Group: baker-group - with tag structure_prediction [87 articles] Export Sort

Recent papers posted by members of the baker-group group with tag structure_prediction

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	Increasing the precision of comparative models with YASARA NOVA - a self-parameterizing force field [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 47, No. 3. (2002), pp. 393-402. by Elmar Krieger, Günther Koraimann, Gert Vriend posted to molecular_simulation optimization structure_prediction by sobolevnrm to the group baker-group on 2009-04-23 12:29:22 as
	Statistical Theory of Protein Sequence Design by Random Mutation [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Arnab Bhattacherjee, Parbati Biswas posted to bioinformatics protein_engineering structure_prediction by sobolevnrm to the group baker-group on 2009-03-28 16:16:11 as
	Building alternate protein structures using the elastic network model [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA. by Qingyi Yang, Kim A. Sharp posted to enhanced_sampling quasiharmonic_models structure_prediction by sobolevnrm to the group baker-group on 2009-03-25 11:36:50 as along with 5 people and 1 group pansapiens klexa abovell oteri middledomain Structural Biology Group TorVergata
	Kemp elimination catalysts by computational enzyme design [My Copy] Nature, Vol. 453, No. 7192. (19 March 2008), pp. 190-195. by Daniela Rothlisberger, Olga Khersonsky, Andrew M. Wollacott, et al.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 along with 12 people and 2 groups barmak7282 baiaixi whitead qbin1304 fralium Diego_Prada apaydin jwm msuarezdiez austin cactus neils Jiang Research Group Biocatalysis and Biotransformation
	Prediction of membrane-protein topology from first principles [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 20. (20 May 2008), pp. 7177-7181. by Andreas Bernsel, Håkan 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 along with 3 people and 1 group sebk druvus superpyrin OPIG
	Monte Carlo refinement of rigid-body protein docking structures with backbone displacement and side-chain optimization. [My Copy] Protein science : a publication of the Protein Society, 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
	A correlation-based method for the enhancement of scoring functions on funnel-shaped energy landscapes [My Copy] 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
	Prediction of the structure of symmetrical protein assemblies [My Copy] 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 along with 4 people and 1 group jwm jmrivort cjeans zwang Supramolecular
	High-resolution structure prediction and the crystallographic phase problem [My Copy] Nature, Vol. 450, No. 7167. (14 October 2007), pp. 259-264. by Bin Qian, Srivatsan Raman, Rhiju Das, et al.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 along with 16 people and 1 group bmduggan newton1234 apaydin aheilbut jwm eckart_bindewald ffranca dgront massivemayhem cjeans zwang cactus boris_aguilar Ema chenway ardalby OPIG
	Prediction of transition metal-binding sites from apo protein structures [My Copy] 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
	Hydrophobic Potential of Mean Force as a Solvation Function for Protein Structure Prediction [My Copy] Structure, Vol. 15, No. 6. (2007), pp. 727-40. by M. S. Lin, N. L. Fawzi, Head T. Gordon posted to structure_prediction solvation by sobolevnrm to the group baker-group on 2007-06-20 12:33:33 as
	PI2PE: protein interface/interior prediction engine [My Copy] Nucleic Acids Research (in press) by H. Tjong, S. Qin, H. X. Zhou posted to structure_prediction software bioinformatics by sobolevnrm to the group baker-group on 2007-06-06 13:11:37 as
	Protein Structure Prediction: Inroads to Biology [My Copy] 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
	SPrCY: comparison of structural predictions in the Saccharomyces cerevisiae genome [My Copy] Bioinformatics, Vol. 20, No. 14. (2004), pp. 2312-4. by T. J. Dolinsky, P. M. J. Burgers, K. Karplus, N. A. Baker posted to structure_prediction database by sobolevnrm to the group baker-group on 2007-05-25 14:13:09 as
	Refinement of homology-based protein structures by molecular dynamics simulation techniques [My Copy] Protein Science, Vol. 13, No. 1. (2004), pp. 211-20. by H. Fan, A. E. Mark posted to structure_prediction by sobolevnrm to the group baker-group on 2007-05-25 14:13:08 as
	Protein structure prediction and analysis using the Robetta server [My Copy] Nucleic Acids Research, Vol. 32, No. S2. (2004), pp. W526-W531. by D. E. 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
	The elastic net algorithm and protein structure prediction [My Copy] Journal of Computational Chemistry, Vol. 23, No. 1. (2002), pp. 77-83. by K. D. Ball, B. Erman, K. A. Dill posted to structure_prediction protein_folding by sobolevnrm to the group baker-group on 2007-05-25 14:06:48 as
	Funnel sculpting for in silico assembly of secondary structure elements of proteins [My Copy] 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
	Distance-dependent, pair potential for protein folding: Results from linear optimization [My Copy] 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
	Linear programming optimization and a double statistical filter for protein threading protocols [My Copy] 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
	Computational Analysis of Sequence Selection Mechanisms [My Copy] 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
	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 [My Copy] Proteins, Vol. 32, No. 4. (1998), pp. 399-413. by Y. N. Vorobjev, J. C. 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
	Steric restrictions in protein folding: An alpha-helix cannot be followed by a contiguous beta-strand [My Copy] Protein Science, Vol. 13, No. 3. (2004), pp. 633-639. by N. C. Fitzkee, G. D. Rose posted to structure_prediction protein_folding bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 14:04:12 as
