Tag secondary_structure [171 articles] Export

Recent papers classified by the tag secondary_structure.

	Effects of hydrophobic and dipole-dipole interactions on the conformational transitions of a model polypeptide [My Copy] The Journal of Chemical Physics, Vol. 127, No. 10. (2007), 105102. by Yan Mu, Yi Q. Gao posted to secondary_structure hydrophobic beta alpha by diasc on 2009-12-15 20:29:53 as
	Stereochemistry of polypeptide chain configurations [My Copy] Journal of Molecular Biology, Vol. 7, No. 1. (July 1963), pp. 95-99. by G.N. Ramachandran,, C. Ramakrishnan,, V. Sasisekharan, posted to secondary_structure beta alpha by diasc on 2009-12-14 21:16:07 as
	Polyproline II helix is the preferred conformation for unfolded polyalanine in water [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 55, No. 3. (2004), pp. 502-507. by Mihaly Mezei, Patrick J. Fleming, Rajgopal Srinivasan, George D. Rose posted to simulation secondary_structure poly-proline peptide by diasc on 2009-12-03 23:28:36 as
	Unfolded state of polyalanine is a segmented polyproline II helix [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 55, No. 3. (2004), pp. 493-501. by Alex Kentsis, Mihaly Mezei, Tatyana Gindin, Roman Osman posted to simulation secondary_structure poly-proline peptide beta alpha by diasc on 2009-12-03 23:25:17 as
	Comparison between the φ Distribution of the Amino Acids in the Protein Database and NMR Data Indicates that Amino Acids have Various φ Propensities in the Random Coil Conformation [My Copy] Journal of Molecular Biology, Vol. 254, No. 2. (24 November 1995), pp. 322-333. by L Serrano, posted to secondary_structure propensity poly-proline experimental beta alpha by diasc on 2009-12-03 22:46:53 as
	Role of backbone solvation and electrostatics in generating preferred peptide backbone conformations: Distributions of phi [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 100, No. 10. (13 May 2003), pp. 5742-5747. by Franc Avbelj, Robert L. Baldwin posted to short-peptides secondary_structure amino by Diego_Prada on 2009-11-18 16:36:07 as
	RNase J1 endonuclease activity as a probe of RNA secondary structure [My Copy] RNA, Vol. 15, No. 7. (July 2009), pp. 1417-1425. by Roula Daou-Chabo, Ciarán Condon posted to secondary_structure rna_structure by morrislab on 2009-10-09 23:58:28 as along with 1 person swapanjain
	Secbase: Database Module To Retrieve Secondary Structure Elements with Ligand Binding Motifs [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Oliver Koch, Jason Cole, Peter Block, Gerhard Klebe posted to secondary_structure oct09 ligand_binding geometric_features binding_motifs by klexa on 2009-10-07 13:46:16 as along with 1 person reyez
	Inferring consensus structure from nucleic acid sequences [My Copy] Comput. Appl. Biosci., Vol. 7, No. 3. (1 July 1991), pp. 347-352. by David K. Y. Chiu, Ted Kolodziejczak posted to trna secondary_structure rna mutual_information covariance_model by jeargle on 2009-10-06 17:51:19 as
	Identifying constraints on the higher-order structure of RNA: continued development and application of comparative sequence analysis methods [My Copy] Nucl. Acids Res., Vol. 20, No. 21. (11 November 1992), pp. 5785-5795. by R. R. Gutell, A. Power, G. Z. Hertz, E. J. Putz, G. D. Stormo posted to trna secondary_structure rna mutual_information covariance_model by jeargle on 2009-10-06 17:48:04 as
	Folding of Polypeptide Chains in Proteins: A Proposed Mechanism for Folding [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 68, No. 9. (September 1971), pp. 2293-2297. by Peter N. Lewis, Frank A. Momany, Harold A. Scheraga posted to secondary_structure alpha_carbon alpha by Vadikus on 2009-09-17 21:11:14 as
