Tag rosetta [105 articles] Export

Recent papers classified by the tag rosetta.

	Macromolecular Modeling with Rosetta [My Copy] Annual Review of Biochemistry, Vol. 77, No. 1. (2008), pp. 363-382. by Rhiju Das, David Baker posted to rosetta review by dgront on 2009-12-04 00:50:07 as along with 10 people bmduggan choonpeng mijam kgutwin carlk phoenixzxl krapnik flbarroso saunders gisle
	Simultaneous prediction of protein folding and docking at high resolution [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 45. (10 November 2009), pp. 18978-18983. by Rhiju Das, Ingemar AndrÃ©, Yang Shen, et al.Yibing Wu, Alexander Lemak, Sonal Bansal, Cheryl H. Arrowsmith, Thomas Szyperski, David Baker posted to unstructured simulation rosetta folding docking das09pdf binding based by paulschlesinger on 2009-11-12 00:10:36 as along with 4 people ahmetbakan apaydin ibuch zwang
	Computational design of affinity and specificity at protein–protein interfaces [My Copy] Current Opinion in Structural Biology, Vol. 19, No. 4. (29 August 2009), pp. 458-463. by John Karanicolas, Brian Kuhlman posted to rosetta review molecular-dynamics interactions design by bmduggan on 2009-10-28 15:28:08 as along with 4 people sobolevnrm VGreiff higueruelo barry
	Generalized ensemble methods for de novo structure prediction [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 5. (3 February 2009), pp. 1415-1420. by Alena Shmygelska, Michael Levitt posted to structure_prediction rosetta energy_function de_novo conformation_serching by rabio on 2009-10-12 10:09:19 as along with 6 people mijam kentsis apaydin nurban hmk amishp
	Muramyl dipeptide-induced differential gene expression in NOD2 mutant and wild-type Crohn's disease patient-derived dendritic cells. [My Copy] Inflammatory bowel diseases, Vol. 14, No. 2. (February 2008), pp. 186-194. by Zuzana Zelinkova, Astrid J. van Beelen, Floor de Kort, et al.Perry D. Moerland, Emiel Ver Loren van Themaat, Anje A. te Velde, Sander J. van Deventer, Esther C. de Jong, Daniel W. Hommes posted to rosetta microarray crohn by ptrobajo on 2009-09-29 16:14:31 as
	Pathway and gene-set activation measurement from mRNA expression data: the tissue distribution of human pathways. [My Copy] Genome biology, Vol. 7, No. 10. (17 October 2006), R93. by David M. Levine, David R. Haynor, John C. Castle, et al.Sergey B. Stepaniants, Matteo Pellegrini, Mao Mao, Jason M. Johnson posted to tissue rosetta pathway humna geneset compendium by ptrobajo on 2009-09-17 10:44:25 as along with 7 people and 1 group daforerog ipark-kaist fisherp dragonrez jfr ealloza heliopais BioinfoCIPF
	Design of a novel globular protein fold with atomic-level accuracy. [My Copy] Science, Vol. 302, No. 5649. (21 November 2003), pp. 1364-1368. by Brian Kuhlman, Gautam Dantas, Gregory C. Ireton, Gabriele Varani, Barry L. Stoddard, David Baker posted to rosetta protein-design by bmduggan on 2009-09-08 19:47:37 as along with 10 people kgutwin Diego_Prada onufriev apaydin dfgreen jwm hmk heymiki kevinchannon ca3295
	Computation of Conformational Coupling in Allosteric Proteins [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (28 August 2009), e1000484. by Brian A. Kidd, David Baker, Wendy E. Thomas posted to sampling rosetta allostery by bmduggan on 2009-09-03 20:49:37 as along with 7 people and 1 group skywalkerus02 sobolevnrm klexa oteri boris_aguilar barry zwang McCammon