	Reduced models of proteins and their applications [My Copy] 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
	The evolution of transmembrane helix kinks and the structural diversity of G protein-coupled receptors [My Copy] 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, J. P. Whitelegge, J. U. Bowie posted to structure_prediction structure correlated_mutations bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 14:02:10 as
	Critical assessment of methods of protein structure prediction (CASP)-round V [My Copy] 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
	The SUPERFAMILY database in 2004: additions and improvements [My Copy] Nucleic Acids Research, Vol. 32 (2004), pp. D235-D239. by M. Madera, C. Vogel, S. K. 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
	Correlated mutations and residue contacts in proteins [My Copy] 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
	Prediction of protein residue contacts with a PDB-derived likelihood matrix [My Copy] Protein Engineering Design and Selection, Vol. 15, No. 9. (2002), pp. 721-5. by M. S. Singer, G. Vriend, R. P. Bywater posted to structure_prediction correlated_mutations bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 13:58:07 as
	A phylogenetic approach to RNA structure prediction [My Copy] Proc Int Conf Intell Syst Mol Biol (1999), pp. 10-7. by V. R. Akmaev, S. T. Kelley, G. D. Stormo posted to structure_prediction correlated_mutations bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 13:57:26 as
	Phylogenetically enhanced statistical tools for RNA structure prediction [My Copy] Bioinformatics, Vol. 16, No. 6. (2000), pp. 501-12. by V. R. Akmaev, S. T. Kelley, G. D. Stormo posted to structure_prediction correlated_mutations bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 13:57:26 as
	Can three-dimensional contacts in protein structures be predicted by analysis of correlated mutations? [My Copy] Protein Engineering, Vol. 7 (1994), pp. 349-358. by I. N. Shindyalov, N. A. Kolchanov, C. Sander posted to structure_prediction correlated_mutations by sobolevnrm to the group baker-group on 2007-05-25 13:57:26 as
	3D-SHOTGUN: a novel, cooperative, fold-recognition meta-predictor [My Copy] 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
	GeneSilico protein structure prediction meta-server [My Copy] Nucleic Acids Res, Vol. 31, No. 13. (2003), pp. 3305-7. by M. A. Kurowski, J. M. Bujnicki posted to structure_prediction database by sobolevnrm to the group baker-group on 2007-05-25 13:55:02 as
	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) [My Copy] (2002) by G. P. S. Raghava posted to structure_prediction software database by sobolevnrm to the group baker-group on 2007-05-25 13:55:02 as
	Protein threading by PROSPECT: a prediction experiment in CASP3 [My Copy] Protein Eng, Vol. 12, No. 11. (1999), pp. 899-907. by Y. Xu, D. Xu, O. H. Crawford, et al. Einstein, F. Larimer, E. Uberbacher, M. A. Unseren, G. Zhang posted to structure_prediction software by sobolevnrm to the group baker-group on 2007-05-25 13:55:02 as
	Assessment of RAPTORâs linear programming approach in CAFASP3 [My Copy] 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
	FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure-dependent gap penalties [My Copy] J Mol Biol, Vol. 310, No. 1. (2001), pp. 243-57. by J. Shi, T. L. Blundell, K. Mizuguchi posted to structure_prediction software bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 13:55:02 as
	Hidden Markov models for detecting remote protein homologies [My Copy] 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
	Critical assessment of methods of protein structure prediction (CASP): round II [My Copy] Proteins, Vol. Suppl 1 (1997), pp. 2-6. by J. Moult, T. Hubbard, S. H. Bryant, K. Fidelis, J. T. Pedersen posted to structure_prediction by sobolevnrm to the group baker-group on 2007-05-25 13:55:02 as
	Critical assessment of methods of protein structure prediction (CASP): round III [My Copy] Proteins, Vol. Suppl 3 (1999), pp. 2-6. by J. Moult, T. Hubbard, K. Fidelis, J. T. Pedersen posted to structure_prediction by sobolevnrm to the group baker-group on 2007-05-25 13:55:02 as
	Predicting protein structure using only sequence information [My Copy] 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
	CAFASP2: the second critical assessment of fully automated structure prediction methods [My Copy] Proteins, Vol. Suppl 5 (2001), pp. 171-83. by D. Fischer, A. Elofsson, L. Rychlewski, et al.F. Pazos, A. Valencia, B. Rost, A. R. Ortiz, Jr posted to structure_prediction bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 13:55:02 as
	Assessment of the CASP4 fold recognition category [My Copy] Proteins, Vol. Suppl 5 (2001), pp. 55-67. by M. J. Sippl, P. Lackner, F. S. Domingues, et al.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
	Combining local-structure, fold-recognition, and new-fold methods for protein structure prediction [My Copy] Proteins (in press) by K. Karplus, R. Karchin, J. Draper, et al.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
	What is the value added by human intervention in protein structure prediction? [My Copy] Proteins, Vol. Suppl 5 (2001), pp. 86-91. by K. Karplus, R. Karchin, C. Barrett, et al.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
	The 2002 olympic games of protein structure prediction [My Copy] 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
	Protein structure prediction and structural genomics [My Copy] 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
	The Pedant genome database [My Copy] Nucleic Acids Research, Vol. 31, No. 1. (2003), pp. 207-211. by D. Frishman, M. Mokrejs, D. Kosykh, et al.G. Karstenmuller, G. Kolesov, I. Zubrzycki, C. Gruber, B. Geier, A. Kaps, A. Volz, C. Wagner, M. Fellenberg, K. Heumann, H. W. Mewes posted to structure_prediction database bioinformatics by sobolevnrm to the group baker-group on 2007-05-25 13:55:02 as
	Knowledge-based selection of targets for structural genomics [My Copy] 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

