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Tag protein_structure [562 articles]

Recent papers classified by the tag protein_structure.
  • An analysis of simultaneous variation in protein structures.
    Protein Eng, Vol. 10, No. 4. (April 1997), pp. 307-316.
    by G Chelvanayagam, A Eggenschwiler, L Knecht, GH Gonnet, SA Benner
    posted to protein_structure by wilbur on 2008-02-29 23:07:35 as ** along with 2 people and 2 groups ana barry structural_bioinformatics Bioinformatics
  • A composite score for predicting errors in protein structure models.
    Protein Sci, Vol. 15, No. 7. (July 2006), pp. 1653-1666.
    by D Eramian, MY Shen, D Devos, F Melo, A Sali, MA Marti-Renom
    posted to protein_structure svm by vavi on 2006-07-25 10:39:39 as ** along with 4 people j3xucite dimka wouterboomsma mijam
  • Visible volume: a robust measure for protein structure characterization.
    J Mol Biol, Vol. 273, No. 1. (17 October 1997), pp. 338-348.
    by L Lo Conte, TF Smith
    posted to protein_structure volume by vavi on 2005-10-09 16:25:58 as ** along with 1 person penka
  • Evolution of function in protein superfamilies, from a structural perspective
    Journal of Molecular Biology, Vol. 307, No. 4. (6 April 2001), pp. 1113-1143.
    by Annabel E Todd, Christine A Orengo, Janet M Thornton
    posted to evolution protein_structure protein_superfamily review by uz_labu_laimi on 2007-03-28 03:54:29 as ** along with 8 people and 2 groups sim82 ana kuhn chad_davis tny sriram_s choonpeng cdallett structural_bioinformatics Bioinformatics
  • Structure-function analysis of C-type animal lectins.
    Methods Enzymol, Vol. 363 (2003), pp. 3-16.
    by ME Taylor, K Drickamer
    posted to function lectin protein_structure by stevanspringer on 2006-03-16 02:50:28 as ** along with 1 person and 3 groups naturecure FAB-lab Boydian_Society Nutritional_Polymorphisms
  • Loop Grafting and the Origins of Enzyme Species
    Science, Vol. 311, No. 5760. (27 January 2006), pp. 475-476.
    by Dan S Tawfik
    posted to function mutagenesis protein_structure by stevanspringer on 2006-03-08 21:48:49 as ** along with 1 group FAB-lab
  • Do Proteins Learn to Evolve? The Hopfield Network as a Basis for the Understanding of Protein Evolution
    Journal of Theoretical Biology, Vol. 202, No. 1. (07 January 2000), pp. 77-86.
    by Leighton Pritchard, Mark J Dufton
    posted to function protein_structure by stevanspringer on 2006-05-24 19:10:40 as ** along with 3 people and 1 group LeightonP pansapiens cmm FAB-lab
  • Robust signals of coevolution of interacting residues in mammalian proteomes identified by phylogeny-aided structural analysis
    Nature Genetics, Vol. 37, No. 12. (13 November 2005), pp. 1367-1371.
    by Sun S Choi, Weimin Li, Bruce T Lahn
    posted to coevolution protein_structure by stevanspringer on 2006-02-07 05:17:01 as ** along with 2 people and 1 group bicko mingzhi FAB-lab
  • The immunoglobulin fold family: sequence analysis and 3D structure comparisons.
    Protein Eng, Vol. 12, No. 7. (July 1999), pp. 563-571.
    by DM Halaby, A Poupon, J Mornon
    posted to protein_structure by stevanspringer on 2005-03-31 21:46:46 as ** along with 1 person and 1 group analogAI FAB-lab
  • Defining epitopes: It's not as easy as it seems.
