chad_davis's algorithm [136 articles] Export

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	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
	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
	Residue contact-count potentials are as effective as residue-residue contact-type potentials for ranking protein decoys. [My Copy] BMC structural biology, Vol. 8 (08 December 2008), 53. by Dan M. Bolser, Ioannis Filippis, Henning Stehr, Jose Duarte, Michael Lappe posted to algorithm binding feature_selection ppi proj_interprets statistics structure validation by chad_davis on 2008-12-18 20:51:09 as along with 3 people tcschen RamuAnandakrishnan krapnik
	Learning to Select Features using their Properties [My Copy] Journal of Machine Learning Research, Vol. 9 (October 2008), pp. 2349-2376. by Eyal Krupka, Amir Navot, Naftali Tishby posted to algorithm classification feature_selection by chad_davis on 2008-11-03 08:25:14 as along with 3 people shpigi sdvillal jjrodriguez
	The Rough Guide to In Silico Function Prediction, or How To Use Sequence and Structure Information To Predict Protein Function [My Copy] PLoS Comput Biol, Vol. 4, No. 10. (31 October 2008), e1000160. by Marco Punta, Yanay Ofran posted to algorithm annotation classification feature_selection review structure by chad_davis on 2008-11-03 08:17:22 as along with 18 people and 1 group kiekyon Thaverkamp niallhaslam daforerog Zalanszabo bpcusack Katje joseph_x_zhou taguchi sjcockell markchen ptrobajo druvus mdstobbe giovenko nilanjanroy reyez GeeSharpMinor microbiology_nijmegen
	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
	PEDANT covers all complete RefSeq genomes. [My Copy] Nucleic acids research (21 October 2008) by Mathias C C. Walter, Thomas Rattei, Roland Arnold, et al.Ulrich Güldener, Martin Münsterkötter, Karamfilka Nenova, Gabi Kastenmüller, Patrick Tischler, Andreas Wölling, Andreas Volz, Norbert Pongratz, Ralf Jost, Hans-Werner W. Mewes, Dmitrij Frishman posted to algorithm annotation classic data_integration database service by chad_davis on 2008-10-27 12:35:52 as along with 1 person guhjy
	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
	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
	Optimal contact map alignment of protein-protein interfaces. [My Copy] Bioinformatics (Oxford, England), Vol. 24, No. 20. (15 October 2008), pp. 2324-2328. by V. Pulim, B. Berger, J. Bienkowska posted to algorithm alignment binding complexes ppi proj_interprets structure by chad_davis on 2008-10-09 18:28:32 as along with 1 person i000
	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
	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
	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
	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
	A tree-based conservation scoring method for short linear motifs in multiple alignments of protein sequences. [My Copy] BMC bioinformatics, Vol. 9 (06 May 2008), 229. by Claudia Chica, Alberto Labarga, Cathryn M. Gould, Rodrigo Lopez, Toby J. Gibson posted to algorithm annotation classification disorder embl evolution ppi statistics service by chad_davis on 2008-10-06 12:49:02 as along with 6 people chica niallhaslam Evangelia cabbagesofdoom biehl alanrw
	The C1C2: a framework for simultaneous model selection and assessment. [My Copy] BMC bioinformatics, Vol. 9, No. 1. (2008) by Martin Eklund, Ola Spjuth, Jarl Wikberg posted to algorithm classification feature_selection proj_stabperf statistics validation by chad_davis on 2008-09-02 12:38:06 as along with 2 people guhjy nuin
	Using 3D Hidden Markov Models that explicitly represent spatial coordinates to model and compare protein structures. [My Copy] BMC Bioinformatics, Vol. 5 (9 January 2004) by V. Alexandrov, M. Gerstein posted to algorithm alignment download structure by chad_davis on 2008-08-29 22:01:20 as along with 1 person Evangelia
	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
	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
	Memory-efficient dynamic programming backtrace and pairwise local sequence alignment. [My Copy] Bioinformatics (Oxford, England) (17 June 2008) by Lee A. A. Newberg posted to algorithm alignment download by chad_davis on 2008-08-12 14:21:27 as along with 4 people ilyashl GustavoLacerda stajich nuin
	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
	MSDmotif: exploring protein sites and motifs [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008), 312. by Adel Golovin, Kim Henrick posted to algorithm complexes database data_integration drug embl structure binding service by chad_davis on 2008-07-17 16:18:19 as along with 6 people pansapiens HawkinsJohnC tjimenez reyez massivemayhem Evangelia
	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
