saunders's library 323 articles Export

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	A model study of protein nascent chain and cotranslational folding using hydrophobic-polar residues. [My Copy] Proteins (6 August 2007) by Hsiao-Mei M. Lu, Jie Liang posted to folding model protein 3d 2d hp co-translation by saunders on 2007-11-22 15:50:06 as along with 1 person and 1 group cdeane OPIG
	Kinetically driven refolding of the hyperstable EBNA1 origin DNA-binding dimeric beta-barrel domain into amyloid-like spherical oligomers. [My Copy] Proteins (6 August 2007) by Eleonora Freire, Cristian Oddo, Lori Frappier, Gonzalo de Prat-Gay posted to co-translation folding protein vivo by saunders on 2007-11-22 15:34:37 as
	An assessment of protein secondary structure prediction methods based on amino acid sequence. [My Copy] Biochimica et biophysica acta, Vol. 439, No. 2. (9 August 1976), pp. 261-273. by P. Argos, J. Schwarz, J. Schwarz posted to structure secondary prediction bias by saunders on 2009-09-24 11:55:08 as
	A critical evaluation of methods for prediction of protein secondary structures. [My Copy] Annual review of biophysics and biophysical chemistry, Vol. 17 (1988), pp. 1-21. by G. E. Schulz posted to structure secondary prediction bias by saunders on 2009-09-24 10:53:23 as
	The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications. [My Copy] Nucleic acids research, Vol. 15, No. 3. (11 February 1987), pp. 1281-1295. by P. M. Sharp, W. H. Li posted to adaption cai calculate codon index by saunders on 2009-06-02 16:09:53 as along with 9 people codonusage mgomes qluo antonkratz dswan operon bjorns gpalidwor aaronsmith
	Mapping PDB chains to UniProtKB entries. [My Copy] Bioinformatics, Vol. 21, No. 23. (1 December 2005), pp. 4297-4301. by A. C. Martin posted to mapping pdb uniprot by saunders on 2008-07-24 10:51:12 as along with 3 people bicko grahamc lpfernandes
	Frustration and hydrophobicity interplay in protein folding and protein evolution. [My Copy] J Chem Phys, Vol. 125, No. 8. (28 August 2006) by L. C. Oliveira, R. T. Silva, V. B. Leite, J. Chahine posted to folding hp mutation protein by saunders on 2007-11-25 15:18:09 as along with 2 people and 1 group kracher rsantana Immunoinformatics
	A model for co-translational translocation: ribosome-regulated nascent polypeptide translocation at the protein-conducting channel. [My Copy] FEBS Lett, Vol. 580, No. 14. (12 June 2006), pp. 3353-3360. by K. Mitra, J. Frank posted to co-translation pause ribosome sensing signal srp translocation by saunders on 2007-11-22 15:28:31 as
	Structure of the E. coli protein-conducting channel bound to a translating ribosome [My Copy] Nature, Vol. 438, No. 7066. (17 November 2005), pp. 318-324. by Kakoli Mitra, Christiane Schaffitzel, Tanvir Shaikh, et al.Florence Tama, Simon Jenni, Charles L. Brooks, Nenad Ban, Joachim Frank posted to co-translation electron microscopy protein ribosome translocation by saunders on 2007-11-22 15:24:41 as along with 3 people aqeel dayjm ruudvanleeuwen
	The EMBL data library. [My Copy] Nucleic acids research, Vol. 14, No. 1. (10 January 1986), pp. 5-9. by G. H. Hamm, G. N. Cameron posted to nucleotide embl database by saunders on 2009-11-12 19:14:57 as
	The Universal Protein Resource (UniProt) 2009. [My Copy] Nucleic acids research, Vol. 37, No. Database issue. (1 January 2009), pp. D169-174. by UniProt Consortium posted to uniprot reference by saunders on 2009-11-12 19:08:24 as along with 12 people barmak7282 azazello badi MarcoAlvarez tfuji nedwards niallhaslam bicko gjuggler lptolik coela sjcockell
