chad_davis's library 527 articles Export

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	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
	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
	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
	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
	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
	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
	MotifVoter: a novel ensemble method for fine-grained integration of generic motif finders. [My Copy] 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 5 people wowalz druvus nuin maximilianh idonaldson
	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
	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
	Incorporating high-throughput proteomics experiments into structural biology pipelines: Identification of the low-hanging fruits. [My Copy] Proteomics, Vol. 8, No. 10. (19 May 2008), pp. 1959-1964. by Roland A. A. 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. [My Copy] BMC genomics, Vol. 9 Suppl 1 (2008) by J. Hecker, J. Y. Yang, J. Cheng posted to algorithm classification disorder proj_disocons review structure by chad_davis on 2008-04-20 11:16:25 as
	Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. [My Copy] Genome research, Vol. 14, No. 6. (June 2004), pp. 1107-1118. by H. Yu, N. M. Luscombe, H. X. Lu, et al.X. Zhu, Y. Xia, J. D. 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 12 people and 1 group kiekyon rsaito thegoose2 robfsouza carlk tharris bicko dragonrez balajis koller cjeans cerca C. elegans / WormBase
	WI-PHI: A weighted yeast interactome enriched for direct physical interactions. [My Copy] 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. [My Copy] Biochim Biophys Acta, Vol. 1764, No. 9. (September 2006), pp. 1498-1511. by P. J. 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. [My Copy] 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 [My Copy] 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 17 people and 1 group Diego_Prada xdeupi 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 [My Copy] 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 [My Copy] Nature, Vol. 450, No. 7170. (29 November 2007), pp. 683-694. by Frank Alber, Svetlana Dokudovskaya, Liesbeth M. Veenhoff, et al.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 9 people mijam bicko neils cjeans zwang CameronNeylon faion phoenixzxl higueruelo
	The molecular architecture of the nuclear pore complex [My Copy] Nature, Vol. 450, No. 7170. (29 November 2007), pp. 695-701. by Frank Alber, Svetlana Dokudovskaya, Liesbeth M. Veenhoff, et al.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 9 people kgutwin MatthiasReimann hadesnumb neils cjeans zwang mkikkawa faion phoenixzxl
	Melina II: a web tool for comparisons among several predictive algorithms to find potential motifs from promoter regions. [My Copy] 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 ensemble gene_regulation proj_credo service by chad_davis on 2007-11-16 13:36:52 as along with 1 person guhjy
	Structural disorder promotes assembly of protein complexes [My Copy] BMC Structural Biology, Vol. 7, No. 1. (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
	The Many Faces of Protein-Protein Interactions: A Compendium of Interface Geometry [My Copy] PLoS computational biology, Vol. 2, No. 9. (29 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 10 people and 2 groups winterschlaefer 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. [My Copy] Protein Sci, Vol. 13, No. 4. (April 2004), pp. 1043-1055. by O. Keskin, C. J. Tsai, H. Wolfson, R. Nussinov posted to non-redundant structure binding by chad_davis on 2007-09-26 14:06:27 as along with 8 people flbarroso marti thomaskelder baaden bicko nickolay henschel ladab
	Reconstitution, activities, and structure of the eukaryotic RNA exosome. [My Copy] Cell, Vol. 127, No. 6. (15 December 2006), pp. 1223-1237. by Q. Liu, J. C. Greimann, C. D. Lima posted to classic complexes experimental structure by chad_davis on 2007-09-18 09:28:38 as along with 2 people martainn jrweir82
	POODLE-L: a two-level SVM prediction system for reliably predicting long disordered regions [My Copy] 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. [My Copy] Mol Biotechnol, Vol. 34, No. 1. (September 2006), pp. 69-93. by C. Rohl, Y. Price, T. B. Fischer, M. Paczkowski, M. F. Zettel, J. Tsai posted to database review structure binding by chad_davis on 2007-09-04 10:55:50 as along with 2 people flbarroso bicko
	Benchmarking of dimeric threading and structure refinement. [My Copy] 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. [My Copy] 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 8 people kaarsinogen bicko mdimmic cjeans selrac iris_2001 wilbur kgutwin
	How optimal are the binding energetics of barnase and barstar? [My Copy] Biophysical journal, Vol. 87, No. 3. (September 2004), pp. 1618-1630. by T. Wang, S. Tomic, R. R. Gabdoulline, R. C. Wade posted to chemistry experimental structure binding by chad_davis on 2007-08-19 12:50:35 as along with 3 people flbarroso dfgreen ras
