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Ключевое слово structure_prediction [102 articles]

Recent papers classified by the tag structure_prediction.
  • Structural prediction of peptides bound to MHC class I.
    J Mol Biol, Vol. 356, No. 2. (17 February 2006), pp. 521-546.
    by T Fagerberg, JC Cerottini, O Michielin
    posted to molecular_dynamics protein simulated_annealing structure_prediction by vavi on 2006-07-31 08:54:09 as **
  • CODA: a combined algorithm for predicting the structurally variable regions of protein models.
    Protein Sci, Vol. 10, No. 3. (March 2001), pp. 599-612.
    by CM Deane, TL Blundell
    posted to hybrid protein structure_prediction by vavi on 2006-08-05 13:07:33 as ** along with 2 people medic0747 cdeane
  • Prediction of loop geometries using a generalized born model of solvation effects
    Proteins: Structure, Function, and Genetics, Vol. 35, No. 2. (1999), pp. 173-183.
    by Chaya S Rapp, Richard A Friesner
    posted to ab_initio molecular_dynamics monte_carlo protein structure_prediction by vavi on 2006-07-31 09:23:54 as **
  • Comparative protein modelling by satisfaction of spatial restraints.
    J Mol Biol, Vol. 234, No. 3. (5 December 1993), pp. 779-815.
    by A Sali, TL Blundell
    posted to protein structure_prediction by vavi on 2006-07-25 13:44:57 as ** along with 11 people dimka bicko chad_davis ttjoseph skhadar dgront rabio massivemayhem medic0747 sebk granujilla
  • Recovery of protein structure from contact maps.
    Fold Des, Vol. 2, No. 5. (1997), pp. 295-306.
    by M Vendruscolo, E Kussell, E Domany
    posted to contact_map structure_prediction by vavi on 2006-06-27 15:42:14 as read along with 3 people dgront babakap mijam
  • Protein fold recognition and dynamics in the space of contact maps
    Proteins: Structure, Function, and Genetics, Vol. 26, No. 4. (1996), pp. 391-410.
    by Leonid Mirny, Eytan Domany
    posted to contact_maps structure_prediction by vavi on 2006-07-02 13:37:50 as **
  • Protein structure prediction and structural genomics.
    Science, Vol. 294, No. 5540. (5 October 2001), pp. 93-96.
    by D Baker, A Sali
    posted to review structure_prediction by vavi on 2006-06-25 13:36:51 as ** along with 7 people and 2 groups ana dgront sriram_s mirzazadeh mingzhi granujilla janasont structural_bioinformatics Bioinformatics
  • Reconstruction of protein structures from a vectorial representation.
    Phys Rev Lett, Vol. 92, No. 21. (28 May 2004)
    by M Porto, U Bastolla, HE Roman, M Vendruscolo
    posted to contact_map structure_comparison structure_prediction by vavi on 2006-06-27 15:48:24 as *** along with 1 person dgront
  • 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 protein review structure_prediction by vavi on 2006-11-29 14:59:03 as ** along with 13 people and 3 groups thaliana jwm bicko KyuhoLee marcius eweaver tny nickolay dgront rsantana mirzazadeh insectopalo barry BioinfoCIPF SGU-CIPF structural_bioinformatics
  • Exploratory studies of ab initio protein structure prediction: multiple copy simulated annealing, AMBER energy functions, and a generalized born/solvent accessibility solvation model.
    Proteins, Vol. 46, No. 1. (1 January 2002), pp. 128-146.
    by Y Liu, DL Beveridge
    posted to ab_initio molecular_dynamics monte_carlo protein simulated_annealing structure_prediction by vavi on 2006-07-31 09:00:25 as **
  • Efficient dynamics in the space of contact maps.
    Fold Des, Vol. 3, No. 5. (1998), pp. 329-336.
    by M Vendruscolo, E Domany
    posted to structure_prediction contact_map by vavi on 2006-06-27 15:45:31 as read
  • Evolution and physics in comparative protein structure modeling.
    Acc Chem Res, Vol. 35, No. 6. (June 2002), pp. 413-421.
    by A Fiser, M Feig, CL Brooks, A Sali
    posted to comparative_modeling structure_prediction by vavi on 2006-10-11 16:51:26 as ** along with 2 people and 2 groups barry insectopalo structural_bioinformatics Bioinformatics
  • notes ArchPRED: a template based loop structure prediction server.