	Identification of structural motifs from protein coordinate data: Secondary structure and first-level supersecondary structure [My Copy] Proteins: Structure, Function, and Genetics, Vol. 3, No. 2. (1988), pp. 71-84. by Frederic M. Richards, Craig E. Kundrot posted to secondary_structure prediction alpha_carbon alpha by Vadikus on 2009-09-17 20:56:01 as along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
	Establishing wild-type levels of catalytic activity on natural and artificial (Î²Î±)8-barrel protein scaffolds [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 10. (10 March 2009), pp. 3704-3709. by JÃ¶rg Claren, Christoph Malisi, Birte HÃ¶cker, Reinhard Sterner posted to secondary_structure scaffold enzyme directed_evolution catalysis barrel by pablocarb on 2009-09-16 13:59:15 as along with 1 person ygygod
	Enzyme evolution: Design by necessity [My Copy] Nature, Vol. 403, No. 6770. (10 February 2000), pp. 606-607. by Gregory A. Petsko posted to secondary_structure evolution enzyme by pablocarb on 2009-09-16 13:12:28 as
	Occurrence of protein structure elements in conserved sequence regions [My Copy] BMC Structural Biology, Vol. 7, No. 1. (09 January 2007), 3. by Einat Sitbon, Shmuel Pietrokovski posted to secondary_structure conservation by pablocarb on 2009-09-16 11:04:29 as along with 2 people and 1 group dfdong Einat structural_bioinformatics
	Relationship between sequence conservation and three-dimensional structure in a large family of esterases, lipases, and related proteins. [My Copy] Protein science : a publication of the Protein Society, Vol. 2, No. 3. (March 1993), pp. 366-382. by M. Cygler, J. D. Schrag, J. L. Sussman, et al.M. Harel, I. Silman, M. K. Gentry, B. P. Doctor posted to secondary_structure enzymes conservation by pablocarb on 2009-09-16 10:49:20 as
	Structural Evidence for Evolution of the beta /alpha Barrel Scaffold by Gene Duplication and Fusion [My Copy] Science, Vol. 289, No. 5484. (1 September 2000), pp. 1546-1550. by Dietmar Lang, Ralf Thoma, Martina Henn-Sax, Reinhard Sterner, Matthias Wilmanns posted to secondary_structure fusion evolution duplication beta_alpha by pablocarb on 2009-09-15 18:30:12 as along with 2 people dfdong echinotrix
	Protein sectors: evolutionary units of three-dimensional structure. [My Copy] Cell, Vol. 138, No. 4. (21 August 2009), pp. 774-786. by Najeeb Halabi, Olivier Rivoire, Stanislas Leibler, Rama Ranganathan posted to structure secondary_structure modularity by pablocarb on 2009-09-15 10:07:09 as along with 10 people and 1 group yyfwuhan cmzmasek dgront robfsouza pansapiens vvoorr biomcgary dayjm jwm jbhiatt Marcotte_Lab
	Analysis of Catalytic Residues in Enzyme Active Sites [My Copy] Journal of Molecular Biology, Vol. 324, No. 1. (15 November 2002), pp. 105-121. by Gail J. Bartlett, Craig T. Porter, Neera Borkakoti, Janet M. Thornton posted to secondary_structure prediction enzyme-promis-paper enzyme catalytic_residues by pablocarb on 2009-09-03 11:13:41 as along with 4 people barmak7282 baaden chrn tny
	Relationship between nuclear magnetic resonance chemical shift and protein secondary structure [My Copy] Journal of Molecular Biology, Vol. 222, No. 2. (November 1991), pp. 311-333. by D. Wishart, B. D. Sykes, F. M. Richards posted to secondary_structure protein nmr by viktor21614 on 2009-08-21 15:07:45 as
	Architecture and secondary structure of an entire HIV-1 RNA genome. [My Copy] Nature, Vol. 460, No. 7256. (6 August 2009), pp. 711-716. by Joseph M. Watts, Kristen K. Dang, Robert J. Gorelick, et al.Christopher W. Leonard, Julian W. Bess, Ronald Swanstrom, Christina L. Burch, Kevin M. Weeks posted to hiv rna secondary_structure by AlexBateman to the group Journal picks on 2009-08-06 10:50:44 as along with 8 people and 1 group samgj jago physics operon wsjames memerman djkt jbhiatt Oxford Virology
	The 13C Chemical-Shift Index: A simple method for the identification of protein secondary structure using 13C chemical-shift data [My Copy] Journal of Biomolecular NMR, Vol. 4, No. 2. (1 March 1994), pp. 171-180. by David S. Wishart, Brian D. Sykes posted to 13c csi nmr secondary_structure by viktor21614 on 2009-08-06 07:59:34 as along with 2 people laurenm apaydin