	Exploring the structure and function paradigm [My Copy] Current Opinion in Structural Biology In Nucleic acids / Sequences and topology, Vol. 18, No. 3. (June 2008), pp. 394-402. by Oliver C. Redfern, Benoit Dessailly, Christine A. Orengo posted to algorithm annotation classification evolution review structure by chad_davis on 2008-07-09 14:50:49 as along with 7 people and 1 group yylin bdessailly robfsouza guhjy paulschlesinger marck janasont Orengo Group Journal Picks
	Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. [My Copy] Bioinformatics (Oxford, England), Vol. 15, No. 7-8. (1 July 1999), pp. 563-577. by Gz Hertz, Gd Stormo posted to algorithm alignment download gene_regulation proj_credo statistics by chad_davis on 2008-07-06 17:25:57 as along with 8 people and 1 group megraw tonamswish wowalz yylin tuck indigoviolet dquest lusk EisenLab
	POIMs: positional oligomer importance matrices--understanding support vector machine-based signal detectors [My Copy] Bioinformatics, Vol. 24, No. 13. (1 July 2008), pp. i6-14. by Soren Sonnenburg, Alexander Zien, Petra Philips, Gunnar Ratsch posted to algorithm classification ensemble proj_credo proj_disocons by chad_davis on 2008-07-05 16:29:44 as along with 2 people babakap papamicd
	Efficient algorithms for accurate hierarchical clustering of huge datasets: tackling the entire protein space [My Copy] Bioinformatics, Vol. 24, No. 13. (1 July 2008), pp. i41-49. by Yaniv Loewenstein, Elon Portugaly, Menachem Fromer, Michal Linial posted to algorithm clustering download evolution by chad_davis on 2008-07-05 16:26:30 as along with 5 people isimpson druvus nklee sconlan nuin
	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
	Open source clustering software. [My Copy] Bioinformatics (Oxford, England), Vol. 20, No. 9. (12 June 2004), pp. 1453-1454. by M. J. de Hoon, S. Imoto, J. Nolan, S. Miyano posted to algorithm clustering download toolkit by chad_davis on 2008-07-04 09:28:18 as along with 25 people and 7 groups dakelley rabio klexa oteri arlam ilyashl matterhorn cswinburne mtagaya macowell davidbroadhurst eme oilcan rahul Ayest balajis piscinero metamerist digisoki wnpx rafamayo atopcu ccr calu karlmicha Structural Biology Group TorVergata Fluid-Mechanics-and-Thermal-Science-Research astro SRL Computational_Systems_Biology XMLDataManagement BUiGEM
	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 complexes data_integration modelling proj_assembly structure binding by chad_davis on 2008-06-29 11:15:36 as along with 1 group structural_bioinformatics
	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
	Intrinsic disorder prediction from the analysis of multiple protein fold recognition models. [My Copy] Bioinformatics (Oxford, England) (25 June 2008) by Liam J. J. Mcguffin posted to algorithm classification data_integration disorder ensemble feature_selection proj_disocons structure service by chad_davis on 2008-06-29 10:59:50 as
	Systematic discovery of in vivo phosphorylation networks. [My Copy] Cell, Vol. 129, No. 7. (29 June 2007), pp. 1415-1426. by R. Linding, L. J. Jensen, G. J. Ostheimer, et al.M. A. van Vugt, C. Jørgensen, I. M. Miron, F. Diella, K. Colwill, L. Taylor, K. Elder, P. Metalnikov, V. Nguyen, A. Pasculescu, J. Jin, J. G. Park, L. D. Samson, J. R. Woodgett, R. B. Russell, P. Bork, M. B. Yaffe, T. Pawson posted to algorithm data_integration embl networks binding by chad_davis on 2008-06-20 11:13:19 as along with 21 people and 2 groups rsaito jaimie nzm nedwards MatthiasReimann ptrobajo guhjy skhadar julius zwang cdppublications lp2 psique robrussell snowcrash larsjuhljensen Evangelia renatomilani carlk daed bouncingbudha SysbioMPI-TCells Durbin group
	Reconstruction of protein backbones from the BriX collection of canonical protein fragments. [My Copy] PLoS computational biology, Vol. 4, No. 5. (May 2008) by L. Baeten, J. Reumers, V. Tur, et al.F. Stricher, T. Lenaerts, L. Serrano, F. Rousseau, J. Schymkowitz posted to algorithm database non-redundant structure by chad_davis on 2008-06-17 16:53:00 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
	Structural characterization of components of protein assemblies by comparative modeling and electron cryo-microscopy. [My Copy] Journal of structural biology, Vol. 149, No. 2. (February 2005), pp. 191-203. by M. Topf, M. L. Baker, B. John, W. Chiu, A. Sali posted to algorithm alignment complexes data_integration modelling proj_assembly structure by chad_davis on 2008-05-28 10:37:06 as along with 1 person and 1 group gcaltabiano structural_bioinformatics

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Result page: 1 2 3 Next

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

chad_davis's algorithm [136 articles] Export

chad_davis's tags