    Nucleic Acids Res, Vol. 34, No. Web Server issue. (1 July 2006)
    by N Fernandez-Fuentes, J Zhai, A Fiser
    posted to fiser loop_modeling server structure_prediction by vavi on 2006-07-24 09:18:59 as *** along with 2 people eckart_bindewald cdeane
  • Protein loop structure prediction with flexible stem geometries.
    Proteins (12 October 2005)
    by M Mönnigmann, C A A Floudas
    posted to loop protein structure_prediction by vavi on 2005-10-20 13:19:50 as *** along with 1 person and 2 groups marcius BioinfoCIPF SGU-CIPF
  • Ab initio protein structure prediction: progress and prospects.
    Annu Rev Biophys Biomol Struct, Vol. 30 (2001), pp. 173-189.
    by R Bonneau, D Baker
    posted to ab_initio protein review structure_prediction by vavi on 2006-07-25 14:29:29 as ** along with 1 person dgront
  • Kemp elimination catalysts by computational enzyme design
    Nature (19 March 2008)
    by Daniela Röthlisberger, Olga Khersonsky, Andrew M Wollacott, 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 protein_engineering structure_prediction by sobolevnrm on 2008-06-27 12:04:48 as read along with 5 people and 1 group jwm msuarezdiez austin cactus neils baker-group
  • Prediction of the structure of symmetrical protein assemblies
    Proceedings of the National Academy of Sciences (31 October 2007), 0702626104.
    by Ingemar Andre, Philip Bradley, Chu Wang, David Baker
    posted to structure_prediction by sobolevnrm on 2007-12-18 12:53:24 as read along with 4 people and 2 groups jwm jmrivort cjeans zwang Supramolecular baker-group
  • High-resolution structure prediction and the crystallographic phase problem
    Nature (14 October 2007)
    by Bin Qian, Srivatsan Raman, Rhiju Das, Philip Bradley, Airlie J Mccoy, Randy J Read, David Baker
    posted to protein_folding structure_prediction by sobolevnrm on 2007-12-17 12:41:20 as read along with 15 people and 2 groups apaydin aheilbut jwm chad_davis eckart_bindewald ffranca dgront massivemayhem cjeans zwang cactus boris_aguilar Ema chenway ardalby baker-group OPIG
  • Monte Carlo refinement of rigid-body protein docking structures with backbone displacement and side-chain optimization
    Protein Sci, Vol. 16, No. 12. (1 December 2007), pp. 2716-2725.
    by Stephan Lorenzen, Yang Zhang
    posted to protein-protein_interactions structure_prediction by sobolevnrm on 2007-12-21 12:26:27 as read along with 1 group baker-group
  • Prediction of membrane-protein topology from first principles
    Proceedings of the National Academy of Sciences, Vol. 105, No. 20. (20 May 2008), pp. 7177-7181.
    by Andreas Bernsel, Hakan Viklund, Jenny Falk, Erik Lindahl, Gunnar von Heijne, Arne Elofsson
    posted to biomembranes protein-membrane_interactions structure_prediction by sobolevnrm on 2008-05-20 20:09:18 as read along with 1 person and 1 group superpyrin baker-group
  • A correlation-based method for the enhancement of scoring functions on funnel-shaped energy landscapes
    Proteins: Structure, Function, and Bioinformatics, Vol. 63, No. 1. (2006), pp. 155-164.
    by Andrew W Stumpff-Kane, Michael Feig
    posted to protein-ligand_interactions structure_prediction by sobolevnrm on 2007-12-18 13:05:11 as read along with 1 group baker-group
  • Computational analysis of alpha-helical membrane protein structure: implications for the prediction of 3D structural models.
    Protein Eng Des Sel, Vol. 17, No. 8. (August 2004), pp. 613-624.
    by TA Eyre, L Partridge, JM Thornton
    posted to computational membrane_protein protein_structure structure_prediction by rmj001 on 2005-01-19 09:56:30 as ** along with 2 people karbak thaliana
  • I-TASSER server for protein 3D structure prediction
    BMC Bioinformatics, Vol. 9 (23 January 2008), 40.
    by Yang Zhang
    posted to structure_prediction by rabio on 2008-04-14 19:28:05 as ** along with 4 people chad_davis mkurc zwang mclarenv
  • Structural genomics analysis of alternative splicing and application to isoform structure modeling.