	The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases. [My Copy] BMC bioinformatics, Vol. 8, No. 1. (2007) by Richard G. Côté, Philip Jones, Lennart Martens, et al.Samuel Kerrien, Florian Reisinger, Quan Lin, Rasko Leinonen, Rolf Apweiler, Henning Hermjakob posted to protein picr cross-reference by saunders on 2009-11-12 19:07:41 as along with 12 people robert druvus whoare chad_davis guhjy dullhunk niallhaslam antonkratz barriot dansullivanblk tny kynn
	GTOP: a database of protein structures predicted from genome sequences. [My Copy] Nucleic acids research, Vol. 30, No. 1. (1 January 2002), pp. 294-298. by Takeshi Kawabata, Satoshi Fukuchi, Keiichi Homma, et al.Motonori Ota, Jiro Araki, Takehiko Ito, Nobuyuki Ichiyoshi, Ken Nishikawa posted to structure protein mrna gtop database by saunders on 2009-11-12 18:33:15 as along with 1 person tny
	The GTOP database in 2009: updated content and novel features to expand and deepen insights into protein structures and functions. [My Copy] Nucleic acids research, Vol. 37, No. Database issue. (January 2009) by Satoshi Fukuchi, Keiichi Homma, Shigetaka Sakamoto, et al.Hideaki Sugawara, Yoshio Tateno, Takashi Gojobori, Ken Nishikawa posted to structure protein mrna gtop database by saunders on 2009-11-12 18:32:14 as along with 2 people tprpip guhjy
	A brighter future for protein structure prediction [My Copy] Nature Structural & Molecular Biology, Vol. 6, No. 2. (01 February 1999), pp. 108-111. by Patrice Koehl, Michael Levitt posted to structure protein prediction holy grail by saunders on 2009-11-12 17:44:40 as
	Predicting protein three-dimensional structure [My Copy] Current Opinion in Biotechnology, Vol. 10, No. 6. (1 December 1999), pp. 583-588. by J. Moult posted to structure protein prediction holy grail by saunders on 2009-11-12 17:43:59 as
	Progress in protein structure prediction. [My Copy] Current opinion in structural biology, Vol. 7, No. 3. (June 1997), pp. 377-387. by D. T. Jones posted to structure protein prediction holy grail by saunders on 2009-11-12 17:40:00 as along with 1 person j3xucite
	Protein structure prediction begins well but ends badly [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 999A. (2009), NA. by Rhodri Saunders, Charlotte M. Deane posted to tertiary structure secondary protein prediction casp bias by saunders on 2009-11-12 14:21:03 as along with 1 group OPIG
	Cotranslational Folding of Proteins [My Copy] Biochemistry (Moscow), Vol. 65, No. 12. (1 December 2000), pp. 1380-1384. by M. A. Basharov posted to timing protein folding co-translation by saunders on 2009-11-11 13:11:04 as
	An expanding arsenal of experimental methods yields an explosion of insights into protein folding mechanisms. [My Copy] Nature structural & molecular biology, Vol. 16, No. 6. (03 June 2009), pp. 582-588. by Alice I. Bartlett, Sheena E. Radford posted to techniques protein global folding experimental by saunders on 2009-11-10 14:02:05 as along with 3 people skywalkerus02 siggi84 melo_mcr
	The Levinthal paradox: yesterday and today. [My Copy] Folding & design, Vol. 2, No. 4. (1997) by M. Karplus posted to structure restriction nonrandom levinthal folding by saunders on 2009-11-10 13:58:42 as along with 1 person faccioli
	Protein thermodynamic structure. [My Copy] IUBMB life, Vol. 61, No. 6. (June 2009), pp. 600-606. by Qinyi Zhao posted to thermodynamic hypothesis global folding by saunders on 2009-11-10 13:54:04 as along with 1 person skywalkerus02
	Mechanism of ribosome assisted protein folding: a new insight into rRNA functions. [My Copy] Biochemical and biophysical research communications, Vol. 384, No. 2. (26 June 2009), pp. 137-140. by Dibyendu Samanta, Anindita Das, Arpita Bhattacharya, Arunima Basu, Debasis Das, Chanchal DasGupta posted to rrna ribosome function folding co-translation by saunders on 2009-11-10 13:52:42 as
