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Ключевое слово casp [48 articles]

Recent papers classified by the tag casp.
  • Rigorous performance evaluation in protein structure modelling and implications for computational biology.
    Philos Trans R Soc Lond B Biol Sci, Vol. 361, No. 1467. (29 March 2006), pp. 453-458.
    by J Moult
    posted to casp protein-structure by wouterboomsma on 2006-04-10 09:46:52 as *** along with 2 people chad_davis cdeane
  • A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction.
    Curr Opin Struct Biol (3 June 2005)
    by John Moult
    posted to casp modeling protein by warlock6x3 on 2005-06-25 17:14:35 as *** along with 9 people and 2 groups ujh nigham thaliana marcius ffranca j3xucite dgront granujilla mingzhi BioinfoCIPF SGU-CIPF
  • RMS/Coverage graphs: A qualitative method for comparing three-dimensional protein structure predictions
    Proteins: Structure, Function, and Genetics, Vol. 37, No. S3. (1999), pp. 15-21.
    by Tim JP Hubbard
    posted to casp rmsd by rabio on 2008-03-31 01:35:32 as **
  • Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models.
    Proteins, Vol. 61 Suppl 7 (26 September 2005), pp. 84-90.
    by Andrzej Koliński, Janusz MM Bujnicki
    posted to ab casp casp6 fold folding initio protein recognition by nigham on 2006-04-21 02:28:26 as *** along with 2 people and 2 groups marcius dgront BioinfoCIPF SGU-CIPF
  • Evaluation of domain prediction in CASP6.
    Proteins, Vol. 61 Suppl 7 (26 September 2005), pp. 183-192.
    by Chin-Hsien H Tai, Woei-Jyh J Lee, James JJ 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
  • Comparative modeling in CASP6 using consensus approach to template selection, sequence-structure alignment, and structure assessment.
    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 predictions submitted for the CASP6 comparative modelling category.
    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 read along with 3 people and 2 groups marcius ffranca magia215 BioinfoCIPF SGU-CIPF
  • TASSER: An automated method for the prediction of protein tertiary structures in CASP6.
    Proteins, Vol. 61 Suppl 7 (26 September 2005), pp. 91-98.
    by Yang Zhang, Adrian KK Arakaki, Jeffrey Skolnick
    posted to casp casp6 folding protein tasser by nigham on 2006-04-24 04:50:11 as *** along with 4 people and 2 groups marcius dgront schuylrp mirzazadeh BioinfoCIPF SGU-CIPF
  • Assessment of fold recognition predictions in CASP6.
    Proteins, Vol. 61 Suppl 7 (26 September 2005), pp. 46-66.
    by Guoli Wang, Yumi Jin, Roland LL 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 CASP6 predictions for new and nearly new fold targets.
    Proteins, Vol. 61 Suppl 7 (26 September 2005), pp. 67-83.
    by James JJ Vincent, Chin-Hsien H Tai, BKK 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
  • The protein structure prediction problem could be solved using the current PDB library.
    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 9 people and 3 groups karbak iakes vavi marcius alexg j3xucite kracher schuylrp jfmuggs BioinfoCIPF Immunoinformatics SGU-CIPF
  • The significance of performance ranking in CASP--response to Marti-Renom et al.
    Structure (Camb), Vol. 10, No. 3. (March 2002)
    by J Moult, K Fidelis, A Zemla, T Hubbard, A Tramontano
    posted to cafasp casp by marcius on 2005-10-20 21:34:47 as read along with 2 groups BioinfoCIPF SGU-CIPF
  • CASP6 data processing and automatic evaluation at the protein structure prediction center.
    Proteins (26 September 2005)
    by Andriy Kryshtafovych, Maciej Milostan, Lukasz Szajkowski, Pawel Daniluk, Krzysztof Fidelis
    posted to cafasp casp model_evaluation by marcius on 2005-10-22 08:59:49 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • Free modeling with Rosetta in CASP6.
    Proteins (26 September 2005)
    by Philip Bradley, Lars Malmström, Bin Qian, Jack Schonbrun, Dylan Chivian, David E E Kim, Jens Meiler, Kira M S M Misura, David Baker
    posted to ab-initio cafasp casp structure_prediction by marcius on 2005-10-22 08:58:20 as *** along with 4 people and 2 groups jwm dgront schuylrp mirzazadeh BioinfoCIPF SGU-CIPF
  • SAM-T04: what's new in protein-structure prediction for CASP6.