	SCOPPI: a structural classification of protein-protein interfaces. [My Copy] Nucleic acids research, Vol. 34, No. Database issue. (1 January 2006) by C. Winter, A. Henschel, W. K. Kim, M. Schroeder posted to annotation classification clustering complexes database binding by chad_davis on 2007-08-15 12:12:11 as along with 10 people and 4 groups winterschlaefer higueruelo sjcockell ana kuhn bicko marcius choonpeng Evangelia kintoki structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
	Empirical potentials and functions for protein folding and binding. [My Copy] 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 2 people and 2 groups kgutwin marcius BioinfoCIPF SGU-CIPF
	Protein-Protein Interactions More Conserved within Species than across Species [My Copy] PLoS computational biology, Vol. 2, No. 7. (21 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 7 people and 2 groups chica RebeccaHamer robfsouza jeremymiller marcius skhadar dquest BioinfoCIPF SGU-CIPF
	PIPER: an FFT-based protein docking program with pairwise potentials. [My Copy] Proteins, Vol. 65, No. 2. (1 November 2006), pp. 392-406. by D. Kozakov, R. Brenke, S. R. 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 [My Copy] J. Biol. Chem., Vol. 271, No. 25. (21 June 1996), pp. 15292-15297. by David M. Ornitz, Jingsong Xu, Jennifer S. Colvin, et al.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 1 person lisa1
	Stability of macromolecular complexes. [My Copy] Proteins, Vol. 48, No. 4. (1 September 2002), pp. 645-653. by N. Brooijmans, K. A. Sharp, I. D. 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. [My Copy] Nucleic Acids Res, Vol. 35, No. Database issue. (January 2007) by M. Sickmeier, J. A. Hamilton, T. Legall, et al.V. Vacic, M. S. Cortese, A. Tantos, B. Szabo, P. Tompa, J. Chen, V. N. Uversky, Z. Obradovic, A. K. 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. [My Copy] EMBO J, Vol. 22, No. 14. (15 July 2003), pp. 3486-3492. by I. M. Nooren, J. M. 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. [My Copy] PLoS computational biology, Vol. 2, No. 11. (17 November 2006) by E. D. Levy, Pereira J. B. Leal, C. Chothia, S. A. Teichmann posted to classification non-redundant structure database binding by chad_davis on 2007-03-21 12:46:03 as along with 3 people and 1 group flbarroso bicko Einat structural_bioinformatics
	Identification of distant homologues of fibroblast growth factors suggests a common ancestor for all beta-trefoil proteins. [My Copy] J Mol Biol, Vol. 302, No. 5. (6 October 2000), pp. 1041-1047. by C. P. Ponting, R. B. Russell posted to embl evolution structure by chad_davis on 2007-03-19 11:03:15 as
	Correlated sequence-signatures as markers of protein-protein interaction. [My Copy] 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. [My Copy] J Mol Recognit, Vol. 18, No. 5. (t 2005), pp. 343-384. by V. N. Uversky, C. J. Oldfield, A. K. 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. [My Copy] Proteins, Vol. 58, No. 1. (1 January 2005), pp. 144-150. by S. Lise, D. T. 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. [My Copy] Biochemistry, Vol. 45, No. 22. (6 June 2006), pp. 6873-6888. by J. Liu, N. B. Perumal, C. J. Oldfield, E. W. Su, V. N. Uversky, A. K. Dunker posted to disorder gene_regulation proj_disocons by chad_davis on 2006-07-21 13:22:46 as
	Fast fitting of atomic structures to low-resolution electron density maps by surface overlap maximization. [My Copy] J Mol Biol, Vol. 338, No. 4. (7 May 2004), pp. 783-793. by H. Ceulemans, R. B. Russell posted to algorithm embl structure by chad_davis on 2006-06-23 09:46:03 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
	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
	R/parallel - speeding up bioinformatics analysis with R [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (22 September 2008), 390. by Gonzalo Vera, Ritsert C. Jansen, Remo L. Suppi posted to algorithm distributed download proj_stabperf toolkit by chad_davis on 2008-10-09 15:13:43 as along with 26 people and 1 group Zephyrus daveGerrard sotacam cassj walshtp dposada jfr Yanno siebert operon talponer guhjy dakelley ptrobajo pengchy shikin robertlischke chrisamiller cisevol druvus renatomilani rdiaz nuin GeeSharpMinor neils jandot BergmanLab
	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
	Identifying Cognate Binding Pairs among a Large Set of Paralogs: The Case of PE/PPE Proteins of Mycobacterium tuberculosis [My Copy] PLoS Comput Biol, Vol. 4, No. 9. (2008), e1000174. by Robert Riley, Matteo Pellegrini, David Eisenberg posted to algorithm evolution ppi proj_interprets by chad_davis on 2008-10-06 13:56:25 as along with 2 people robfsouza Ema

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structure	236
binding	152
algorithm	136
review	112
embl	98
proj_disocons	82
database	81
complexes	80
classic	79
classification	79
proj_assembly	66
evolution	64
statistics	64
networks	58
disorder	53
modelling	49
service	46
feature_selection	44
ppi	42
proj_credo	40
data_integration	36
download	36
gene_regulation	30
yeast	29
annotation	28
proj_interprets	27
toolkit	25
validation	24
clustering	22
experimental	20
alignment	19
microarray	18
disease	16
chemistry	15
non-redundant	12
proj_stabperf	11
ensemble	10
data_mining	9
mpi	9
docking	8
drug	7
proj_cct	6
proj_bachelor	4
distributed	3

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