Tag casp [72 articles] Export

Recent papers classified by the tag casp.

	Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models. [My Copy] Proteins (26 September 2005) by Andrzej Koliński, Janusz M M. Bujnicki posted to structure_prediction fold_recognition de_novo comparative_modeling casp cabs by rabio on 2009-12-16 12:22:12 as along with 5 people and 2 groups mijam mcbla nigham marcius dgront BioinfoCIPF SGU-CIPF
	A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. [My Copy] Current opinion in structural biology, Vol. 15, No. 3. (3 June 2005), pp. 285-289. by John Moult posted to prediction casp by krapnik on 2009-12-01 14:22:55 as along with 13 people and 2 groups timhubbard flbarroso mcbla ujh nigham thaliana warlock6x3 marcius ffranca j3xucite dgront granujilla mingzhi BioinfoCIPF SGU-CIPF
	Protein structure prediction begins well but ends badly [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 999A. (2009), NA. by Rhodri Saunders, Charlotte M. Deane posted to tertiary structure secondary protein prediction casp bias by saunders to the group OPIG on 2009-11-12 14:21:06 as
	Protein-binding site prediction based on three-dimensional protein modeling [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 77, No. S9. (2009), pp. 152-156. by Mina Oh, Keehyoung Joo, Jooyoung Lee posted to protein_structure prediction model ligand_binding casp by hryk on 2009-10-24 09:07:00 as along with 3 people and 1 group HawkinsJohnC AliC reyez Orengo Group Journal Picks
	Automatic annotation of protein function. [My Copy] Current opinion in structural biology, Vol. 15, No. 3. (June 2005), pp. 267-274. by Alfonso Valencia posted to casp by timhubbard on 2009-08-29 12:59:48 as along with 7 people and 2 groups sgoetz tjimenez dimka kuhn marcius eweaver bootsy BioinfoCIPF SGU-CIPF
	Structure prediction for CASP8 with all-atom refinement using Rosetta [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 77, No. S9. (20 July 2009), pp. 89-99. by Srivatsan Raman, Robert Vernon, James Thompson, et al.Michael Tyka, Ruslan Sadreyev, Jimin Pei, David Kim, Elizabeth Kellogg, Frank DiMaio, Oliver Lange, Lisa Kinch, Will Sheffler, Bong-Hyun Kim, Rhiju Das, Nick V. Grishin, David Baker posted to protein_3d_prediction casp by timhubbard on 2009-08-29 12:55:23 as along with 2 people and 1 group AliC j3xucite Orengo Group Journal Picks
	Assessment of the protein-structure refinement category in CASP8. [My Copy] Proteins, Vol. 9999, No. 9999. (20 July 2009), NA. by Justin L. Maccallum, Lan Hua, Michael J. Schnieders, Vijay S. Pande, Matthew P. Jacobson, Ken A. Dill posted to protein_3d_prediction casp by timhubbard on 2009-08-29 12:53:59 as along with 1 person and 1 group ppgardne Journal picks
	Target domain definition and classification in CASP8 [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 77, No. S9. (2009), pp. 10-17. by Michael L. Tress, Iakes Ezkurdia, Jane S. Richardson posted to casp by ppgardne to the group Journal picks on 2009-07-15 21:23:22 as along with 1 person and 1 group AliC Orengo Group Journal Picks
	Critical assessment of methods of protein structure prediction-Round VII. [My Copy] Proteins, Vol. 69 Suppl 8, No. S8. (5 October 2007), pp. 3-9. by J. Moult, K. Fidelis, A. Kryshtafovych, B. Rost, T. Hubbard, A. Tramontano posted to casp tjph by timhubbard on 2009-07-13 21:22:44 as along with 5 people mijam mcbla j3xucite nigham saunders
	New tools and expanded data analysis capabilities at the protein structure prediction center [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 69, No. S8. (2007), pp. 19-26. by Andriy Kryshtafovych, Andreas Prlic, Zinoviy Dmytriv, et al.Pawel Daniluk, Maciej Milostan, Volker Eyrich, Tim Hubbard, Krzysztof Fidelis posted to casp tjph by timhubbard on 2009-07-13 21:21:45 as along with 1 person TRHvidsten
	Critical assessment of methods of protein structure prediction (CASP)--round 6. [My Copy] Proteins, Vol. 61 Suppl 7 (2005), pp. 3-7. by J. Moult, K. Fidelis, B. Rost, T. Hubbard, A. Tramontano posted to casp tjph by timhubbard on 2009-07-13 08:47:22 as along with 5 people j3xucite dgront aengisch schuylrp saunders