    Proteins (26 September 2005)
    by Kevin Karplus, Sol Katzman, George Shackleford, Martina Koeva, Jenny Draper, Bret Barnes, Marcia Soriano, Richard Hughey
    posted to cafasp casp sequence_alignment structure_prediction by marcius on 2005-10-22 09:10:38 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • Empirical limits for template-based protein structure prediction: the CASP5 example.
    FEBS Lett, Vol. 579, No. 5. (14 February 2005), pp. 1203-1207.
    by B Contreras-Moreira, I Ezkurdia, ML Tress, A Valencia
    posted to bioinformatics cafasp casp protein_structure by marcius on 2005-10-22 00:54:18 as read along with 3 people and 2 groups karbak iakes magia215 BioinfoCIPF SGU-CIPF
  • Reliability of assessment of protein structure prediction methods.
    Structure (Camb), Vol. 10, No. 3. (March 2002), pp. 435-440.
    by MA Marti-Renom, MS Madhusudhan, A Fiser, B Rost, A Sali
    posted to cafasp casp by marcius on 2005-10-20 21:34:30 as read along with 1 person and 2 groups dgront BioinfoCIPF SGU-CIPF
  • The prediction of protein function at CASP6.
    Proteins (26 September 2005)
    by Simonetta Soro, Anna Tramontano
    posted to casp protein_function by marcius on 2005-10-22 08:55:56 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • Protein structure prediction using a variety of profile libraries and 3D verification.
    Proteins (26 September 2005)
    by Kentaro Tomii, Takatsugu Hirokawa, Chie Motono
    posted to bioinformatics cafasp casp model_assessment structure_prediction by marcius on 2005-10-22 09:11:09 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • Protein structure prediction in CASP6 using CHIMERA and FAMS.
    Proteins (26 September 2005)
    by Mayuko Takeda-Shitaka, Genki Terashi, Daisuke Takaya, Kazuhiko Kanou, Mitsuo Iwadate, Hideaki Umeyama
    posted to bioinformatics cafasp casp sequence_alignment structure_prediction by marcius on 2005-10-22 09:11:43 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • Progress over the first decade of CASP experiments.
    Proteins (26 September 2005)
    by Andriy Kryshtafovych, Ceslovas Venclovas, Krzysztof Fidelis, John Moult
    posted to casp review structure_prediction by marcius on 2005-10-22 08:55:22 as ** along with 4 people and 2 groups bicko ffranca schuylrp granujilla BioinfoCIPF SGU-CIPF
  • SPARKS 2 and SP(3) servers in CASP 6.
    Proteins (26 September 2005)
    by Hongyi Zhou, Yaoqi Zhou
    posted to cafasp casp comparative_modeling model_assessment protein_structure structure_prediction by marcius on 2005-10-22 08:56:27 as *** along with 1 person and 2 groups j3xucite BioinfoCIPF SGU-CIPF
  • RNA 3D structure prediction: (1) assessing rna 3D structure similarity from 2D structure similarity.
    Genome Inform Ser Workshop Genome Inform, Vol. 15, No. 2. (2004), pp. 112-120.
    by JE Barreda D C, Y Shigenobu, E Ichiishi, CA Del Carpio M
    posted to casp comparative_modeling rna secondary_structure structure by marcius on 2005-12-20 06:19:07 as ** along with 1 person and 2 groups eckart_bindewald BioinfoCIPF SGU-CIPF
  • Prediction of novel and analogous folds using fragment assembly and fold recognition.
    Proteins (26 September 2005)
    by D T T Jones, K Bryson, A Coleman, L J J McGuffin, M I I Sadowski, J S S Sodhi, J J J Ward
    posted to cafasp casp comparative_modeling model_assessment protein_fragments protein_structure structure_prediction by marcius on 2005-10-22 08:57:29 as **** along with 2 groups BioinfoCIPF SGU-CIPF
  • Scoring docking models with evolutionary information.
