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Group: baker-group - with tag structure_prediction [84 articles]

グループ baker-group のメンバーが最近追加した論文の一覧 with tag structure_prediction
  • 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 to the group baker-group on 2008-06-27 12:04:48 as read along with 5 people jwm msuarezdiez austin cactus neils
  • 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 to the group baker-group on 2008-05-20 20:09:19 as read along with 1 person superpyrin
  • 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 to the group baker-group on 2007-12-21 12:26:27 as read
  • 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 to the group baker-group on 2007-12-18 13:05:12 as read
  • 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 to the group baker-group on 2007-12-18 12:53:24 as read along with 4 people and 1 group jwm jmrivort cjeans zwang Supramolecular
  • 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 to the group baker-group on 2007-12-17 12:41:21 as read along with 15 people and 1 group apaydin aheilbut jwm chad_davis eckart_bindewald ffranca dgront massivemayhem cjeans zwang cactus boris_aguilar Ema chenway ardalby OPIG
  • Prediction of transition metal-binding sites from apo protein structures
    Proteins (in press)
    by M Babor, S Gerzon, B Raveh, V Sobolev, M Edelman
    posted to structure_prediction software metalloregulation bioinformatics by sobolevnrm to the group baker-group on 2007-08-06 14:33:01 as read
  • Hydrophobic Potential of Mean Force as a Solvation Function for Protein Structure Prediction
    Structure, Vol. 15, No. 6. (2007), pp. 727-40.
    by MS Lin, NL Fawzi, Head T Gordon
    posted to structure_prediction solvation by sobolevnrm to the group baker-group on 2007-06-20 12:33:33 as read
  • PI2PE: protein interface/interior prediction engine
    Nucleic Acids Research (in press)
    by H Tjong, S Qin, HX Zhou
    posted to structure_prediction software bioinformatics by sobolevnrm to the group baker-group on 2007-06-06 13:11:37 as read
  • Protein Structure Prediction: Inroads to Biology
    Molecular Cell, Vol. 20 (2005), pp. 811-9.
    by D Petrey, B Honig
    posted to structure_prediction by sobolevnrm to the group baker-group on 2007-05-25 14:19:26 as read
  • SPrCY: comparison of structural predictions in the Saccharomyces cerevisiae genome
    Bioinformatics, Vol. 20, No. 14. (2004), pp. 2312-4.
    by TJ Dolinsky, PMJ Burgers, K Karplus, NA Baker
    posted to structure_prediction database by sobolevnrm to the group baker-group on 2007-05-25 14:13:09 as read
  • Refinement of homology-based protein structures by molecular dynamics simulation techniques
    Protein Science, Vol. 13, No. 1. (2004), pp. 211-20.
    by H Fan, AE Mark
    posted to structure_prediction by sobolevnrm to the group baker-group on 2007-05-25 14:13:08 as read
  • Protein structure prediction and analysis using the Robetta server
    Nucleic Acids Research, Vol. 32, No. S2. (2004), pp. W526-W531.
    by DE Kim, D Chivian, D Baker
    posted to structure_prediction software by sobolevnrm to the group baker-group on 2007-05-25 14:10:46 as read
  • The elastic net algorithm and protein structure prediction
    Journal of Computational Chemistry, Vol. 23, No. 1. (2002), pp. 77-83.
    by KD Ball, B Erman, KA Dill
    posted to structure_prediction protein_folding by sobolevnrm to the group baker-group on 2007-05-25 14:06:48 as read
  • Funnel sculpting for in silico assembly of secondary structure elements of proteins
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 100, No. 19. (2003), pp. 10700-10705.
    by B Fain, M Levitt
    posted to structure_prediction protein_folding by sobolevnrm to the group baker-group on 2007-05-25 14:06:15 as read
  • Distance-dependent, pair potential for protein folding: Results from linear optimization
    Proteins, Vol. 41, No. 1. (2000), pp. 40-46.
    by D Tobi, R Elber
    posted to structure_prediction by sobolevnrm to the group baker-group on 2007-05-25 14:05:56 as read
  • Linear programming optimization and a double statistical filter for protein threading protocols
    Proteins, Vol. 45, No. 3. (2001), pp. 241-261.
    by J Meller, R Elber
    posted to structure_prediction by sobolevnrm to the group baker-group on 2007-05-25 14:05:56 as read
  • Computational Analysis of Sequence Selection Mechanisms
    Structure, Vol. 12 (2004), pp. 547-557.
    by L Meyerguz, C Grasso, J Kleinberg, R Elber
    posted to structure_prediction protein_folding by sobolevnrm to the group baker-group on 2007-05-25 14:05:56 as read
  • Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model
    Proteins, Vol. 32, No. 4. (1998), pp. 399-413.