    Proc Natl Acad Sci U S A (14 December 2005)
    by Peng Wang, Bo Yan, Jun-Tao T Guo, Chindo Hicks, Ying Xu
    posted to bioinformatics evolution sequence structural_genomics structure_prediction by marcius on 2005-12-22 03:26:15 as ** along with 4 people and 2 groups Cortel shuns penka antonkratz 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
  • 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
  • Threading thrills and threats.
    Structure, Vol. 4, No. 1. (15 January 1996), pp. 15-19.
    by MJ Sippl, H Flöckner
    posted to computational_biology review statistical_potentials structure_prediction by marcius on 2005-10-26 19:18:59 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 genomics.
    Brief Bioinform, Vol. 2, No. 2. (May 2001), pp. 111-125.
    by DT Jones
    posted to review structural_genomics structure_prediction by marcius on 2005-12-22 06:51:11 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • Modeling RNA tertiary structure from patterns of sequence variation.
    Methods Enzymol, Vol. 317 (2000), pp. 491-510.
    by F Michel, M Costa, C Massire, E Westhof
    posted to review rna structure_prediction by marcius on 2005-12-22 22:45:59 as ** along with 2 groups 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
  • Evolutionarily conserved networks of residues mediate allosteric communication in proteins.
    Nat Struct Biol, Vol. 10, No. 1. (January 2003), pp. 59-69.
    by GM Süel, SW Lockless, MA Wall, R Ranganathan
    posted to bioinformatics biophysics sequence_alignment statistical_potentials structure_prediction by marcius on 2006-01-20 23:09:56 as ** along with 15 people and 3 groups lna dimka eckart_bindewald gbart analogAI nirfriedman dgront caporaso choonpeng efge carlescorbi mingzhi yalexeev weisblum ca3295 biomedical-nlp BioinfoCIPF SGU-CIPF
  • Combining evolutionary and structural information for local protein structure prediction.
    Proteins, Vol. 56, No. 4. (1 September 2004), pp. 782-794.
    by J Pei, NV Grishin
    posted to bioinformatics biophysics sequence_alignment statistical_potentials structure_prediction by marcius on 2006-01-20 23:19:35 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • Structure-derived hydrophobic potential. Hydrophobic potential derived from X-ray structures of globular proteins is able to identify native folds.
    J Mol Biol, Vol. 224, No. 3. (5 April 1992), pp. 725-732.
    by G Casari, MJ Sippl
    posted to computational_biology review statistical_potentials structure_prediction by marcius on 2005-10-26 19:19:29 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • High-resolution protein folding with a transferable potential
    PNAS, Vol. 102, No. 52. (27 December 2005), pp. 18914-18919.
    by Isaac A Hubner, Eric J Deeds, Eugene I Shakhnovich
    posted to ab-initio biophysics protein_structure structure_prediction by marcius on 2006-02-07 02:17:31 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • Assessment of predictions submitted for the CASP6 comparative modelling category.
    Proteins (26 September 2005)
    by Michael Tress, Iakes Ezkurdia, Osvaldo Graña, Gonzalo López, Alfonso Valencia
    posted to cafasp casp comparative_modeling protein_structure structure_prediction by marcius on 2005-10-22 08:59:31 as **** along with 3 people and 2 groups nigham ffranca magia215 BioinfoCIPF SGU-CIPF
  • Evolutionarily Conserved Pathways of Energetic Connectivity in Protein Families
    Science, Vol. 286, No. 5438. (08 October 1999), pp. 295-299.
    by Steve W Lockless, Rama Ranganathan
    posted to bioinformatics biophysics sequence_alignment statistical_potentials structure_prediction by marcius on 2006-01-20 23:11:47 as ** along with 15 people and 5 groups stevanspringer Einat eckart_bindewald analogAI dgront caporaso sriram_s choonpeng Haggan rabio mottonen zambujo mingzhi bethbromley ca3295 structural_bioinformatics FAB-lab biomedical-nlp 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
  • Knowledge-based potentials for proteins.
    Curr Opin Struct Biol, Vol. 5, No. 2. (April 1995), pp. 229-235.
    by MJ Sippl
    posted to computational_biology review statistical_potentials structure_prediction by marcius on 2005-10-26 19:19:08 as ** along with 4 people and 2 groups chad_davis eckart_bindewald tolot27 janasont 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
  • Five hierarchical levels of sequence-structure correlation in proteins.