    Nat Biotechnol, Vol. 17, No. 10. (October 1999), pp. 936-937.
    by NS Greenspan, E Di Cera
    posted to combinatorial function mutagenesis protein_structure by stevanspringer on 2007-04-13 00:07:24 as ** along with 1 group FAB-lab
  • Selection and evolution of enzymes from a partially randomized non-catalytic scaffold
    Nature, Vol. 448, No. 7155., pp. 828-831.
    by Burckhard Seelig, Jack W Szostak
    posted to adaptation combinatorial protein_structure by stevanspringer on 2007-08-27 22:54:20 as ** along with 3 people and 2 groups aheilbut dpollard zwang EisenLab FAB-lab
  • Error and attack tolerance of complex networks
    Nature, Vol. 406, No. 6794. (27 July 2000), pp. 378-382.
    by Reka Albert, Hawoong Jeong, Albert-Laszlo Barabasi
    posted to protein_structure by shivaram on 2005-10-10 20:53:34 as ** along with 14 people and 2 groups dylanwalker tjpp korakot alexisgallagher cmmorel balicea yoh mmt jaspervoskuilen timflutre thehajime karfunkel Evangelia stefanoallesina Philosophy_of_Information Blog_and_Wiki_Research
  • The large-scale organization of metabolic networks.
    Nature, Vol. 407, No. 6804. (5 October 2000), pp. 651-654.
    by H Jeong, B Tombor, R Albert, ZN Oltvai, AL Barabási
    posted to protein_structure by shivaram on 2005-10-10 20:51:47 as ** along with 21 people and 2 groups shikin camster snuppepuppan jpmague mague alexisgallagher bjorns Borelli lfriedl cmmorel alexg Shirakawa ddahlem gcalda grahamc jrbanga karfunkel Evangelia shung pmendes stefanoallesina dbk-lab kdl
  • Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level.
    Nucleic Acids Res, Vol. 29, No. 13. (1 July 2001), pp. 2860-2874.
    by NM Luscombe, RA Laskowski, JM Thornton
    posted to protein_dna protein_structure by shantanu on 2006-02-07 18:32:29 as ** along with 1 person and 8 groups medic0747 structural_bioinformatics MathBio Biostatistics Bioinformatics microRNA Computational_Systems_Biology EvolutionaryComputation Computational-Neurobiology
  • Recent advances in Cys-loop receptor structure and function
    Nature, Vol. 440, No. 7083. (23 March 2006), pp. 448-455.
    by Steven M Sine, Andrew G Engel
    posted to protein_structure by shantanu on 2006-04-05 19:20:33 as ** along with 2 people and 8 groups barry frooonk structural_bioinformatics MathBio Biostatistics Bioinformatics microRNA Computational_Systems_Biology EvolutionaryComputation Computational-Neurobiology
  • Helix to helix packing in proteins.
    J Mol Biol, Vol. 145, No. 1. (5 January 1981), pp. 215-250.
    by C Chothia, M Levitt, D Richardson
    posted to protein_structure by shantanu on 2006-01-28 07:28:09 as ** along with 1 person and 8 groups ana structural_bioinformatics MathBio Biostatistics Bioinformatics microRNA Computational_Systems_Biology EvolutionaryComputation Computational-Neurobiology
  • Molecular cloning and characterization of a unique 60 kDa/72 kDa antigen gene encoding enzyme I of the phosphoenolpyruvate: sugar phosphotransferase system (PTS) of Mycoplasma hyopneumoniae.
    Journal of biochemistry, Vol. 128, No. 2. (August 2000), pp. 261-269.
    by TL Chung, L Farh, YL Chen, D Shiuan
    posted to protein_structure promoters primer_extension mycoplasma by shana on 2008-06-23 04:12:59 as ***
  • A putative transcription factor inducing mobility in Mycoplasma pneumoniae.
    Microbiology (Reading, England), Vol. 148, No. Pt 12. (December 2002), pp. 3764-3765.
    by E Bornberg-Bauer, J Weiner
    posted to transcription sigma protein_structure mycoplasma bioinformatics by shana on 2008-06-23 03:36:30 as *****
  • Why are both ends of the polypeptide chain on the outside of proteins?