	High-resolution structure prediction and the crystallographic phase problem [My Copy] Nature, Vol. 450, No. 7167. (14 October 2007), pp. 259-264. by Bin Qian, Srivatsan Raman, Rhiju Das, et al.Philip Bradley, Airlie J. McCoy, Randy J. Read, David Baker posted to structure-prediction rosetta molecular-dynamics by bmduggan on 2009-09-02 19:58:03 as along with 16 people and 2 groups newton1234 apaydin aheilbut jwm eckart_bindewald ffranca dgront massivemayhem cjeans zwang cactus sobolevnrm boris_aguilar Ema chenway ardalby baker-group OPIG
	Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling. [My Copy] Nature methods, Vol. 6, No. 8. (August 2009), pp. 551-552. by Daniel J. Mandell, Evangelos A. Coutsias, Tanja Kortemme posted to design loop prediction rosetta by tcschen on 2009-08-06 23:26:49 as along with 1 person mijam
	A Comprehensive Analysis of the Structure-Function Relationship in Proteins Based on Local Structure Similarity [My Copy] PLoS ONE, Vol. 4, No. 7. (15 July 2009), e6266. by Torgeir R. Hvidsten, Astrid Lægreid, Andriy Kryshtafovych, Gunnar Andersson, Krzysztof Fidelis, Jan Komorowski posted to localdescriptors rosetta by TRHvidsten on 2009-07-26 12:03:57 as
	Improving NMR protein structure quality by Rosetta refinement: A molecular replacement study [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA. by Theresa A. Ramelot, Srivatsan Raman, Alexandre P. Kuzin, et al.Rong Xiao, Li-Chung Ma, Thomas B. Acton, John F. Hunt, Gaetano T. Montelione, David Baker, Michael A. Kennedy posted to crystallography methods modelling molecular_replacement nmr protein rosetta structure by pansapiens on 2009-06-29 06:27:14 as along with 2 people sunhwan neils
	Kemp elimination catalysts by computational enzyme design [My Copy] Nature, Vol. 453, No. 7192. (19 March 2008), pp. 190-195. by Daniela Rothlisberger, Olga Khersonsky, Andrew M. Wollacott, et al.Lin Jiang, Jason DeChancie, Jamie Betker, Jasmine L. Gallaher, Eric A. Althoff, Alexandre Zanghellini, Orly Dym, Shira Albeck, Kendall N. Houk, Dan S. Tawfik, David Baker posted to enzyme molecular recognition rosetta by whitead to the group Jiang Research Group on 2009-05-26 09:15:42 as along with 12 people and 2 groups barmak7282 baiaixi qbin1304 fralium Diego_Prada apaydin jwm msuarezdiez austin cactus neils sobolevnrm Biocatalysis and Biotransformation baker-group
	Physically realistic homology models built with ROSETTA can be more accurate than their templates. [My Copy] Proc Natl Acad Sci U S A, Vol. 103, No. 14. (4 April 2006), pp. 5361-5366. by K. M. Misura, D. Chivian, C. A. Rohl, D. E. Kim, D. Baker posted to homology-model post-defense rosetta by kgutwin on 2009-05-20 07:38:28 as along with 7 people krapnik j3xucite jwm balajis dgront bilab BioNica
	Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. [My Copy] Proteins, Vol. 69, No. S8. (25 September 2007), pp. 118-128. by Rhiju Das, Bin Qian, Srivatsan Raman, et al.Robert Vernon, James Thompson, Philip Bradley, Sagar Khare, Michael D D. Tyka, Divya Bhat, Dylan Chivian, David E E. Kim, William H H. Sheffler, Lars Malmström, Andrew M M. Wollacott, Chu Wang, Ingemar Andre, David Baker posted to casp post-defense predictions rosetta structure ab-initio by kgutwin on 2009-05-20 07:37:22 as along with 3 people mcbla jwm Ema