	Structural determinants of protein folding. [My Copy] Cellular and molecular life sciences : CMLS, Vol. 66, No. 14. (1 July 2009), pp. 2341-2361. by Tse Siang S. Kang, R. Manjunatha Kini posted to structure review protein function folding by saunders on 2009-11-10 13:51:48 as along with 1 person skywalkerus02
	Structural dynamics and folding of beta-lactoglobulin probed by heteronuclear NMR. [My Copy] Biochimica et biophysica acta, Vol. 1790, No. 6. (June 2009), pp. 527-537. by Kazumasa Sakurai, Tsuyoshi Konuma, Masanori Yagi, Yuji Goto posted to protein nmr folding dynamics by saunders on 2009-11-10 13:49:26 as
	A synonymous polymorphism in a common MDR1 (ABCB1) haplotype shapes protein function. [My Copy] Biochimica et biophysica acta, Vol. 1794, No. 5. (May 2009), pp. 860-871. by King Leung L. Fung, Michael M. Gottesman posted to synonymous structure protein mutation mdr1 abcb1 by saunders on 2009-11-10 13:48:44 as
	Structural conservation of a short, functional, peptide-sequence motif. [My Copy] Frontiers in bioscience : a journal and virtual library, Vol. 14 (2009), pp. 1143-1151. by Susan Fox-Erlich, Martin R. Schiller, Michael R. Gryk posted to unstructured structure signalling conserved by saunders on 2009-11-10 13:47:54 as
	The ribosome as a platform for co-translational processing, folding and targeting of newly synthesized proteins. [My Copy] Nature structural & molecular biology, Vol. 16, No. 6. (June 2009), pp. 589-597. by Günter Kramer, Daniel Boehringer, Nenad Ban, Bernd Bukau posted to role ribosome review protein folding co-translational by saunders on 2009-11-10 13:10:28 as along with 4 people siggi84 bratwurst redondoself reyez
	tRNA over-expression in breast cancer and functional consequences. [My Copy] Nucleic acids research (25 September 2009) by Mariana Pavon-Eternod, Suzanna Gomes, Renaud Geslain, Qing Dai, Marsha Rich R. Rosner, Tao Pan posted to usage trna concentration codon cancer breast by saunders on 2009-11-03 14:23:17 as
	Clustering of codons with rare cognate tRNAs in human genes suggests an extra level of expression regulation. [My Copy] PLoS genetics, Vol. 5, No. 7. (3 July 2009), e1000548. by Joanna L. Parmley, Martijn A. Huynen posted to usage trna slow human codons codon cluster by saunders on 2009-11-03 14:11:30 as along with 4 people danatcaret hrogers bpcusack djkt
	Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. [My Copy] Bioinformatics, Vol. 22, No. 13. (1 July 2006), pp. 1658-1659. by W. Li, A. Godzik posted to protein nucleotide clustering by saunders on 2009-11-02 09:46:49 as along with 6 people and 2 groups pablocarb guhjy eweaver indigoviolet caporaso gisle EisenLab biomedical-nlp
	Rare Codons Cluster [My Copy] PLoS ONE, Vol. 3, No. 10. (15 October 2008), e3412. by Thomas F. Clarke, Patricia L. Clark posted to usage minmax measure codon by saunders on 2009-11-02 09:38:23 as along with 1 person cabbagesofdoom
	Biased codon usage near intron-exon junctions: selection on splicing enhancers, splice-site recognition or something else? [My Copy] Trends in Genetics, Vol. 21, No. 5. (May 2005), pp. 256-259. by Jean-Vincent Chamary, Laurence D. Hurst posted to usage synonymous exon codon boundaries by saunders on 2009-10-30 12:12:47 as along with 2 people setar bpcusack
	Exonic splicing regulatory elements skew synonymous codon usage near intron-exon boundaries in mammals. [My Copy] Molecular biology and evolution, Vol. 24, No. 8. (1 August 2007), pp. 1600-1603. by Joanna L. Parmley, Laurence D. Hurst posted to usage exon codon boundaries by saunders on 2009-10-30 12:04:00 as along with 1 person and 2 groups dchughes G4ID Genetics-of-Gambling
	Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 96, No. 8. (13 April 1999), pp. 4482-4487. by Laurent Duret, Dominique Mouchiroud posted to usage exon codon boundaries by saunders on 2009-10-30 11:59:55 as along with 4 people and 1 group robfsouza thegoose2 tharris bjorns C. elegans / WormBase