    Proteins, Vol. 55, No. 2. (1 May 2004), pp. 219-222.
    by S Hovmöller, T Zhou
    posted to protein_structure by rubendrr on 2005-11-29 16:03:11 as ** along with 1 person and 1 group Cortel cytoskeleton-and-afm
  • 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
  • Protein Evolution with Dependence Among Codons Due to Tertiary Structure
    Mol Biol Evol, Vol. 20, No. 10. (1 October 2003), pp. 1692-1704.
    by Douglas M Robinson, David T Jones, Hirohisa Kishino, Nick Goldman, Jeffrey L Thorne
    posted to evolution protein_structure substitution by redelings on 2006-08-29 20:49:21 as ** along with 2 people penka tale
  • Assessing Site-Interdependent Phylogenetic Models of Sequence Evolution
    Mol Biol Evol, Vol. 23, No. 9. (1 September 2006), pp. 1762-1775.
    by Nicolas Rodrigue, Herve Philippe, Nicolas Lartillot
    posted to evolution protein_structure substitution by redelings on 2006-08-29 20:37:12 as ** along with 2 people penka tale
  • Site interdependence attributed to tertiary structure in amino acid sequence evolution
    Gene, Vol. 347, No. 2. (14 March 2005), pp. 207-217.
    by Nicolas Rodrigue, Nicolas Lartillot, David Bryant, Herve Philippe
    posted to evolution protein_structure substitution by redelings on 2006-08-29 20:35:35 as ** along with 1 person penka
  • Protein stability promotes evolvability
    PNAS, Vol. 103, No. 15. (11 April 2006), pp. 5869-5874.
    by Jesse D Bloom, Sy T Labthavikul, Christopher R Otey, Frances H Arnold
    posted to evolution protein_folding protein_structure by redelings on 2006-08-30 18:38:49 as ** along with 10 people and 2 groups rklancer Retchless lna Einat penka cmm BioNica Cristiano wilbur cdeane structural_bioinformatics FAB-lab
  • A seven-helix coiled coil
    PNAS, Vol. 103, No. 42. (17 October 2006), pp. 15457-15462.
    by Jie Liu, Qi Zheng, Yiqun Deng, Chao-Sheng Cheng, Neville R Kallenbach, Min Lu
    posted to buried_polar_interactions cavity helixhelix_interfaces protein_design protein_structure by namtonthat on 2006-10-19 00:24:29 as read
  • Recoverable one-dimensional encoding of protein three-dimensional structures.
    Bioinformatics (18 February 2005)
    by Akira R R Kinjo, Ken Nishikawa
    posted to protein_structure by mtw on 2006-07-15 17:06:56 as **** along with 4 people and 2 groups karbak ana barry penka structural_bioinformatics Bioinformatics
  • Medium- and long-range interaction parameters between amino acids for predicting three-dimensional structures of proteins.
    Macromolecules, Vol. 9, No. 6. (c 1976), pp. 945-950.
    by S Tanaka, HA Scheraga
    posted to force_field interaction_hierarchy intro knowledge_based_potentials protein_folding protein_structure by mcbla on 2007-07-08 10:12:15 as ** along with 4 people and 2 groups ana thaliana dgront aengisch structural_bioinformatics Bioinformatics
  • 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
  • How different amino acid sequences determine similar protein structures: The structure and evolutionary dynamics of the globins
    Journal of Molecular Biology, Vol. 136, No. 3. (25 January 1980), pp. 225-230.
    by Arthur M Lesk, Cyrus Chothia
    posted to biophysics comparative_modeling evolution protein_structure by marcius on 2006-04-30 01:12:36 as ** along with 2 people and 4 groups ana barry structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
  • Comparative molecular dynamics-Similar folds and similar motions?
    Proteins (17 October 2005)
    by Andrew Pang, Yalini Arinaminpathy, Mark S P S Sansom, Philip C C Biggin
    posted to biophysics computational_biology molecular_dynamics protein_structure by marcius on 2005-10-22 16:56:55 as **** along with 2 groups BioinfoCIPF SGU-CIPF
  • Structural biologyProteins downhill all the way
    Nature, Vol. 442, No. 7100. (19 July 2006), pp. 255-256.
    by Jeffery W Kelly
    posted to biophysics folding news protein_structure views by marcius on 2006-07-20 10:06:15 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • Atom-by-atom analysis of global downhill protein folding
    Nature, Vol. 442, No. 7100. (14 June 2006), pp. 317-321.
    by Mourad Sadqi, David Fushman, Victor Muñoz
    posted to biophysics folding protein_structure by marcius on 2006-07-20 10:05:38 as ** along with 4 people and 2 groups wouterboomsma choonpeng gisle huyun110 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 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
  • 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
  • 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
  • Evaluating the usefulness of protein structure models for molecular replacement.
