan, W. S. Noble posted to algorithm annotation clustering evolution networks proj_assembly by chad_davis on 2008-10-15 09:16:29 as along with 1 person grahamc
	Assembly reflects evolution of protein complexes. [My Copy] Nature, Vol. 453, No. 7199. (26 June 2008), pp. 1262-1265. by Emmanuel D. Levy, Elisabetta B. Erba, Carol V. Robinson, Sarah A. Teichmann posted to complexes evolution experimental ppi proj_assembly structure by chad_davis on 2008-10-14 14:51:52 as along with 11 people and 1 group robfsouza chica noraziz psique marck paulschlesinger neils jwm zwang faion phoenixzxl KeatingJClub
	Fitting a Geometric Graph to a Protein-Protein Interaction Network. [My Copy] Bioinformatics (14 March 2008) by Desmond J. J. Higham, Marija Rasajski, Natasa Przulj posted to algorithm networks ppi proj_assembly by chad_davis on 2008-10-14 10:36:47 as along with 10 people and 1 group tmmurali AbnerCYH grahamc bootsy maralena scienbox lidaiqiang1981 paolomarcatili guhjy mariap3636 untranet
	Homology modelling of protein-protein complexes: a simple method and its possibilities and limitations [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008) by Guillaume Launay, Thomas Simonson posted to algorithm binding complexes modelling proj_assembly structure by chad_davis on 2008-10-10 07:36:29 as along with 1 person lptolik
	Modifying the DPClus algorithm for identifying protein complexes based on new topological structures [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008) by Min Li, Jianer Chen, Jianxin Wang, Bin Hu, Gang Chen posted to algorithm clustering complexes download networks proj_assembly by chad_davis on 2008-10-09 15:22:18 as along with 2 people diamantis neils
	Protein Structure Fitting and Refinement Guided by Cryo-EM Density [My Copy] 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 algorithm complexes data_integration modelling proj_assembly structure by chad_davis on 2008-10-08 16:10:16 as along with 1 person and 1 group noraziz KeatingJClub
	Structural characterization of assemblies from overall shape and subcomplex compositions. [My Copy] Structure, Vol. 13, No. 3. (March 2005), pp. 435-445. by F. Alber, M. F. Kim, A. Sali posted to algorithm binding complexes data_integration modelling ppi proj_assembly structure by chad_davis on 2008-10-08 15:51:24 as along with 1 person faion
	Computational methods for the prediction of protein interactions. [My Copy] Curr Opin Struct Biol, Vol. 12, No. 3. (June 2002), pp. 368-373. by A. Valencia, F. Pazos posted to algorithm ppi proj_assembly proj_interprets review by chad_davis on 2008-10-08 15:48:08 as along with 4 people bicko Robinder eckart_bindewald marti
	An efficient algorithm for large-scale detection of protein families [My Copy] Nucl. Acids Res., Vol. 30, No. 7. (1 April 2002), pp. 1575-1584. by A. J. Enright, S. Van Dongen, C. A. Ouzounis posted to algorithm clustering download networks proj_assembly toolkit by chad_davis on 2008-10-08 12:48:58 as along with 22 people and 2 groups jperkins calderonv nedwards dakelley druvus treangen carlk cgaugain johanviklund camster operon knaseanka indigoviolet skhadar nirfriedman dgront entropy gcalda GustavoLacerda hpaces RebeccaHamer Borelli dbk-lab EisenLab
	Interactome data and databases: different types of protein interaction. [My Copy] Comparative and functional genomics, Vol. 5, No. 2. (2004), pp. 173-178. by De Las, A. de Luis posted to networks ppi proj_assembly proj_interprets review by chad_davis on 2008-10-08 10:56:48 as
	APID: Agile Protein Interaction DataAnalyzer. [My Copy] Nucleic acids research, Vol. 34, No. Web Server issue. (1 July 2006) by C. Prieto, De Las posted to data_integration database download networks ppi proj_assembly proj_interprets service by chad_davis on 2008-10-08 10:53:05 as along with 1 person satre