	VARNA: Interactive drawing and editing of the RNA secondary structure [My Copy] Bioinformatics, Vol. 25, No. 15. (1 August 2009), pp. 1974-1975. by Kevin Darty, Alain Denise, Yann Ponty posted to rna secondary_structure by AlexBateman to the group Journal picks on 2009-07-20 14:29:42 as along with 1 person cassj
	Alignments grow, secondary structure prediction improves [My Copy] Proteins: Structure, Function, and Genetics, Vol. 46, No. 2. (2002), pp. 197-205. by Dariusz Przybylski, Burkhard Rost posted to secondary_structure by mcbla on 2009-06-01 19:59:46 as along with 2 people rabio yoonk
	Review: protein secondary structure prediction continues to rise. [My Copy] J Struct Biol, Vol. 134, No. 2-3. (n 2001), pp. 204-218. by B. Rost posted to secondary_structure by mcbla on 2009-06-01 19:51:21 as along with 1 person dgront
	A simple method to predict protein flexibility using secondary chemical shifts. [My Copy] Journal of the American Chemical Society, Vol. 127, No. 43. (2 November 2005), pp. 14970-14971. by Mark V. Berjanskii, David S. Wishart posted to nmr protein scs secondary_structure by viktor21614 on 2009-05-13 17:49:09 as along with 6 people and 1 group laurabailey rpetrenko dsekaran apaydin yongzhao allmensch TSRI_MGL
	Probability-based protein secondary structure identification using combined NMR chemical-shift data. [My Copy] Protein science : a publication of the Protein Society, Vol. 11, No. 4. (April 2002), pp. 852-861. by Yunjun Wang, Oleg Jardetzky posted to nmr protein scs secondary_structure by viktor21614 on 2009-05-13 17:48:22 as along with 1 person kumar_physics
	Reaction path study of conformational transitions and helix formation in a tetrapeptide [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 86, No. 18. (1989), pp. 6963-6967. by R. Czerminski, R. Elber posted to hexapeptide secondary_structure short-peptides by Diego_Prada on 2008-12-18 19:37:34 as
	Building native protein conformation from highly approximate backbone torsion angles. [My Copy] Proc Natl Acad Sci U S A, Vol. 102, No. 45. (8 November 2005), pp. 16227-16232. by H. Gong, P. J. Fleming, G. D. Rose posted to secondary_structure by Diego_Prada on 2008-10-07 20:32:05 as along with 2 people j3xucite allmensch
	Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features [My Copy] Biopolymers, Vol. 22, No. 12. (December 1983), pp. 2577-2637. by Wolfgang Kabsch, Christian Sander posted to secondary_structure by Diego_Prada on 2008-10-07 20:29:54 as along with 33 people dfdong barmak7282 Vadikus j3xucite scampos TLVincent maria_hauser pablocarb rpetrenko carlosjavierna mijam wqia007 dsmueller niallhaslam saunders jwm sebk pjcite kaarsinogen lna chad_davis wouterboomsma penka ffranca dgront choonpeng rabio gisle medic0747 martainn chgjb mschofie marti
	Does secondary structure determine tertiary structure in proteins? [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 61, No. 2. (2005), pp. 338-343. by Haipeng Gong, George D. Rose posted to secondary_structure by Diego_Prada on 2008-10-07 20:28:11 as
	A physical basis for protein secondary structure. [My Copy] Proc Natl Acad Sci U S A, Vol. 96, No. 25. (7 December 1999), pp. 14258-14263. by R. Srinivasan, G. D. Rose posted to secondary_structure by Diego_Prada on 2008-10-07 20:24:21 as along with 2 people and 1 group saunders Einat structural_bioinformatics
	Protein secondary structure prediction based on position-specific scoring matrices. [My Copy] Journal of molecular biology, Vol. 292, No. 2. (17 September 1999), pp. 195-202. by D. T. Jones posted to prediction secondary_structure by dandaman on 2008-04-24 17:30:53 as along with 11 people rpetrenko kgutwin pjcite chad_davis wouterboomsma j3xucite dgront rabio rph saunders granujilla
