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タグ: rosetta [63 articles]

Recent papers classified by the tag rosetta.
  • Modeling structurally variable regions in homologous proteins with rosetta.
    Proteins, Vol. 55, No. 3. (15 May 2004), pp. 656-677.
    by CA Rohl, CE Strauss, D Chivian, D Baker
    posted to baker loop prediction rosetta by vavi on 2006-05-31 14:05:20 as read along with 5 people and 1 group jwm yongzhao thamelry Alan hmk TSRI_MGL
  • Prospects for ab initio protein structural genomics.
    J Mol Biol, Vol. 306, No. 5. (9 March 2001), pp. 1191-1199.
    by KT Simons, C Strauss, D Baker
    posted to 3d_prediction fragment_library genomic_3d_prediction protein rosetta by thamelry on 2006-01-11 09:21:56 as read
  • Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design.
    Nucleic Acids Res, Vol. 33, No. 18. (2005), pp. 5861-5867.
    by Gong Cheng, Bin Qian, Ram Samudrala, David Baker
    posted to energy functional interactions residues rosetta structural by sriram_s on 2006-03-24 23:51:27 as *** along with 6 people and 3 groups bicko Einat marcius alexg nickolay ladab structural_bioinformatics BioinfoCIPF SGU-CIPF
  • Protein structure prediction using Rosetta.
    Methods Enzymol, Vol. 383 (2004), pp. 66-93.
    by CA Rohl, CE Strauss, KM Misura, D Baker
    posted to structure rosetta protein prediction by saunders on 2008-07-08 15:02:11 as ** along with 4 people nigham thaliana dgront JimmyMac
  • Reduced models of proteins and their applications
    Polymer, Vol. 45, No. 2. (January 2004), pp. 511-524.
    by Andrzej Kolinski, Jeffrey Skolnick
    posted to cabs continuous_moodels lattice_models monte_carlo reduced_models review rosetta sicho strutcture_prediction unres by rabio on 2006-12-11 13:01:23 as read along with 1 person iantunbridge
  • Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions.
    J Mol Biol, Vol. 268, No. 1. (25 April 1997), pp. 209-225.
    by KT Simons, C Kooperberg, E Huang, D Baker
    posted to rosetta by mijam on 2008-02-23 23:44:32 as ** along with 6 people and 2 groups ana jwm vavi wouterboomsma j3xucite hmk structural_bioinformatics Bioinformatics
  • De novo prediction of three-dimensional structures for major protein families.
    J Mol Biol, Vol. 322, No. 1. (6 September 2002), pp. 65-78.
    by R Bonneau, CE Strauss, CA Rohl, D Chivian, P Bradley, L Malmström, T Robertson, D Baker
    posted to rosetta by mijam on 2008-02-23 23:44:15 as ** along with 1 person jwm
  • Maintaining solvent accessible surface area under rotamer substitution for protein design
    Journal of Computational Chemistry, Vol. 28, No. 8. (2007), pp. 1336-1341.
    by Andrew Leaver-Fay, Glenn L Butterfoss, Jack Snoeyink, Brian Kuhlman
    posted to rosetta by jwm on 2007-11-09 09:21:29 as ** along with 1 person jwagoner
  • Structure-based protocol for identifying mutations that enhance protein-protein binding affinities.
    J Mol Biol, Vol. 371, No. 5. (31 August 2007), pp. 1392-1404.
    by DW Sammond, ZM Eletr, C Purbeck, RJ Kimple, DP Siderovski, B Kuhlman
    posted to rosetta by jwm on 2007-11-09 09:18:37 as ** along with 1 person TOchi
  • Mis-translation of a Computationally Designed Protein Yields an Exceptionally Stable Homodimer: Implications for Protein Engineering and Evolution
    Journal of Molecular Biology, Vol. 362, No. 5. (6 October 2006), pp. 1004-1024.
    by Gautam Dantas, Alexander L Watters, Bradley M Lunde, Ziad M Eletr, Nancy G Isern, Toby Roseman, Jan Lipfert, Sebastian Doniach, Martin Tompa, Brian Kuhlman, Barry L Stoddard, Gabriele Varani, David Baker
    posted to protein_design rosetta by jwm on 2007-11-09 09:16:48 as ** along with 1 person lundbra
  • High-resolution structural validation of the computational redesign of human U1A protein.