	CASP5 target classification. [My Copy] Proteins, Vol. 53 Suppl 6 (2003), pp. 340-351. by L. N. Kinch, Y. Qi, T. J. Hubbard, N. V. Grishin posted to tjph casp by timhubbard on 2009-07-13 08:34:30 as
	Critical assessment of methods of protein structure prediction (CASP)-round V. [My Copy] Proteins, Vol. 53 Suppl 6, No. S6. (2003), pp. 334-339. by J. Moult, K. Fidelis, A. Zemla, T. Hubbard posted to tjph casp by timhubbard on 2009-07-13 08:34:13 as along with 1 person j3xucite
	The significance of performance ranking in CASP--response to Marti-Renom et al. [My Copy] Structure (Camb), Vol. 10, No. 3. (March 2002) by J. Moult, K. Fidelis, A. Zemla, T. Hubbard, A. Tramontano posted to tjph casp by timhubbard on 2009-07-13 07:37:59 as along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
	Assessment of novel fold targets in CASP4: predictions of three-dimensional structures, secondary structures, and interresidue contacts. [My Copy] Proteins, Vol. Suppl 5 (2001), pp. 98-118. by A. M. Lesk, L. Lo Conte, T. J. Hubbard posted to casp tjph by timhubbard on 2009-07-13 07:33:15 as
	Prediction targets of CASP4. [My Copy] Proteins, Vol. Suppl 5 (2001), pp. 8-12. by A. Murzin, T. J. Hubbard posted to casp tjph by timhubbard on 2009-07-13 07:32:57 as
	Critical assessment of methods of protein structure prediction (CASP): round IV. [My Copy] Proteins, Vol. Suppl 5 (2001), pp. 2-7. by J. Moult, K. Fidelis, A. Zemla, T. Hubbard posted to casp tjph by timhubbard on 2009-07-13 07:31:49 as
	RMS/coverage graphs: a qualitative method for comparing three-dimensional protein structure predictions. [My Copy] Proteins, Vol. Suppl 3 (1999), pp. 15-21. by T. J. Hubbard posted to casp tjph by timhubbard on 2009-07-13 07:28:47 as along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
	Analysis and assessment of ab initio three-dimensional prediction, secondary structure, and contacts prediction. [My Copy] Proteins, Vol. Suppl 3 (1999), pp. 149-170. by C. A. Orengo, J. E. Bray, T. Hubbard, L. LoConte, I. Sillitoe posted to casp tjph by timhubbard on 2009-07-13 07:28:26 as along with 1 person and 1 group sillitoe Orengo Group Journal Picks
	Critical assessment of methods of protein structure prediction (CASP): round III. [My Copy] Proteins, Vol. Suppl 3 (1999), pp. 2-6. by J. Moult, T. Hubbard, K. Fidelis, J. T. Pedersen posted to casp tjph by timhubbard on 2009-07-13 07:28:02 as
	Critical assessment of methods of protein structure prediction (CASP): round II. [My Copy] Proteins, Vol. Suppl 1 (1997), pp. 2-6. by J. Moult, T. Hubbard, S. H. Bryant, K. Fidelis, J. T. Pedersen posted to casp tjph by timhubbard on 2009-07-12 00:18:50 as
	Numerical criteria for the evaluation of ab initio predictions of protein structure. [My Copy] Proteins, Vol. Suppl 1 (1997), pp. 140-150. by A. Zemla, C. Venclovas, A. Reinhardt, K. Fidelis, T. J. Hubbard posted to casp tjph by timhubbard on 2009-07-12 00:07:14 as
	Fold recognition and ab initio structure predictions using hidden Markov models and beta-strand pair potentials. [My Copy] Proteins, Vol. 23, No. 3. (November 1995), pp. 398-402. by T. J. Hubbard, J. Park posted to casp protein_3d_prediction tjph by timhubbard on 2009-07-11 23:56:57 as
	Template-based modeling and free modeling by I-TASSER in CASP7 [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 69, No. S8. (2007), pp. 108-117. by Yang Zhang posted to casp post-defense predictions structure tasser ab-initio by kgutwin on 2009-05-20 07:39:31 as
	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
	Assessment of CASP7 structure predictions for template free targets [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 69, No. S8. (2007), pp. 57-67. by Ralf Jauch, Hock C. Yeo, Prasanna R. Kolatkar, Neil D. Clarke posted to casp by mcbla on 2009-04-20 21:31:41 as
	QMEAN: A comprehensive scoring function for model quality assessment. [My Copy] Proteins (11 October 2007) by Pascal Benkert, Silvio C E C. Tosatto, Dietmar Schomburg posted to casp force function mean potentials scoring statistical by larian on 2009-01-16 09:25:08 as along with 4 people cat_hutchinson68 j3xucite sebk cdeane