    by YN Vorobjev, JC Almagro, J Hermans
    posted to structure_prediction solvation protein_folding electrostatics by sobolevnrm to the group baker-group on 2007-05-25 14:05:56 as read
  • Steric restrictions in protein folding: An alpha-helix cannot be followed by a contiguous beta-strand
    Protein Science, Vol. 13, No. 3. (2004), pp. 633-639.
    by NC Fitzkee, GD Rose
    posted to structure_prediction protein_folding bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 14:04:12 as read
  • Reduced models of proteins and their applications
    Polymer, Vol. 45, No. 2. (2004), pp. 511-524.
    by A Kolinski, J Skolnick
    posted to structure_prediction multiscale by sobolevnrm to the group baker-group on 2007-05-25 14:03:37 as read
  • The evolution of transmembrane helix kinks and the structural diversity of G protein-coupled receptors
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 101, No. 4. (2004), pp. 959-963.
    by S Yohannan, S Faham, D Yang, JP Whitelegge, JU Bowie
    posted to structure_prediction structure correlated_mutations bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 14:02:10 as read
  • Critical assessment of methods of protein structure prediction (CASP)-round V
    Proteins, Vol. 53, No. S6. (2003), pp. 334-339.
    by J Moult, K Fidelis, A Zemla, T Hubbard
    posted to structure_prediction bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 14:02:10 as read
  • The SUPERFAMILY database in 2004: additions and improvements
    Nucleic Acids Research, Vol. 32 (2004), pp. D235-D239.
    by M Madera, C Vogel, SK Kummerfeld, C Chothia, J Gough
    posted to structure_prediction software by sobolevnrm to the group baker-group on 2007-05-25 14:01:00 as read
  • Correlated mutations and residue contacts in proteins
    Proteins, Vol. 18, No. 4. (1994), pp. 309-17.
    by U Gobel, C Sander, R Schneider, A Valencia
    posted to structure_prediction correlated_mutations bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 13:58:07 as read
  • Prediction of protein residue contacts with a PDB-derived likelihood matrix
    Protein Engineering Design and Selection, Vol. 15, No. 9. (2002), pp. 721-5.
    by MS Singer, G Vriend, RP Bywater
    posted to structure_prediction correlated_mutations bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 13:58:07 as read
  • A phylogenetic approach to RNA structure prediction
    Proc Int Conf Intell Syst Mol Biol (1999), pp. 10-7.
    by VR Akmaev, ST Kelley, GD Stormo
    posted to structure_prediction correlated_mutations bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 13:57:26 as read
  • Phylogenetically enhanced statistical tools for RNA structure prediction
    Bioinformatics, Vol. 16, No. 6. (2000), pp. 501-12.
    by VR Akmaev, ST Kelley, GD Stormo
    posted to structure_prediction correlated_mutations bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 13:57:26 as read
  • Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations?
    Protein Engineering, Vol. 7 (1994), pp. 349-358.
    by IN Shindyalov, NA Kolchanov, C Sander
    posted to structure_prediction correlated_mutations by sobolevnrm to the group baker-group on 2007-05-25 13:57:26 as read
  • 3D-SHOTGUN: a novel, cooperative, fold-recognition meta-predictor
    Proteins, Vol. 51, No. 3. (2003), pp. 434-41.
    by D Fischer
    posted to structure_prediction bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 13:55:02 as read
  • GeneSilico protein structure prediction meta-server
    Nucleic Acids Res, Vol. 31, No. 13. (2003), pp. 3305-7.
    by MA Kurowski, JM Bujnicki
    posted to structure_prediction database by sobolevnrm to the group baker-group on 2007-05-25 13:55:02 as read
  • RPFOLD : Recognition of protein fold from sequence and predicted secondary structure using standard sequence searching methods; Fifth Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP5)
    (2002)
    by GPS Raghava
    posted to structure_prediction software database by sobolevnrm to the group baker-group on 2007-05-25 13:55:02 as read
  • Protein threading by PROSPECT: a prediction experiment in CASP3
    Protein Eng, Vol. 12, No. 11. (1999), pp. 899-907.
    by Y Xu, D Xu, OH Crawford, Einstein, F Larimer, E Uberbacher, MA Unseren, G Zhang
    posted to structure_prediction software by sobolevnrm to the group baker-group on 2007-05-25 13:55:02 as read
  • Assessment of RAPTORâs linear programming approach in CAFASP3
    Proteins, Vol. In press (2003)
    by J Xu, M Li
    posted to structure_prediction software by sobolevnrm to the group baker-group on 2007-05-25 13:55:02 as read
  • FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties
    J Mol Biol, Vol. 310, No. 1. (2001), pp. 243-57.