	PRISM: protein interactions by structural matching. [My Copy] Nucleic acids research, Vol. 33, No. Web Server issue. (1 July 2005) by U. Ogmen, O. Keskin, A. S. Aytuna, R. Nussinov, A. Gursoy posted to algorithm binding ppi proj_assembly proj_interprets structure service by chad_davis on 2008-10-07 10:15:00 as along with 4 people apaydin bicko j3xucite henschel
	GraphCrunch: a tool for large network analyses [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008) by Tijana Milenkovic, Jason Lai, Natasa Przulj posted to algorithm clustering distributed download networks proj_assembly service by chad_davis on 2008-10-06 16:41:38 as along with 7 people grahamc laughcry barriot guhjy maralena dullhunk ptrobajo
	Analyzing Protein Interaction Networks Using Structural Information [My Copy] Annual Review of Biochemistry, Vol. 77, No. 1. (2008) by Christina Kiel, Pedro Beltrao, Luis Serrano posted to data_integration embl networks ppi proj_assembly proj_interprets review structure by chad_davis to the group structural_bioinformatics on 2008-09-17 16:51:19 as along with 11 people msuarezdiez flbarroso kshameer Borelli bicko neils Evangelia grahamc paolomarcatili phoenixzxl zwang
	Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces. [My Copy] BMC bioinformatics, Vol. 9, No. 1. (2008) by Andrew Bordner, Andrey Gorin posted to annotation binding clustering database non-redundant proj_assembly proj_interprets structure service by chad_davis on 2008-09-16 10:09:39 as along with 6 people somak bicko robfsouza guhjy neils phoenixzxl
	STRING 7--recent developments in the integration and prediction of protein interactions. [My Copy] Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007) by C. von Mering, L. J. Jensen, M. Kuhn, et al.S. Chaffron, T. Doerks, B. Krüger, B. Snel, P. Bork posted to classic data_integration database embl ppi proj_assembly service by chad_davis on 2008-09-16 09:59:56 as along with 16 people anf dragonrez druvus Cortel wenhui guhjy kuhn balajis fisherp raiyar massivemayhem larsjuhljensen higueruelo renatomilani carlk bicko
	United we stand: combining structural methods [My Copy] Current Opinion in Structural Biology, Vol. In Press, Corrected Proof by Nathan P. Cowieson, Bostjan Kobe, Jennifer L. Martin posted to complexes data_integration proj_assembly review structure by chad_davis on 2008-09-13 10:54:58 as along with 2 people dgront paulschlesinger
	DAPID: a 3D-domain annotated protein-protein interaction database. [My Copy] Genome informatics. International Conference on Genome Informatics, Vol. 17, No. 2. (2006), pp. 206-215. by Y. C. Chen, H. C. Chen, J. M. Yang posted to database ppi proj_assembly proj_interprets service structure by chad_davis on 2008-08-26 18:18:15 as along with 1 person bicko
	PPiClust: EFFICIENT CLUSTERING OF 3D PROTEIN-PROTEIN INTERACTION INTERFACES. [My Copy] Journal of bioinformatics and computational biology, Vol. 6, No. 3. (June 2008), pp. 415-433. by Z. Aung, S. H. Tan, S. K. Ng, K. L. 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
	HOMCOS: a server to predict interacting protein pairs and interacting sites by homology modeling of complex structures. [My Copy] Nucleic acids research, Vol. 36, No. Web Server issue. (1 July 2008) by N. Fukuhara, T. Kawabata posted to binding algorithm complexes modelling proj_assembly structure service by chad_davis on 2008-08-21 16:31:17 as along with 2 people bicko guhjy
	Protein Complex Evolution Does Not Involve Extensive Network Rewiring [My Copy] 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 4 people zufar noraziz phoenixzxl cabbagesofdoom
	Ensemble Non-negative Matrix Factorization Methods for Clustering Protein-Protein Interactions [My Copy] Bioinformatics (12 June 2008), btn286. by Derek Greene, Gerard Cagney, Nevan Krogan, Padraig Cunningham posted to algorithm clustering complexes ensemble proj_assembly binding by chad_davis on 2008-08-05 15:26:09 as along with 4 people colmryan svozil zwang grahamc