    Structure, Vol. 14, No. 5. (May 2006), pp. 847-856.
    by N Dobson, G Dantas, D Baker, G Varani
    posted to protein_design protein_redesign rosetta by jwm on 2007-11-09 09:15:49 as **
  • Computational design of protein-protein interactions.
    Curr Opin Chem Biol, Vol. 8, No. 1. (February 2004), pp. 91-97.
    by T Kortemme, D Baker
    posted to rosetta by jwm on 2007-11-09 13:40:20 as ** along with 5 people jteyra lna bicko hmk cjeans
  • High-resolution Structural and Thermodynamic Analysis of Extreme Stabilization of Human Procarboxypeptidase by Computational Protein Design.
    J Mol Biol (2 December 2006)
    by Gautam Dantas, Colin Corrent, Steve L L Reichow, James J J Havranek, Ziad M M Eletr, Nancy G G Isern, Brian Kuhlman, Gabriele Varani, Ethan A A Merritt, David Baker
    posted to protein_design protein_redesign rosetta by jwm on 2007-11-09 09:15:23 as ** along with 1 person kentsis
  • A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins.
    J Mol Biol, Vol. 332, No. 2. (12 September 2003), pp. 449-460.
    by G Dantas, B Kuhlman, D Callender, M Wong, D Baker
    posted to protein_design protein_structure_prediction rosetta by jwm on 2007-11-09 09:13:45 as ** along with 2 people leelarcombe bethbromley
  • Toward High-Resolution de Novo Structure Prediction for Small Proteins
    Science, Vol. 309, No. 5742. (16 September 2005), pp. 1868-1871.
    by Philip Bradley, Kira M Misura, David Baker
    posted to rosetta by jwm on 2007-11-12 17:06:42 as ** along with 8 people and 4 groups BragilMassoud ana barry thaliana vavi marcius gbart thamelry structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
  • Native protein sequences are close to optimal for their structures.
    Proc Natl Acad Sci U S A, Vol. 97, No. 19. (12 September 2000), pp. 10383-10388.
    by B Kuhlman, D Baker
    posted to protein_structure_prediction rosetta by jwm on 2007-11-09 09:11:52 as ** along with 2 people analogAI gisle
  • Computational redesign of endonuclease DNA binding and cleavage specificity
    Nature, Vol. 441, No. 7093. (1 June 2006), pp. 656-659.
    by Justin Ashworth, James J Havranek, Carlos M Duarte, Django Sussman, Raymond J Monnat, Barry L Stoddard, David Baker
    posted to rosetta by jwm on 2007-11-12 17:06:08 as ** along with 3 people and 1 group apaydin aalibes condon beta
  • 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
  • A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys.
    Nucleic Acids Res, Vol. 32, No. 17. (2004), pp. 5147-5162.
    by Y Chen, T Kortemme, T Robertson, D Baker, G Varani
    posted to rosetta by jwm on 2007-11-09 13:38:11 as ** along with 1 person medic0747
  • Computational redesign of protein-protein interaction specificity.
    Nat Struct Mol Biol, Vol. 11, No. 4. (April 2004), pp. 371-379.
    by T Kortemme, LA Joachimiak, AN Bullock, AD Schuler, BL Stoddard, D Baker
    posted to rosetta by jwm on 2007-11-09 13:37:56 as ** along with 6 people jteyra lna bicko ruvido cjeans tale
  • Automated de novo prediction of native-like RNA tertiary structures
    PNAS (28 August 2007), 0703836104.
    by Rhiju Das, David Baker
    posted to protein_structure_prediction rosetta by jwm on 2007-11-09 09:10:17 as ** along with 6 people and 2 groups reyez marcius eckart_bindewald zwang physics Ema BioinfoCIPF SGU-CIPF
  • Recapitulation and Design of Protein Binding Peptide Structures and Sequences
    Journal of Molecular Biology, Vol. In Press, Corrected Proof
    by Vanita D Sood, David Baker
    posted to rosetta by jwm on 2007-11-09 14:01:24 as ** along with 2 people and 1 group shuns anita structure-bii
  • 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_structure_prediction rosetta by jwm on 2007-11-09 09:07:36 as ** along with 15 people and 2 groups ardalby apaydin aheilbut chad_davis eckart_bindewald ffranca dgront massivemayhem cjeans zwang cactus sobolevnrm boris_aguilar Ema chenway OPIG baker-group
  • A simple physical model for binding energy hot spots in protein-protein complexes.