	Protein-Protein Docking with Backbone Flexibility [My Copy] Journal of Molecular Biology, Vol. 373, No. 2. (19 October 2007), pp. 503-519. by Chu Wang, Philip Bradley, David Baker posted to docking post-defense rosetta by kgutwin on 2009-05-20 07:36:57 as along with 6 people and 2 groups mijam csrocha barry jwm xdeupi Ema structural_bioinformatics Bioinformatics
	Toward High-Resolution de Novo Structure Prediction for Small Proteins [My Copy] Science, Vol. 309, No. 5742. (16 September 2005), pp. 1868-1871. by Philip Bradley, Kira M. S. Misura, David Baker posted to ab-initio post-defense predictions rosetta structure by kgutwin on 2009-05-19 04:17:00 as along with 11 people and 4 groups ucbcjbm paddydu BragilMassoud ana barry thaliana jwm vavi marcius gbart thamelry structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
	Towards Knowledge Discovery from cDNA Microarray Gene Expression Data [My Copy] In PKDD '00: Proceedings of the 4th European Conference on Principles of Data Mining and Knowledge Discovery (2000), pp. 470-475. by Henryk J. Komorowski, Torgeir R. Hvidsten, Tor K. Jenssen, et al.Dyre Tjeldvoll, Eivind Hovig, Arne K. Sanvik, Astrid L\aegreid posted to rosetta by TRHvidsten on 2009-04-28 10:19:00 as
	[New knowledge derived from measurement of gene expression with the DNA microarray method] [My Copy] Tidsskrift for den Norske lægeforening : tidsskrift for praktisk medicin, ny række, Vol. 121, No. 10. (20 April 2001), pp. 1229-1232. by J. Komorowski, T. R. Hvidsten, T. K. Jenssen, et al.D. Tjeldvoll, E. Hovig, A. Laegreid, A. K. Sandvik posted to rosetta by TRHvidsten on 2009-04-28 10:17:31 as
	Modelling prognostic power of cardiac tests using rough sets. [My Copy] Artificial intelligence in medicine, Vol. 15, No. 2. (February 1999), pp. 167-191. by J. Komorowski, A. Ohrn posted to rosetta by TRHvidsten on 2009-04-28 10:14:28 as
	Learning rough set classifiers from gene expressions and clinical data [My Copy] Fundam. Inf., Vol. 53, No. 2. (2002), pp. 155-183. by Herman Midelfart, Jan Komorowski, Kristin Norsett, Fekadu Yadetie, Arne K. Sandvik, Astrid L\aegreid posted to rosetta by TRHvidsten on 2009-04-28 10:08:24 as
	Predicting gene function from gene expressions and ontologies. [My Copy] Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (2001), pp. 299-310. by T. R. Hvidsten, J. Komorowski, A. K. Sandvik, A. Laegreid posted to rosetta by TRHvidsten on 2009-04-25 14:16:44 as
	Predicting gene ontology biological process from temporal gene expression patterns. [My Copy] Genome Res, Vol. 13, No. 5. (May 2003), pp. 965-979. by A. Lagreid, T. R. Hvidsten, H. Midelfart, J. Komorowski, A. K. Sandvik posted to rosetta by TRHvidsten on 2009-04-25 14:15:58 as along with 3 people klees mr_abali macavity1g
	Learning rule-based models of biological process from gene expression time profiles using Gene Ontology [My Copy] Bioinformatics, Vol. 19, No. 9. (12 June 2003), pp. 1116-1123. by Torgeir R. Hvidsten, Astrid Laegreid, Jan Komorowski posted to rosetta by TRHvidsten on 2009-04-25 14:15:28 as
	Markers of Adenocarcinoma Characteristic of the Site of Origin: Development of a Diagnostic Algorithm [My Copy] Clin Cancer Res, Vol. 11, No. 10. (15 May 2005), pp. 3766-3772. by Jayne L. Dennis, Torgeir R. Hvidsten, Ernst C. Wit, et al.Jan Komorowski, Alexandra K. Bell, Ian Downie, Jacqueline Mooney, Caroline Verbeke, Christopher Bellamy, Nicol W. Keith, Karin A. Oien posted to rosetta by TRHvidsten on 2009-04-25 14:14:59 as