    Bioinformatics, Vol. 21, No. suppl_2. (1 September 2005)
    by Alejandro Giorgetti, Domenico Raimondo, Adriana Erica E Miele, Anna Tramontano
    posted to comparative_modeling protein_structure by marcius on 2005-10-22 08:54:54 as ** along with 1 person and 2 groups ffranca BioinfoCIPF SGU-CIPF
  • Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation.
    Proc Natl Acad Sci U S A, Vol. 101, No. 43. (26 October 2004), pp. 15346-15351.
    by B Qian, AR Ortiz, D Baker
    posted to biophysics clustering comparative_modeling protein_structure structure_prediction by marcius on 2005-10-22 05:00:32 as **** along with 4 people and 4 groups ana barry lna dgront structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
  • PDB-UF: database of predicted enzymatic functions for unannotated protein structures from structural genomics.
    BMC Bioinformatics, Vol. 7, No. 1. (6 February 2006)
    by Marcin von Grotthuss, Dariusz Plewczynski, Krzysztof Ginalski, Leszek Rychlewski, Eugene I Shakhnovich
    posted to bioinformatics databases protein_function protein_structure by marcius on 2006-02-27 20:16:54 as ** along with 2 people and 3 groups sim82 caporaso biomedical-nlp 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
  • Comparing graph representations of protein structure for mining family-specific residue-based packing motifs.
    J Comput Biol, Vol. 12, No. 6. (g 2005), pp. 657-671.
    by J Huan, D Bandyopadhyay, W Wang, J Snoeyink, J Prins, A Tropsha
    posted to bioinformatics protein_structure by marcius on 2005-10-22 00:48:33 as ** along with 3 people and 2 groups pansapiens aalibes shuns BioinfoCIPF SGU-CIPF
  • Prediction of protein thermostability with a direction- and distance-dependent knowledge-based potential.
    Protein Sci, Vol. 14, No. 10. (October 2005), pp. 2682-2692.
    by C Hoppe, D Schomburg
    posted to model_assessment protein_structure protein_threading by marcius on 2006-01-19 19:51:53 as ** along with 2 groups BioinfoCIPF SGU-CIPF
  • Crossing the species barrier
    Nature Structural & Molecular Biology, Vol. 12, No. 10., pp. 831-831.
    by Hwa-Ping Feng
    posted to disease protein_interactions protein_structure by marcius on 2005-10-21 21:59:01 as ** along with 2 groups 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 computational_biology evolution protein_folding protein_structure structural_genomics by marcius on 2005-10-21 21:56:14 as read along with 9 people and 3 groups neils karbak iakes vavi alexg j3xucite kracher schuylrp jfmuggs BioinfoCIPF Immunoinformatics SGU-CIPF
  • 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 computational_biology model_assessment protein_structure by marcius on 2005-10-21 21:55:27 as * along with 4 people and 2 groups karbak dgront aengisch rabio BioinfoCIPF SGU-CIPF
  • Discrimination of native loop conformations in membrane proteins: decoy library design and evaluation of effective energy scoring functions.
    Proteins, Vol. 52, No. 4. (1 September 2003), pp. 492-509.
    by LR Forrest, TB Woolf
    posted to computational_biology model_assessment protein_structure software by marcius on 2005-10-21 21:08:44 as * along with 1 person and 2 groups thaliana BioinfoCIPF SGU-CIPF
  • Sequence evolution and the mechanism of protein folding.
    Biophys J, Vol. 79, No. 4. (October 2000), pp. 1787-1799.
    by AR Ortiz, J Skolnick
    posted to biophysics computational_biology evolution protein_structure by marcius on 2005-10-21 20:27:05 as read along with 2 people and 2 groups penka cjeans BioinfoCIPF SGU-CIPF
  • MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading.
    Proteins, Vol. 49, No. 3. (15 November 2002), pp. 350-364.
    by L Lu, H Lu, J Skolnick
    posted to computational_biology protein_interactions protein_structure by marcius on 2005-10-21 19:36:56 as *** along with 5 people and 5 groups ana bicko chad_davis sangeetha ruvido structural_bioinformatics Bioinformatics insilicodrug 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
  • 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
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