	Analysis of an optimal hidden Markov model for secondary structure prediction [My Copy] BMC Structural Biology, Vol. 6 (13 December 2006), 25. by Juliette Martin, Jean-Francois Gibrat, Francois Rodolphe posted to secondary_structure by bobychan on 2008-04-04 00:21:18 as
	Protein secondary structure prediction for a single-sequence using hidden semi-Markov models [My Copy] BMC Bioinformatics, Vol. 7, No. 1. (2006) by Zafer Aydin, Yucel Altunbasak, Mark Borodovsky posted to secondary_structure by bobychan on 2008-04-04 00:19:39 as along with 1 person isakemalp
	Recoverable one-dimensional encoding of three-dimensional protein structures [My Copy] Bioinformatics, Vol. 21, No. 10. (15 May 2005), pp. 2167-2170. by Akira R. Kinjo, Ken Nishikawa posted to secondary_structure by rabio on 2008-03-25 17:44:38 as along with 2 people eweaver mirzazadeh
	CRNPRED: Highly accurate prediction of one-dimensional protein structures by large-scale critical random networks [My Copy] BMC Bioinformatics, Vol. 7 (05 September 2006), 401. by Akira R. Kinjo, Ken Nishikawa posted to 1-d_structure secondary_structure by rabio on 2008-03-25 17:40:15 as
	Secondary structure assignment that accurately reflects physical and evolutionary characteristics. [My Copy] BMC Bioinformatics, Vol. 6 Suppl 4 (1 December 2005) by M. V. Cubellis, F. Cailliez, S. C. Lovell posted to secondary_structure by bobychan on 2008-03-19 18:56:13 as along with 1 person and 1 group Einat structural_bioinformatics
	Protein secondary structure assignment revisited: a detailed analysis of different assignment methods [My Copy] BMC Structural Biology, Vol. 5, No. 1. (2005) by Juliette Martin, Guillaume Letellier, Antoine Marin, Jean F. Taly, Alexandre de Brevern, Jean F. Gibrat posted to secondary_structure by bobychan on 2008-03-19 18:53:42 as along with 1 person and 1 group Einat structural_bioinformatics
	Identification and Classification of Conserved RNA Secondary Structures in the Human Genome [My Copy] PLoS Comput Biol, Vol. 2, No. 4. (21 April 2006), e33. by Jakob S. Pedersen, Gill Bejerano, Adam Siepel, et al.Kate Rosenbloom, Kerstin Lindblad-Toh, Eric S. Lander, Jim Kent, Webb Miller, David Haussler posted to genome-wide rna rna_folding secondary_structure by raylim on 2008-03-08 23:09:43 as along with 14 people and 2 groups rb_india guhjy NicholasErho marcius eckart_bindewald tardigrade arcticrasta tabu mtagaya Eonwe ilh djkt tale hpaces BioinfoCIPF SGU-CIPF
	Exploiting the past and the future in protein secondary structure prediction [My Copy] Bioinformatics, Vol. 15, No. 11. (November 1999), pp. 937-946. by Pierre Baldi, Søren Brunak, Paolo Frasconi, Giovanni Soda, Gianluca Pollastri posted to secondary_structure by rabio on 2008-02-02 11:05:16 as along with 3 people and 1 group dgront paolo girschick Bioinformatics
	Improved secondary structure predictions for a nicotinic receptor subunit: incorporation of solvent accessibility and experimental data into a two-dimensional representation. [My Copy] Biophys J, Vol. 76, No. 5. (May 1999), pp. 2329-2345. by N. Le Novère, P. J. Corringer, J. P. Changeux posted to nachrs secondary_structure solvent_accessibility topology by lenov on 2007-12-18 23:32:11 as
	Exploring genomic dark matter: A critical assessment of the performance of homology search methods on noncoding RNA [My Copy] Genome Research, Vol. 17, No. 1. (6 January 2007), pp. 117-125. by Eva K. Freyhult, Jonathan P. Bollback, Paul P. Gardner posted to homology noncoding rna search secondary_structure by eckart_bindewald on 2007-10-29 04:02:12 as along with 12 people and 2 groups parnell natstreet druvus jfr ppgardne gpalidwor dchughes aswin bjhaugen jayster4 yoanjacquemin evaf G4ID Genetics-of-Gambling