	Discovering regulatory binding-site modules using rule-based learning [My Copy] Genome Research, Vol. 15, No. 6. (June 2005), pp. 856-866. by Torgeir R. Hvidsten, Bartosz Wilczyński, Andriy Kryshtafovych, Jerzy Tiuryn, Jan Komorowski, Krzysztof Fidelis posted to rosetta by TRHvidsten on 2009-04-25 14:14:28 as
	Generalized modeling of enzyme-ligand interactions using proteochemometrics and local protein substructures [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 65, No. 3. (2006), pp. 568-579. by Helena Strömbergsson, Andriy Kryshtafovych, Peteris Prusis, et al.Krzysztof Fidelis, Jarl E. S. Wikberg, Jan Komorowski, Torgeir R. Hvidsten posted to interactions localdescriptors rosetta by TRHvidsten on 2009-04-25 14:13:40 as
	Rough Sets in Bioinformatics [My Copy] Transactions on Rough Sets VII (2007), pp. 225-243. by Torgeir Hvidsten, Jan Komorowski posted to rosetta by TRHvidsten on 2009-04-25 14:12:53 as
	Revealing cell cycle control by combining model-based detection of periodic expression with novel cis-regulatory descriptors [My Copy] BMC Systems Biology, Vol. 1, No. 1. (2007), 45. by Claes Andersson, Torgeir Hvidsten, Anders Isaksson, Mats Gustafsson, Jan Komorowski posted to rosetta by TRHvidsten on 2009-04-25 14:12:01 as
	Gene expression trends and protein features effectively complement each other in gene function prediction [My Copy] Bioinformatics, Vol. 25, No. 3. (1 February 2009), pp. 322-330. by Krzysztof Wabnik, Torgeir R. Hvidsten, Anna Kedzierska, et al.Jelle Van Leene, Geert De Jaeger, Gerrit T. S. Beemster, Jan Komorowski, Martin T. R. Kuiper posted to rosetta by TRHvidsten on 2009-04-25 14:11:17 as along with 5 people and 1 group grimplet jfr guhjy dswan tmmurali Bioinformatics
	Prediction of protein structural class with Rough Sets [My Copy] BMC Bioinformatics, Vol. 7, No. 1. (2006), 20. by Youfang Cao, Shi Liu, Lida Zhang, Jie Qin, Jiang Wang, Kexuan Tang posted to rosetta by TRHvidsten on 2009-04-25 14:08:56 as
	Gene expression based classification of gastric carcinoma [My Copy] Cancer Letters, Vol. 210, No. 2. (July 2004), pp. 227-237. by K. Norsett posted to rosetta by TRHvidsten on 2009-04-25 14:05:02 as
	Aetiology-specific patterns in end-stage heart failure patients identified by functional annotation and classification of microarray data. [My Copy] European journal of heart failure : journal of the Working Group on Heart Failure of the European Society of Cardiology, Vol. 8, No. 4. (June 2006), pp. 381-389. by V. Beisvag, P. K. Lehre, H. Midelfart, et al.H. Aass, O. Geiran, A. K. Sandvik, A. Laegreid, J. Komorowski, O. Ellingsen posted to rosetta by TRHvidsten on 2009-04-25 14:04:34 as
	Computational proteomics analysis of HIV-1 protease interactome [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 68, No. 1. (2007), pp. 305-312. by Aleksejs Kontijevskis, Jarl E. S. Wikberg, Jan Komorowski posted to rosetta by TRHvidsten on 2009-04-25 13:56:09 as
	Rough set-based proteochemometrics modeling of G-protein-coupled receptor-ligand interactions [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 63, No. 1. (2006), pp. 24-34. by Helena Strömbergsson, Peteris Prusis, Herman Midelfart, Maris Lapinsh, Jarl E. S. Wikberg, Jan Komorowski posted to rosetta by TRHvidsten on 2009-04-25 13:55:52 as
	Construction of Rough Set-Based Classifiers for Predicting HIV Resistance to Nucleoside Reverse Transcriptase Inhibitors [My Copy] Granular Computing: At the Junction of Rough Sets and Fuzzy Sets (2008), pp. 249-258. by Marcin Kierczak, Witold Rudnicki, Jan Komorowski posted to rosetta by TRHvidsten on 2009-04-25 13:55:21 as