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protein_structure	101
review	49
bioinformatics	47
statistical_potentials	43
comparative_modeling	41
casp	40
biophysics	36
computational_biology	36
cafasp	33
sequence_alignment	27
ab-initio	24
protein_sequence	18
rna	18
model_assessment	15
algorithms	13
contact_maps	10
protein	10
structure_comparison	10
membrane_protein	9
structural_genomics	9
structure_alignment	9
computational	8
monte_carlo	8
benchmark	6
evolution	6
protein_fragments	6
sequence_comparison	6
water-mediated_contacts	6
structure_fragments	5
threading	5
15872	4
ab_initio	4
loop_modeling	4
protein_engineering	4
protein_folding	4
rosetta	4
cabs	3
clustering	3
comparative_genomics	3
contact_map	3
databases	3
folding	3
homology_analogy	3
indels	3
lattice_models	3
microarray	3
model_evaluation	3
model_refinement	3
modeling	3
molecular_dynamics	3
multiple_structure_comparison	3
pca	3
protein-ligand_interactions	3
protein_evolution	3
protein_universe	3
pseudoknot	3
reduced_models	3
secondary_structure	3
sequence	3
sequence-structure	3
sequence_structure	3
servers	3
structure	3
structure_classification	3
structure_core	3
structure_flexible	3
ace	2
biomembranes	2
chemical_shift	2
de_novo	2
dec09	2
enhanced_sampling	2
fold_recognition	2
molecular_simulation	2
multicanonical_ensemble	2
ncrna	2
nmr	2
optimization	2
protein-membrane_interactions	2
protein-protein_interactions	2
protein-structure	2
protein_interaction	2
protein_thermodynamics	2
quasiharmonic_models	2
replica_method	2
sequence_analysis	2
sicho	2
simulated_annealing	2
structural_model	2
structure_similarity	2
tools	2
web_servers	2
allostery	1
blast_search	1
coiled_coil	1
complex_proteins	1
hybrid	1
protein_homology	1
similarity	1
simulations	1

Group: baker-group - with tag structure_prediction [87 articles] Export Sort

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