	ProCope - Protein Complex Prediction and Evaluation [My Copy] Bioinformatics (17 July 2008), btn376. by Jan Krumsiek, Caroline C. Friedel, Ralf Zimmer posted to algorithm complexes data_integration proj_assembly structure toolkit service by chad_davis on 2008-08-03 22:03:17 as along with 4 people carlk saket zwang guhjy
	Understanding and Predicting Protein Assemblies With 3D Structures. [My Copy] Comparative and functional genomics, Vol. 4, No. 4. (2003), pp. 410-415. by P. Aloy, R. B. Russell posted to algorithm classic complexes data_integration embl modelling proj_assembly structure binding by chad_davis on 2008-08-03 18:17:16 as
	Inference of macromolecular assemblies from crystalline state. [My Copy] Journal of molecular biology, Vol. 372, No. 3. (21 September 2007), pp. 774-797. by E. Krissinel, K. Henrick posted to algorithm annotation complexes database embl proj_assembly structure validation binding service by chad_davis on 2008-07-13 16:28:44 as along with 3 people marti rico bicko
	The social network of a cell: Recent advances in interactome mapping. [My Copy] Biotechnology annual review, Vol. 14 (2008), pp. 1-28. by S. Charbonnier, O. Gallego, A. C. Gavin posted to data_integration embl networks proj_assembly review by chad_davis on 2008-07-09 19:38:51 as
	Bacterial cell division protein FtsZ assembles into protofilament sheets and minirings, structural homologs of tubulin polymers. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 93, No. 1. (9 January 1996), pp. 519-523. by H. P. Erickson, D. W. Taylor, K. A. Taylor, D. Bramhill posted to complexes proj_assembly structure binding by chad_davis on 2008-07-07 16:07:55 as
	Designing succinct structural alphabets [My Copy] Bioinformatics, Vol. 24, No. 13. (1 July 2008), pp. i182-189. by Shuai C. Li, Dongbo Bu, Xin Gao, Jinbo Xu, Ming Li posted to algorithm alignment annotation chemistry feature_selection proj_assembly structure by chad_davis on 2008-07-05 16:11:37 as along with 1 person marck
	PSIbase: a database of Protein Structural Interactome map (PSIMAP) [My Copy] Bioinformatics, Vol. 21, No. 10. (15 May 2005), pp. 2541-2543. by Sungsam Gong, Giseok Yoon, Insoo Jang, et al.Dan Bolser, Panos Dafas, Michael Schroeder, Hansol Choi, Yoobok Cho, Kyungsook Han, Sunghoon Lee, Hwanho Choi, Michael Lappe, Liisa Holm, Sangsoo Kim, Donghoon Oh, Jonghwa Bhak posted to algorithm database proj_assembly structure binding service by chad_davis on 2008-07-01 14:43:04 as along with 1 person medic0747
	Homology-based modeling of 3D structures of protein-protein complexes using alignments of modified sequence profiles. [My Copy] International journal of biological macromolecules (21 May 2008) by Petras J J. Kundrotas, Marc F F. Lensink, Emil Alexov posted to algorithm alignment binding complexes data_integration modelling proj_assembly structure by chad_davis to the group structural_bioinformatics on 2008-06-29 11:15:36 as
	Using indirect protein-protein interactions for protein complex prediction. [My Copy] Journal of bioinformatics and computational biology, Vol. 6, No. 3. (June 2008), pp. 435-466. by H. N. Chua, K. Ning, W. K. Sung, H. W. Leong, L. Wong posted to algorithm clustering complexes networks proj_assembly binding by chad_davis on 2008-06-29 11:14:25 as
	Taking advantage of local structure descriptors to analyze interresidue contacts in protein structures and protein complexes [My Copy] 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

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structure	86
complexes	79
algorithm	69
binding	61
ppi	42
networks	35
modelling	32
proj_interprets	32
data_integration	31
database	19
embl	19
clustering	17
review	17
download	16
evolution	16
service	15
classic	14
alignment	12
experimental	12
annotation	11
docking	10
web_service	9
non-redundant	8
yeast	8
statistics	7
validation	6
chemistry	4
ensemble	3
feature_selection	3
toolkit	3
microarray	2
proj_stabperf	2
data_mining	1
disorder	1
distributed	1
em	1
mycoplasma	1
proj_disocons	1

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