	Feature Selection for Microarray Data Analysis Using Mutual Information and Rough Set Theory [My Copy] Artificial Intelligence Applications and Innovations (2006), pp. 492-499. by Wengang Zhou, Chunguang Zhou, Guixia Liu, Hong Zhu posted to rosetta by TRHvidsten on 2009-04-25 13:55:05 as
	De Novo Determination of Protein Backbone Structure from Residual Dipolar Couplings Using Rosetta [My Copy] Journal of the American Chemical Society, Vol. 124, No. 11. (1 March 2002), pp. 2723-2729. by Carol A. Rohl, David Baker posted to experimental_restraints nmr rosetta by mcbla on 2009-04-20 17:14:52 as along with 1 person dgront
	Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2006), NA. by Philip Bradley, David Baker posted to de_novo rosetta by dgront on 2009-03-16 02:30:41 as along with 2 people zwang wouterboomsma
	Prediction of membrane protein structures with complex topologies using limited constraints [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 5. (3 February 2009), pp. 1409-1414. by P. Barth, B. Wallner, D. Baker posted to rosetta transmembrane by dgront on 2009-03-06 06:15:19 as along with 10 people and 2 groups rph sebk barry krapnik viktor21614 paulschlesinger zwang apaydin agrossfield amishp OPIG structural_bioinformatics
	Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins. [My Copy] Proteins, Vol. 34, No. 1. (1 January 1999), pp. 82-95. by K. T. Simons, I. Ruczinski, C. Kooperberg, B. A. Fox, C. Bystroff, D. Baker posted to potential rosetta statpot structure by kgutwin on 2009-02-23 16:27:59 as along with 1 person dgront
	Detecting Protein Function and Protein-Protein Interactions from Genome Sequences [My Copy] Science, Vol. 285, No. 5428. (30 July 1999), pp. 751-753. by Edward M. Marcotte, Matteo Pellegrini, Ho-Leung Ng, Danny W. Rice, Todd O. Yeates, David Eisenberg posted to fussion interaction protein rosetta by yonatanf on 2009-01-30 17:08:30 as along with 10 people and 1 group bicko Robinder lfriedl balajis opheliav gurkanbebek ruvido cjeans Evangelia iris_2001 kdl
	Free modeling with Rosetta in CASP6. [My Copy] Proteins (26 September 2005) by Philip Bradley, Lars Malmström, Bin Qian, et al.Jack Schonbrun, Dylan Chivian, David E E. Kim, Jens Meiler, Kira M S M. Misura, David Baker posted to casp fragment prediction rosetta structure by saunders on 2009-01-06 10:02:12 as along with 6 people and 2 groups krapnik jwm marcius dgront schuylrp mirzazadeh BioinfoCIPF SGU-CIPF
	Improved side-chain modeling for protein-protein docking. [My Copy] Protein Sci, Vol. 14, No. 5. (May 2005), pp. 1328-1339. by C. Wang, O. Schueler-Furman, D. Baker posted to docking rosetta rotamers by dgront on 2008-12-30 00:42:27 as along with 11 people and 3 groups csrocha barry aqeel jwm bicko yongzhao blackbart bluvsh1 hmk selrac Evangelia structural_bioinformatics Bioinformatics TSRI_MGL
	Prediction of structures of multidomain proteins from structures of the individual domains. [My Copy] Protein Sci (22 December 2006) by Andrew M M. Wollacott, Alexandre Zanghellini, Paul Murphy, David Baker posted to rosetta by dgront on 2008-12-28 06:07:11 as along with 5 people wouterboomsma choonpeng zwang IrinaMoreira rph
	Advances in Rosetta protein structure prediction on massively parallel systems [My Copy] IBM J. Res. Dev., Vol. 52, No. 1. (2008), pp. 7-17. by S. Raman, B. Qian, D. Baker, R. C. Walker posted to hpc rosetta by kgutwin on 2008-11-19 23:19:17 as along with 1 person j3xucite