	Progress over the first decade of CASP experiments. [My Copy] Proteins (26 September 2005) by Andriy Kryshtafovych, Ceslovas Venclovas, Krzysztof Fidelis, John Moult posted to assessment casp progress by saunders on 2009-01-06 13:30:33 as along with 5 people and 2 groups bicko marcius ffranca schuylrp granujilla BioinfoCIPF SGU-CIPF
	Progress from CASP6 to CASP7. [My Copy] Proteins, Vol. 69 Suppl 8 (2007), pp. 194-207. by A. Kryshtafovych, K. Fidelis, J. Moult posted to assessment casp progress by saunders on 2009-01-06 13:30:01 as
	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
	Evaluation of 3D-Jury on CASP7 models [My Copy] BMC Bioinformatics, Vol. 8 (21 August 2007), 304. by László Kaján, Leszek Rychlewski posted to casp comparative_modeling by mcbla on 2008-11-24 00:26:42 as along with 1 person rabio
	Problem Solved* (sort of) [My Copy] Science*, Vol. 321, No. 5890. (8 August 2008), pp. 784-786. by Robert F. Service posted to casp review by dgront on 2008-09-22 14:55:54 as along with 3 people krisjack reyez paulschlesinger
	The protein structure prediction problem could be solved using the current PDB library. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 4. (25 January 2005), pp. 1029-1034. by Y. Zhang, J. Skolnick posted to casp homology modelling pdb prediction protein structure by neils on 2008-06-12 07:42:10 as along with 14 people and 3 groups Lombardo_7 semin xingwuliu mijam sschurer karbak iakes vavi marcius alexg j3xucite kracher schuylrp jfmuggs BioinfoCIPF Immunoinformatics SGU-CIPF
	RMS/Coverage graphs: A qualitative method for comparing three-dimensional protein structure predictions [My Copy] Proteins: Structure, Function, and Genetics, Vol. 37, No. S3. (1999), pp. 15-21. by Tim J. P. Hubbard posted to casp rmsd by rabio on 2008-03-31 01:35:32 as along with 1 person mijam
	Rigorous performance evaluation in protein structure modelling and implications for computational biology. [My Copy] Philos Trans R Soc Lond B Biol Sci, Vol. 361, No. 1467. (29 March 2006), pp. 453-458. by J. Moult posted to casp modelling by cdeane on 2007-11-22 09:47:29 as along with 2 people chad_davis wouterboomsma
	TASSER: An automated method for the prediction of protein tertiary structures in CASP6. [My Copy] Proteins, Vol. 61 Suppl 7 (26 September 2005), pp. 91-98. by Yang Zhang, Adrian K. K. Arakaki, Jeffrey Skolnick posted to casp by dgront on 2007-06-05 14:09:58 as along with 4 people and 2 groups nigham marcius schuylrp mirzazadeh BioinfoCIPF SGU-CIPF
	Polyadenylation factor CPSF-73 is the pre-mRNA 3'-end-processing endonuclease [My Copy] Nature (26 November 2006) by Corey R. Mandel, Syuzo Kaneko, Hailong Zhang, et al.Damara Gebauer, Vasupradha Vethantham, James L. Manley, Liang Tong posted to casp by ecattell on 2007-05-30 10:58:40 as
	Revisiting the prediction of protein function at CASP6 [My Copy] FEBS Journal, Vol. 273, No. 13. (July 2006), pp. 2977-2983. by Pellegrini-Calace, Marialuisa, Soro, Simonetta, Tramontano, Anna posted to casp protein_function by marcius on 2006-08-31 17:02:04 as along with 2 groups BioinfoCIPF SGU-CIPF
	Reliability of assessment of protein structure prediction methods. [My Copy] Structure (Camb), Vol. 10, No. 3. (March 2002), pp. 435-440. by M. A. Marti-Renom, M. S. Madhusudhan, A. Fiser, B. Rost, A. Sali posted to casp comparative_modeling by dgront on 2006-07-17 16:58:59 as along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
	Progress in Modeling of Protein Structures and Interactions [My Copy] Science, Vol. 310, No. 5748. (28 October 2005), pp. 638-642. by Ora Schueler-Furman, Chu Wang, Phil Bradley, Kira Misura, David Baker posted to capri casp ppi-review review by bicko on 2006-06-21 14:30:25 as along with 18 people and 3 groups krapnik rabio ucbcjbm paddydu flbarroso thaliana jwm vavi KyuhoLee marcius eweaver tny nickolay dgront rsantana mirzazadeh insectopalo barry BioinfoCIPF SGU-CIPF structural_bioinformatics
	CAFASP-1: critical assessment of fully automated structure prediction methods. [My Copy] Proteins, Vol. Suppl 3 (1999), pp. 209-217. by D. Fischer, C. Barret, K. Bryson, et al.A. Elofsson, A. Godzik, D. Jones, K. J. Karplus, L. A. Kelley, R. M. MacCallum, K. Pawowski, B. Rost, L. Rychlewski, M. Sternberg posted to casp by dgront on 2006-05-25 12:53:07 as