    Proteins, Vol. 60, No. 2. (1 August 2005), pp. 275-280.
    by M Tress, D de Juan, O Graña, MJ Gómez, P Gómez-Puertas, JM González, G López, A Valencia
    posted to bioinformatics cafasp casp protein_interactions by marcius on 2005-10-22 09:02:06 as ** along with 3 people and 2 groups bicko ameetsoni cjeans BioinfoCIPF SGU-CIPF
  • Revisiting the prediction of protein function at CASP6
    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
  • Protein loop structure prediction with flexible stem geometries.
    Proteins (12 October 2005)
    by M Mönnigmann, C A A Floudas
    posted to cafasp casp loop_modeling protein_structure structure_prediction by marcius on 2005-10-22 09:06:47 as ** along with 1 person and 2 groups vavi BioinfoCIPF SGU-CIPF
  • Assessment of disorder predictions in CASP6.
    Proteins (26 September 2005)
    by Yumi Jin, Roland L L Dunbrack
    posted to bioinformatics cafasp casp model_evaluation protein_disorder by marcius on 2005-10-22 09:09:32 as ** along with 2 people and 2 groups niallhaslam chad_davis BioinfoCIPF SGU-CIPF
  • MaxSub: an automated measure for the assessment of protein structure prediction quality.
    Bioinformatics, Vol. 16, No. 9. (September 2000), pp. 776-785.
    by N Siew, A Elofsson, L Rychlewski, D Fischer
    posted to bioinformatics cafasp casp model_evaluation by marcius on 2005-10-21 21:01:19 as ** along with 4 people and 2 groups granujilla BragilMassoud dgront biehl BioinfoCIPF SGU-CIPF
  • Domain definition and target classification for CASP6.
    Proteins (26 September 2005)
    by Michael Tress, Chin-Hsien H Tai, Guoli Wang, Iakes Ezkurdia, Gonzalo López, Alfonso Valencia, Byungkook Lee, Roland L L Dunbrack
    posted to cafasp casp protein_domains by marcius on 2005-10-22 09:01:23 as *** along with 2 groups BioinfoCIPF SGU-CIPF
  • Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM.
    Proteins (26 September 2005)
    by David E E Kim, Dylan Chivian, Lars Malmström, David Baker
    posted to cafasp casp protein_domains ab-initio by marcius on 2005-10-22 09:07:40 as *** along with 1 person and 2 groups jwm BioinfoCIPF SGU-CIPF
  • Can correct protein models be identified?
    Protein Sci, Vol. 12, No. 5. (May 2003), pp. 1073-1086.
    by B Wallner, A Elofsson
    posted to cafasp casp model_assessment by marcius on 2005-10-21 21:10:50 as ** along with 1 person and 2 groups j3xucite BioinfoCIPF SGU-CIPF
  • All are not equal: A benchmark of different homology modeling programs
    Protein Sci, Vol. 14, No. 5. (1 May 2005), pp. 1315-1327.
    by Bjorn Wallner, Arne Elofsson
    posted to cafasp casp comparative_modeling by marcius on 2006-03-02 03:40:24 as ** along with 6 people and 2 groups cdeane karbak eweaver BioNica rsantana hmk BioinfoCIPF SGU-CIPF
  • Practical lessons from protein structure prediction.
    Nucleic Acids Res, Vol. 33, No. 6. (2005), pp. 1874-1891.
    by K Ginalski, NV Grishin, A Godzik, L Rychlewski
    posted to cafasp casp comparative_modeling model_assessment structure_prediction by marcius on 2005-12-22 06:53:06 as ** along with 7 people and 4 groups ana aalibes thaliana okarsligil duartemolha dgront mirzazadeh structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
  • PROTEIN REFINEMENT: A NEW CHALLENGE FOR CASP IN ITS 10TH ANNIVERSARY
    Bioinformatics, Vol. 21, No. 3. (01 February 2005), 277.
    by Alfonso Valencia
    posted to casp protein_structure structure_prediction by karbak on 2005-03-09 23:51:16 as ***
  • 3D-Jury: a simple approach to improve protein structure predictions.
    Bioinformatics, Vol. 19, No. 8. (22 May 2003), pp. 1015-1018.
    by K Ginalski, A Elofsson, D Fischer, L Rychlewski
    posted to casp consensus protein_structure structure_prediction by karbak on 2005-03-15 04:34:04 as *** along with 3 people dgront schuylrp mijam
  • LiveBench-8: the large-scale, continuous assessment of automated protein structure prediction.