    Proc Natl Acad Sci U S A, Vol. 99, No. 22. (29 October 2002), pp. 14116-14121.
    by T Kortemme, D Baker
    posted to protein_design rosetta by jwm on 2007-11-09 13:36:20 as ** along with 5 people and 1 group skoddet hmk lna bicko cjeans Nielsen group
  • Design, activity, and structure of a highly specific artificial endonuclease.
    Mol Cell, Vol. 10, No. 4. (October 2002), pp. 895-905.
    by BS Chevalier, T Kortemme, MS Chadsey, D Baker, RJ Monnat, BL Stoddard
    posted to protein_design rosetta by jwm on 2007-11-09 13:36:06 as **
  • Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection.
    Nucleic Acids Res, Vol. 34, No. 17. (2006)
    by D Chivian, D Baker
    posted to rosetta by jwm on 2007-11-09 13:57:26 as ** along with 2 people dgront rabio
  • Physically realistic homology models built with ROSETTA can be more accurate than their templates.
    Proc Natl Acad Sci U S A, Vol. 103, No. 14. (4 April 2006), pp. 5361-5366.
    by KM Misura, D Chivian, CA Rohl, DE Kim, D Baker
    posted to rosetta by jwm on 2007-11-09 13:57:18 as ** along with 4 people balajis dgront bilab BioNica
  • ROSETTALIGAND: Protein-small molecule docking with full side-chain flexibility.
    Proteins (13 September 2006)
    by Jens Meiler, David Baker
    posted to rosetta by jwm on 2007-11-09 13:53:51 as ** along with 3 people and 1 group BragilMassoud kuhn yongzhao TSRI_MGL
  • Ab initio methods.
    Methods Biochem Anal, Vol. 44 (2003), pp. 547-557.
    by D Chivian, T Robertson, R Bonneau, D Baker
    posted to rosetta by jwm on 2007-11-12 17:37:59 as **
  • New algorithms and an in silico benchmark for computational enzyme design.
    Protein Sci, Vol. 15, No. 12. (December 2006), pp. 2785-2794.
    by A Zanghellini, L Jiang, AM Wollacott, G Cheng, J Meiler, EA Althoff, D Röthlisberger, D Baker
    posted to rosetta by jwm on 2007-11-09 13:53:42 as **
  • 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 rosetta by jwm on 2007-11-12 17:37:50 as ** along with 1 person and 2 groups marcius 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 rosetta by jwm on 2007-11-12 17:37:42 as ** along with 4 people and 2 groups marcius dgront schuylrp mirzazadeh BioinfoCIPF SGU-CIPF
  • Modeling the structure of mAb 14B7 bound to the anthrax protective antigen.
    Proteins (1 August 2007)
    by Arvind Sivasubramanian, Jennifer A A Maynard, Jeffrey J J Gray
    posted to rosetta by jwm on 2007-11-09 13:52:38 as **
  • Prediction of CASP6 structures using automated Robetta protocols.
    Proteins, Vol. 61 Suppl 7 (2005), pp. 157-166.
    by D Chivian, DE Kim, L Malmström, J Schonbrun, CA Rohl, D Baker
    posted to rosetta by jwm on 2007-11-12 17:37:34 as ** along with 1 person schuylrp
  • 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 rosetta by jwm on 2007-11-09 13:51:29 as ** along with 4 people and 2 groups jmrivort cjeans zwang sobolevnrm Supramolecular baker-group
  • Protein-Protein Docking with Backbone Flexibility
    Journal of Molecular Biology, Vol. 373, No. 2. (19 October 2007), pp. 503-519.
    by Chu Wang, Philip Bradley, David Baker
    posted to rosetta by jwm on 2007-11-09 13:51:22 as ** along with 3 people and 2 groups barry xdeupi Ema structural_bioinformatics Bioinformatics
  • De Novo Computational Design of Retro-Aldol Enzymes
    Science, Vol. 319, No. 5868. (7 March 2008), pp. 1387-1391.
    by Lin Jiang, Eric A Althoff, Fernando R Clemente, Lindsey Doyle, Daniela Rothlisberger, Alexandre Zanghellini, Jasmine L Gallaher, Jamie L Betker, Fujie Tanaka, Carlos F Barbas, Donald Hilvert, Kendall N Houk, Barry L Stoddard, David Baker
    posted to protein_design rosetta by jwm on 2008-04-07 13:38:39 as ** along with 10 people and 3 groups ucbcjbm barry aalibes aprasad dgront zwang sobolevnrm davidlott msuarezdiez scienbox McCammon structural_bioinformatics baker-group
  • 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_design rosetta by jwm on 2008-04-07 13:37:16 as ** along with 5 people and 1 group sobolevnrm austin neils cactus msuarezdiez baker-group
  • A ?solvated rotamer? approach to modeling water-mediated hydrogen bonds at protein-protein interfaces
    Proteins: Structure, Function, and Bioinformatics, Vol. 58, No. 4. (2005), pp. 893-904.