	LiveBench-1: continuous benchmarking of protein structure prediction servers. [My Copy] Protein Sci, Vol. 10, No. 2. (February 2001), pp. 352-361. by J. M. Bujnicki, A. Elofsson, D. Fischer, L. Rychlewski posted to casp threading by dgront on 2006-05-23 17:06:55 as
	LiveBench-8: the large-scale, continuous assessment of automated protein structure prediction. [My Copy] Protein Sci, Vol. 14, No. 1. (January 2005), pp. 240-245. by L. Rychlewski, D. Fischer posted to casp server by dgront on 2006-05-23 17:04:33 as along with 1 person karbak
	Protein structure prediction of CASP5 comparative modeling and fold recognition targets using consensus alignment approach and 3D assessment. [My Copy] Proteins, Vol. 53 Suppl 6 (2003), pp. 410-417. by K. Ginalski, L. Rychlewski posted to casp by dgront on 2006-05-23 16:35:43 as along with 1 person nigham
	Automated prediction of CASP-5 structures using the Robetta server. [My Copy] Proteins, Vol. 53 Suppl 6 (2003), pp. 524-533. by D. Chivian, D. E. Kim, L. Malmström, et al.P. Bradley, T. Robertson, P. Murphy, C. E. Strauss, R. Bonneau, C. A. Rohl, D. Baker posted to casp by dgront on 2006-05-23 16:26:23 as
	Comparative modeling in CASP6 using consensus approach to template selection, sequence-structure alignment, and structure assessment. [My Copy] Proteins, Vol. 61 Suppl 7 (2005), pp. 99-105. by C. Venclovas, M. Margelevicius posted to casp casp6 folding homology modeling protein by nigham on 2006-04-24 09:41:12 as along with 1 person schuylrp
	Assessment of CASP6 predictions for new and nearly new fold targets. [My Copy] Proteins, Vol. 61 Suppl 7 (26 September 2005), pp. 67-83. by James J. J. Vincent, Chin-Hsien H. Tai, B. K. K. Sathyanarayana, Byungkook Lee posted to ab casp casp6 fold folding initio new protein by nigham on 2006-04-21 09:44:38 as along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
	Assessment of fold recognition predictions in CASP6. [My Copy] Proteins, Vol. 61 Suppl 7 (26 September 2005), pp. 46-66. by Guoli Wang, Yumi Jin, Roland L. L. Dunbrack posted to casp casp6 fold folding protein recognition by nigham on 2006-04-20 03:09:00 as along with 3 people and 2 groups marcius schuylrp janasont BioinfoCIPF SGU-CIPF
	Assessment of predictions submitted for the CASP6 comparative modelling category. [My Copy] Proteins, Vol. 61 Suppl 7 (26 September 2005), pp. 27-45. by Michael Tress, Iakes Ezkurdia, Osvaldo Graña, Gonzalo López, Alfonso Valencia posted to casp casp6 comparative folding homology modeling protein by nigham on 2006-04-18 02:55:28 as along with 3 people and 2 groups marcius ffranca magia215 BioinfoCIPF SGU-CIPF
	Evaluation of domain prediction in CASP6. [My Copy] Proteins, Vol. 61 Suppl 7 (26 September 2005), pp. 183-192. by Chin-Hsien H. Tai, Woei-Jyh J. Lee, James J. J. Vincent, Byungkook Lee posted to casp casp6 folding prediction protein by nigham on 2006-04-12 07:08:26 as along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF

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cafasp	75
structure_prediction	40
comparative_modeling	22
protein_structure	22
bioinformatics	21
model_evaluation	21
model_assessment	18
tjph	15
protein	13
ab-initio	11
structure	10
protein_domains	9
review	9
casp6	8
folding	8
prediction	8
rosetta	7
protein_function	6
sequence_alignment	6
threading	5
fold	3
homology	3
loop_modeling	3
modeling	3
protein_3d_prediction	3
protein_disorder	3
protein_fragments	3
protein_interactions	3
protein_threading	3
rna	3
secondary_structure	3
structure_alignment	3
ab	2
assessment	2
bias	2
cabs	2
initio	2
modelling	2
pdb	2
post-defense	2
predictions	2
progress	2
recognition	2
secondary	2
server	2
structure-prediction	2
tasser	2
tertiary	2
1st-yr-report	1
algorithms	1
capri	1
comparative	1
consensus	1
de_novo	1
fold_recognition	1
force	1
fragment	1
function	1
hmm	1
ligand_binding	1
mean	1
model	1
new	1
potentials	1
ppi-review	1
protein-structure	1
protein_structure_prediction	1
rmsd	1
scoring	1
statistical	1
strutcture_prediction	1

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