    Protein Sci, Vol. 14, No. 1. (January 2005), pp. 240-245.
    by L Rychlewski, D Fischer
    posted to casp protein_structure structure_prediction by karbak on 2005-03-15 00:54:10 as *** along with 1 person dgront
  • Scoring function for automated assessment of protein structure template quality
    Proteins: Structure, Function, and Bioinformatics, Vol. 57, No. 4., pp. 702-710.
    by Yang Zhang, Jeffrey Skolnick
    posted to algorithms casp protein_structure structure_prediction by karbak on 2005-03-15 01:37:18 as *** along with 5 people and 2 groups marcius dgront aengisch rabio granujilla BioinfoCIPF SGU-CIPF
  • Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home.
    Proteins, Vol. 69, No. S8. (25 September 2007), pp. 118-128.
    by Rhiju Das, Bin Qian, Srivatsan Raman, 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 protein_structure_prediction rosetta by jwm on 2007-11-09 09:10:34 as ** along with 1 person Ema
  • Polyadenylation factor CPSF-73 is the pre-mRNA 3'-end-processing endonuclease
    Nature (26 November 2006)
    by Corey R Mandel, Syuzo Kaneko, Hailong Zhang, Damara Gebauer, Vasupradha Vethantham, James L Manley, Liang Tong
    posted to casp by ecattell on 2007-05-30 10:58:40 as **
  • CAFASP-1: critical assessment of fully automated structure prediction methods.
    Proteins, Vol. Suppl 3 (1999), pp. 209-217.
    by D Fischer, C Barret, K Bryson, A Elofsson, A Godzik, D Jones, KJ Karplus, LA Kelley, RM MacCallum, K Pawowski, B Rost, L Rychlewski, M Sternberg
    posted to casp by dgront on 2006-05-25 12:53:07 as read
  • LiveBench-1: continuous benchmarking of protein structure prediction servers.
    Protein Sci, Vol. 10, No. 2. (February 2001), pp. 352-361.
    by JM Bujnicki, A Elofsson, D Fischer, L Rychlewski
    posted to casp threading by dgront on 2006-05-23 17:06:55 as read
  • Problem Solved* (*sort of)
    Science, Vol. 321, No. 5890. (8 August 2008), pp. 784-786.
    by Robert F Service
    posted to review casp by dgront on 2008-09-22 14:55:54 as read along with 2 people reyez paulschlesinger
  • Critical assessment of methods of protein structure prediction (CASP)--round 6.
    Proteins, Vol. 61 Suppl 7 (2005), pp. 3-7.
    by J Moult, K Fidelis, B Rost, T Hubbard, A Tramontano
    posted to casp by dgront on 2007-06-05 13:47:40 as ** along with 4 people j3xucite aengisch schuylrp saunders
  • Protein structure prediction of CASP5 comparative modeling and fold recognition targets using consensus alignment approach and 3D assessment.
    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 read along with 1 person nigham
  • Automated prediction of CASP-5 structures using the Robetta server.
    Proteins, Vol. 53 Suppl 6 (2003), pp. 524-533.
    by D Chivian, DE Kim, L Malmström, P Bradley, T Robertson, P Murphy, CE Strauss, R Bonneau, CA Rohl, D Baker
    posted to casp by dgront on 2006-05-23 16:26:23 as read
  • Progress in Modeling of Protein Structures and Interactions
    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 13 people and 3 groups thaliana jwm vavi KyuhoLee marcius eweaver tny nickolay dgront rsantana mirzazadeh insectopalo barry BioinfoCIPF SGU-CIPF structural_bioinformatics
  • Rosetta predictions in CASP5: successes, failures, and prospects for complete automation.
    Proteins, Vol. 53 Suppl 6 (2003), pp. 457-468.
    by P Bradley, D Chivian, J Meiler, KM Misura, CA Rohl, WR Schief, WJ Wedemeyer, O Schueler-Furman, P Murphy, J Schonbrun, CE Strauss, D Baker
    posted to casp structure-prediction by bicko on 2005-10-17 16:06:54 as **
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