    by Lin Jiang, Brian Kuhlman, Tanja Kortemme, David Baker
    posted to rosetta by jwm on 2007-11-12 17:16:53 as ** along with 3 people msuarezdiez skoddet apaydin
  • 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 rosetta by jwm on 2007-11-09 13:48:18 as ** along with 12 people and 2 groups thaliana vavi bicko KyuhoLee marcius eweaver tny nickolay dgront rsantana mirzazadeh insectopalo BioinfoCIPF SGU-CIPF
  • Potential functions for hydrogen bonds in protein structure prediction and design.
    Adv Protein Chem, Vol. 72 (2005), pp. 1-38.
    by AV Morozov, T Kortemme
    posted to rosetta by jwm on 2007-11-12 17:15:29 as **
  • Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility.
    Proteins, Vol. 60, No. 2. (1 August 2005), pp. 187-194.
    by O Schueler-Furman, C Wang, D Baker
    posted to rosetta by jwm on 2007-11-09 13:48:10 as ** along with 3 people and 2 groups barry bicko bluvsh1 structural_bioinformatics Bioinformatics
  • Improved side-chain modeling for protein-protein docking.
    Protein Sci, Vol. 14, No. 5. (May 2005), pp. 1328-1339.
    by C Wang, O Schueler-Furman, D Baker
    posted to rosetta by jwm on 2007-11-09 13:48:03 as ** along with 9 people and 3 groups barry aqeel bicko yongzhao blackbart bluvsh1 hmk selrac Evangelia structural_bioinformatics Bioinformatics TSRI_MGL
  • Efficient Monte Carlo trial moves for polypeptide simulations.
    J Chem Phys, Vol. 123, No. 17. (1 November 2005)
    by MR Betancourt
    posted to protein_simulation rosetta by jwm on 2007-11-12 17:23:38 as ** along with 1 person dgront
  • High-resolution protein-protein docking
    Current Opinion in Structural Biology, Vol. 16, No. 2. (April 2006), pp. 183-193.
    by Jeffrey J Gray
    posted to rosetta by jwm on 2007-11-12 17:13:38 as ** along with 6 people higueruelo aqeel ima bluvsh1 ruvido cjeans
  • Design of a novel globular protein fold with atomic-level accuracy.
    Science, Vol. 302, No. 5649. (21 November 2003), pp. 1364-1368.
    by B Kuhlman, G Dantas, GC Ireton, G Varani, BL Stoddard, D Baker
    posted to protein_denovo_design protein_design protein_engineering rosetta by jwm on 2007-11-07 12:00:44 as ** along with 5 people ca3295 chad_davis hmk heymiki kevinchannon
  • A tetrapeptide fragment-based design method results in highly stable artificial proteins.
    Proteins, Vol. 68, No. 4. (1 September 2007), pp. 839-849.
    by R Dallüge, J Oschmann, O Birkenmeier, C Lücke, H Lilie, R Rudolph, C Lange
    posted to rosetta by jwm on 2007-11-09 13:45:28 as **
  • Design of protein conformational switches.
    Curr Opin Struct Biol, Vol. 16, No. 4. (August 2006), pp. 525-530.
    by XI Ambroggio, B Kuhlman
    posted to rosetta by jwm on 2007-11-12 17:11:19 as ** along with 4 people marck rabio kevinchannon bethbromley
  • The backrub motion: how protein backbone shrugs when a sidechain dances.
    Structure, Vol. 14, No. 2. (February 2006), pp. 265-274.
    by IW Davis, WB Arendall, DC Richardson, JS Richardson
    posted to protein_design rosetta validation by jwm on 2007-11-12 17:21:19 as ** along with 2 people and 2 groups ana nigham structural_bioinformatics Bioinformatics
  • Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations.
    J Mol Biol, Vol. 331, No. 1. (1 August 2003), pp. 281-299.
    by JJ Gray, S Moughon, C Wang, O Schueler-Furman, B Kuhlman, CA Rohl, D Baker
    posted to rosetta by jwm on 2007-11-09 13:45:05 as ** along with 1 person hmk
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