    Appl Bioinformatics, Vol. 3, No. 2-3. (2004), pp. 97-104.
    by C Bystroff, Y Shao, X Yuan
    posted to bioinformatics biophysics sequence-structure sequence_alignment statistical_potentials structure_prediction by marcius on 2006-01-20 23:13:49 as ** along with 2 people and 2 groups eweaver rabio BioinfoCIPF SGU-CIPF
  • The relation between the divergence of sequence and structure in proteins.
    EMBO J, Vol. 5, No. 4. (April 1986), pp. 823-826.
    by C Chothia, AM Lesk
    posted to evolution structure structure_alignment structure_prediction by marcius on 2005-12-20 00:56:52 as read along with 7 people and 6 groups ana pansapiens jwm Einat xdeupi ffranca insectopalo structural_bioinformatics Radiation_Damage Stressosome Bioinformatics BioinfoCIPF SGU-CIPF
  • Generalized protein structure prediction based on combination of fold-recognition with de novo folding and evaluation of models.
    Proteins (26 September 2005)
    by Andrzej Koliński, Janusz M M Bujnicki
    posted to ab-initio bioinformatics comparative_modeling model_assessment structure_prediction by marcius on 2005-10-22 09:12:12 as *** along with 2 people and 2 groups nigham dgront BioinfoCIPF SGU-CIPF
  • Assessment of CASP6 predictions for new and nearly new fold targets.
    Proteins (26 September 2005)
    by James J J Vincent, Chin-Hsien H Tai, B K K Sathyanarayana, Byungkook Lee
    posted to ab-initio cafasp casp model_evaluation structure_prediction by marcius on 2005-10-22 09:12:32 as ** along with 1 person and 2 groups nigham BioinfoCIPF SGU-CIPF
  • The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling
    Bioinformatics, Vol. 22, No. 2. (15 January 2006), pp. 195-201.
    by Konstantin Arnold, Lorenza Bordoli, Jurgen Kopp, Torsten Schwede
    posted to algorithms protein_structure servers structure_prediction by marcius on 2006-02-02 05:48:58 as ** along with 2 people and 2 groups chad_davis ffranca BioinfoCIPF SGU-CIPF
  • Natural-like function in artificial WW domains
    Nature, Vol. 437, No. 7058., pp. 579-583.
    by William P Russ, Drew M Lowery, Prashant Mishra, Michael B Yaffe, Rama Ranganathan
    posted to bioinformatics biophysics sequence_alignment statistical_potentials structure_prediction by marcius on 2006-01-20 23:06:18 as ** along with 6 people and 5 groups ana barry balajis caporaso bethbromley ca3295 structural_bioinformatics Bioinformatics biomedical-nlp BioinfoCIPF SGU-CIPF
  • Automated de novo prediction of native-like RNA tertiary structures
    PNAS (28 August 2007), 0703836104.
    by Rhiju Das, David Baker
    posted to ab-initio rna structure_prediction by marcius on 2007-09-01 10:46:02 as ** along with 6 people and 2 groups jwm eckart_bindewald zwang physics Ema reyez BioinfoCIPF SGU-CIPF
  • The SWISS-MODEL Repository: new features and functionalities.
    Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006)
    by J Kopp, T Schwede
    posted to databases protein_structure structure_prediction by marcius on 2006-01-13 23:58:03 as ** along with 1 person and 2 groups miguel BioinfoCIPF SGU-CIPF
  • Computer modeling 16 S ribosomal RNA
    Journal of Molecular Biology, Vol. 221, No. 3. (5 October 1991), pp. 889-907.
    by John M Hubbard, John E Hearst
    posted to algorithms bioinformatics rna structure_prediction by marcius on 2006-09-07 13:31:07 as ** along with 1 person and 2 groups eckart_bindewald BioinfoCIPF SGU-CIPF
  • Boltzmann's principle, knowledge-based mean fields and protein folding. An approach to the computational determination of protein structures.
    J Comput Aided Mol Des, Vol. 7, No. 4. (August 1993), pp. 473-501.
    by MJ Sippl
    posted to computational_biology review statistical_potentials structure_prediction by marcius on 2005-10-26 19:19:19 as read along with 3 people and 2 groups dgront aengisch mcbla BioinfoCIPF SGU-CIPF
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