	Prolinks: a database of protein functional linkages derived from coevolution. [My Copy] Genome Biol, Vol. 5, No. 5. (2004) by P. M. Bowers, M. Pellegrini, M. J. Thompson, J. Fierro, T. O. Yeates, D. Eisenberg posted to fusion gene prolinks rosetta stone by csanford on 2008-10-27 20:38:05 as along with 8 people and 1 group shung pcahan1 lfriedl balajis opheliav tny sanchezbuelna chasmand kdl
	A combined algorithm for genome-wide prediction of protein function. [My Copy] Nature, Vol. 402, No. 6757. (4 November 1999), pp. 83-86. by E. M. Marcotte, M. Pellegrini, M. J. Thompson, T. O. Yeates, D. Eisenberg posted to rosetta stone by Robinder on 2008-10-23 17:03:06 as along with 7 people and 1 group jperkins dragonrez shivaram lfriedl ruvido cjeans carlk kdl
	Consistent blind protein structure generation from NMR chemical shift data [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 12. (25 March 2008), pp. 4685-4690. by Yang Shen, Oliver Lange, Frank Delaglio, et al.Paolo Rossi, James M. Aramini, Gaohua Liu, Alexander Eletsky, Yibing Wu, Kiran K. Singarapu, Alexander Lemak, Alexandr Ignatchenko, Cheryl H. Arrowsmith, Thomas Szyperski, Gaetano T. Montelione, David Baker, Ad Bax posted to experimental_restraints nmr protein_structure rosetta by dgront on 2008-08-21 21:38:43 as along with 7 people and 1 group siggi84 babakap zwang biehl sunhwan skoddet apaydin Nielsen group
	Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and bayesian scoring functions [My Copy] Journal of Molecular Biology, Vol. 268, No. 1. (25 April 1997), pp. 209-225. by K. Simons posted to ab_initio protein rosetta by joule on 2008-07-22 16:18:52 as along with 12 people and 2 groups chemrahul82 paddydu Diego_Prada reyez guxiyou ana jwm vavi wouterboomsma j3xucite hmk mijam structural_bioinformatics Bioinformatics

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protein_design	15
structure	12
protein	9
casp	7
review	7
post-defense	6
prediction	6
protein_structure_prediction	6
nmr	5
experimental_restraints	4
modeling	4
stone	4
threading	4
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comparative_modeling	3
de_novo	3
design	3
docking	3
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predictions	3
structure-prediction	3
allostery	2
enzyme	2
folding	2
fusion	2
gene	2
localdescriptors	2
loop	2
membrane	2
methods	2
molecular	2
molecular-dynamics	2
ppi_design	2
protein_redesign	2
rdc	2
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alternatives	1
baker	1
based	1
binding	1
cabs	1
clustering	1
compendium	1
conformation_serching	1
continuous_models	1
crohn	1
crystallography	1
das09pdf	1
data	1
denovo	1
determination	1
energy	1
energy_function	1
fragment	1
fragment_library	1
free_energy	1
functional	1
fussion	1
geneset	1
genomic_3d_prediction	1
homology-model	1
hpc	1
humna	1
interaction	1
lattice_models	1
microarray	1
modelling	1
molecular_replacement	1
monte_carlo	1
negative_design	1
popcorn	1
potential	1
ppi_homology	1
predict	1
prolinks	1
protein-design	1
protein_denovo_design	1
protein_engineering	1
protein_simulation	1
protein_structure	1
reduced_models	1
refs_mp	1
residues	1
rotamers	1
sampling	1
sicho	1
simulation	1
simulation_methods	1
software	1
statpot	1
structural	1
tissue	1
transmembrane	1
unres	1
unstructured	1
validation	1

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