    by J Shi, TL Blundell, K Mizuguchi
    posted to structure_prediction software bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 13:55:02 as read
  • Hidden Markov models for detecting remote protein homologies
    Bioinformatics, Vol. 14, No. 10. (1998), pp. 846-56.
    by K Karplus, C Barrett, R Hughey
    posted to structure_prediction bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 13:55:02 as read
  • Critical assessment of methods of protein structure prediction (CASP): round II
    Proteins, Vol. Suppl 1 (1997), pp. 2-6.
    by J Moult, T Hubbard, SH Bryant, K Fidelis, JT Pedersen
    posted to structure_prediction by sobolevnrm to the group baker-group on 2007-05-25 13:55:02 as read
  • Critical assessment of methods of protein structure prediction (CASP): round III
    Proteins, Vol. Suppl 3 (1999), pp. 2-6.
    by J Moult, T Hubbard, K Fidelis, JT Pedersen
    posted to structure_prediction by sobolevnrm to the group baker-group on 2007-05-25 13:55:02 as read
  • Predicting protein structure using only sequence information
    Proteins, Vol. Suppl 3 (1999), pp. 121-5.
    by K Karplus, C Barrett, M Cline, M Diekhans, L Grate, R Hughey
    posted to structure_prediction bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 13:55:02 as read
  • CAFASP2: the second critical assessment of fully automated structure prediction methods
    Proteins, Vol. Suppl 5 (2001), pp. 171-83.
    by D Fischer, A Elofsson, L Rychlewski, F Pazos, A Valencia, B Rost, AR Ortiz, Jr
    posted to structure_prediction bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 13:55:02 as read
  • Assessment of the CASP4 fold recognition category
    Proteins, Vol. Suppl 5 (2001), pp. 55-67.
    by MJ Sippl, P Lackner, FS Domingues, A Prlic, R Malik, A Andreeva, M Wiederstein
    posted to structure_prediction bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 13:55:02 as read
  • Combining local-structure, fold-recognition, and new-fold methods for protein structure prediction
    Proteins (in press)
    by K Karplus, R Karchin, J Draper, J Casper, Mandel Y Gutfreund, M Diekhans, R Hughey
    posted to structure_prediction bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 13:55:02 as read
  • What is the value added by human intervention in protein structure prediction?
    Proteins, Vol. Suppl 5 (2001), pp. 86-91.
    by K Karplus, R Karchin, C Barrett, S Tu, M Cline, M Diekhans, L Grate, J Casper, R Hughey
    posted to structure_prediction bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 13:55:02 as read
  • The 2002 olympic games of protein structure prediction
    Protein Eng, Vol. 16, No. 3. (2003), pp. 157-60.
    by D Fischer, L Rychlewski
    posted to structure_prediction bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 13:55:02 as read
  • Protein structure prediction and structural genomics
    Science, Vol. 294, No. 5540. (2001), pp. 93-96.
    by D Baker, A Sali
    posted to structure_prediction by sobolevnrm to the group baker-group on 2007-05-25 13:55:02 as read
  • The Pedant genome database
    Nucleic Acids Research, Vol. 31, No. 1. (2003), pp. 207-211.
    by D Frishman, M Mokrejs, D Kosykh, G Karstenmuller, G Kolesov, I Zubrzycki, C Gruber, B Geier, A Kaps, A Volz, C Wagner, M Fellenberg, K Heumann, HW Mewes
    posted to structure_prediction database bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 13:55:02 as read
  • Knowledge-based selection of targets for structural genomics
    Protein Engineering, Vol. 15, No. 3. (2002), pp. 169-183.
    by D Frishman
    posted to structure_prediction software bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 13:55:02 as read
  • Detection of reliable and unexpected protein fold predictions using 3D-Jury
    Nucleic Acids Research, Vol. 31, No. 13. (2003), pp. 3291-3292.
    by K Ginalski, L Rychlewski
    posted to structure_prediction software bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 13:55:02 as read
  • Large-scale protein structure modeling of the Sacchromyces cerevisiae genome
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 95, No. 23. (1998), pp. 13597-13602.
    by R Sanchez, A Sali
    posted to structure_prediction database by sobolevnrm to the group baker-group on 2007-05-25 13:55:02 as read
  • GTOP: a database of protein structures predicted from genome sequences
    Nucleic Acids Res, Vol. 30, No. 1. (2002), pp. 294-8.
    by T Kawabata, S Fukuchi, K Homma, M Ota, J Araki, T Ito, N Ichiyoshi, K Nishikawa
    posted to structure_prediction database by sobolevnrm to the group baker-group on 2007-05-25 13:55:02 as read
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