	SimulFold: Simultaneously Inferring RNA Structures Including Pseudoknots, Alignments, and Trees Using a Bayesian MCMC Framework [My Copy] PLoS Comput Biol, Vol. 3, No. 8. (10 August 2007), e149. by Irmtraud M. Meyer, István Miklós posted to pseudoknots rna secondary_structure by raylim on 2007-09-20 19:53:04 as along with 4 people jmallos zwang cabbagezs bertelsen
	Pure multiple RNA secondary structure alignments: a progressive profile approach. [My Copy] IEEE/ACM Trans Comput Biol Bioinform, Vol. 1, No. 1. (r 2004), pp. 53-62. by M. Höchsmann, B. Voss, R. Giegerich posted to alignments rna_forester secondary_structure by raylim on 2007-09-11 05:59:50 as along with 1 person emidio_capriotti
	Secondary structure based analysis and classification of biological interfaces: identification of binding motifs in protein protein interactions [My Copy] Bioinformatics In Bioinformatics, Vol. 23, No. 15. (1 August 2007), pp. 1909-1918. by Mainak Guharoy, Pinak Chakrabarti posted to interactions motifs protein-protein secondary_structure by grahamc on 2007-06-05 19:23:04 as along with 2 people dfdong bicko
	RNAbor: a web server for RNA structural neighbors. [My Copy] Nucleic Acids Res (25 May 2007) by Eva Freyhult, Vincent Moulton, Peter Clote posted to server sequence-structure secondary_structure rna by marcius to the group SGU-CIPF on 2007-06-04 10:14:23 as along with 2 people and 1 group sebastien_vigneau evaf BioinfoCIPF
	Unexpected point mutations activate cryptic 3' splice sites by perturbing a natural secondary structure within a yeast intron. [My Copy] Genes Dev., Vol. 5, No. 7. (1 July 1991), pp. 1252-1263. by J. O. Deshler, J. J. Rossi posted to 3ss intron secondary_structure splice_site by raylim on 2007-04-30 05:52:28 as
	Structure of tau exon 10 splicing regulatory element RNA and destabilization by mutations of frontotemporal dementia and parkinsonism linked to chromosome 17 [My Copy] PNAS, Vol. 96, No. 14. (6 July 1999), pp. 8229-8234. by Luca Varani, Masato Hasegawa, Maria G. Spillantini, et al.Michael J. Smith, Jill R. Murrell, Bernardino Ghetti, Aaron Klug, Michel Goedert, Gabriele Varani posted to exon rna secondary_structure splicing_regulatory_element by raylim on 2007-04-30 03:16:59 as
	The iStem, a Long-Range RNA Secondary Structure Element Required for Efficient Exon Inclusion in the Drosophila Dscam Pre-mRNA [My Copy] Mol. Cell. Biol., Vol. 25, No. 23. (1 December 2005), pp. 10251-10260. by Jenny M. Kreahling, Brenton R. Graveley posted to dscam exon_inclusion intron pre_mrna secondary_structure by raylim on 2007-04-30 02:57:08 as

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rna	228
bioinformatics	81
biophysics	36
structure	30
algorithms	24
prediction	17
review	13
folding	12
software	12
ncrna	10
statistics	9
alignment	7
protein_structure	7
alpha	6
computational_biology	6
databases	6
fold_space	6
sequence_alignment	6
servers	6
structure_classification	6
noncoding	5
phylogeny	5
protein	5
beta	4
evolution	4
mrna	4
nmr	4
pseudoknot	4
alternative_splicing	3
casp	3
clustering	3
comparative_modeling	3
conservation	3
dna	3
enzyme	3
experimental	3
genome	3
interaction	3
microarray	3
partition_function	3
poly-proline	3
programming	3
ribosome	3
sequence	3
sequence-structure	3
server	3
structure_alignment	3
structure_prediction	3
suboptimal	3
tools	3
trna	3
virus	3
alpha_carbon	2
comparative	2
constraint	2
covariance_model	2
energy	2
evolutionary	2
exon	2
intron	2
mutual_information	2
peptide	2
scs	2
secondary	2
short-peptides	2
simulation	2
splice_site	2
splice_sites	2
splicing	2
translation_initiation	2
unread	2
amino	1
beta_alpha	1
catalysis	1
catalytic_residues	1
computational_prediction	1
dscam	1
ecoli	1
enzymes	1
genetic	1
graph	1
hiv	1
hydrophobic	1
interactions	1
interactive	1
mfe	1
mirna	1
motif	1
nar	1
periodic_pattern	1
predictprotein_server	1
propensity	1
protein_structure_and_function	1
rna_folding	1
rna_forester	1
rna_motifs	1
rnaalifold	1
scaffold	1
solvent_accessibility	1
translational_efficiency	1

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