	Co-variation of tRNA Abundance and Codon Usage inEscherichia coliat Different Growth Rates [My Copy] Journal of Molecular Biology, Vol. 260, No. 5. (2 August 1996), pp. 649-663. by H. Dong posted to usage trna mrna ecoli concentration codon by saunders on 2009-10-27 15:13:25 as
	Studies on the relationships between the synonymous codon usage and protein secondary structural units. [My Copy] Biochemical and biophysical research communications, Vol. 269, No. 3. (24 March 2000), pp. 692-696. by S. K. Gupta, S. Majumdar, T. K. Bhattacharya, T. C. Ghosh posted to usage structure protein codon by saunders on 2009-10-26 18:17:26 as along with 1 person gpalidwor
	Codon-usage bias versus gene conversion in the evolution of yeast duplicate genes. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 103, No. 39. (26 September 2006), pp. 14412-14416. by Yeong-Shin S. Lin, Jake K. Byrnes, Jenn-Kang K. Hwang, Wen-Hsiung H. Li posted to usage trna gene evolution conversion codon by saunders on 2009-10-26 12:32:05 as along with 1 person bpcusack
	Codon usage and replicative strategies of hepatitis A virus. [My Copy] Virus research, Vol. 127, No. 2. (August 2007), pp. 158-163. by Rosa M. Pintó, Lluis Aragonès, M. Isabel Costafreda, Enric Ribes, Albert Bosch posted to virus usage infection hepatitis deoptimised codon by saunders on 2009-10-26 12:28:53 as
	Slow peptide bond formation by proline and other N-alkylamino acids in translation. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 106, No. 1. (6 January 2009), pp. 50-54. by Michael Y. Pavlov, Richard E. Watts, Zhongping Tan, Virginia W. Cornish, Måns Ehrenberg, Anthony C. Forster posted to slow proline peptide codon bond addition by saunders on 2009-10-26 12:23:51 as
	Silent mutations result in HlyA hypersecretion by reducing intracellular HlyA protein aggregates. [My Copy] Biotechnology and bioengineering, Vol. 101, No. 5. (1 December 2008), pp. 967-974. by Prateek Gupta, Kelvin H. Lee posted to tructure synonymous secretion protein mutation function by saunders on 2009-10-26 12:20:23 as
	Queueing phase transition: theory of translation. [My Copy] Physical review letters, Vol. 102, No. 19. (15 May 2009) by M. Carmen Romano, Marco Thiel, Ian Stansfield, Celso Grebogi posted to transition slow model folding codons by saunders on 2009-10-26 12:14:50 as
	Generic algorithm to predict the speed of translational elongation: implications for protein biogenesis. [My Copy] PloS one, Vol. 4, No. 4. (2009) by Gong Zhang, Zoya Ignatova posted to usage ribosome domain codon boundaries attenuation by saunders on 2009-10-26 12:13:55 as along with 1 person Vincent_Rouilly
	Protein structure and the sequential structure of mRNA: alpha-helix and beta-sheet signals at the nucleotide level. [My Copy] Proteins, Vol. 25, No. 2. (June 1996), pp. 237-252. by S. Brunak, J. Engelbrecht posted to usage structure protein machine link learning codon by saunders on 2009-10-23 11:06:15 as along with 2 people jengeldk msafi
	Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity [My Copy] BMC Bioinformatics, Vol. 6, No. 1. (2005) by Fran Supek, Kristian Vlahovicek posted to usage measure codon by saunders on 2009-10-23 11:00:45 as along with 2 people operon marenzelleria
	Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes [My Copy] BMC Evolutionary Biology, Vol. 4, No. 1. (2004) by Xiu F. Wan, Dong Xu, Andris Kleinhofs, Jizhong Zhou posted to usage relationship codon cg by saunders on 2009-10-23 10:59:22 as along with 3 people codonusage operon msafi
	Folding type specific secondary structure propensities of synonymous codons Folding type specific secondary structure propensities of synonymous codons [My Copy] Nanobioscience, IEEE Transactions on In Nanobioscience, IEEE Transactions on, Vol. 2, No. 3. (2003), pp. 150-157. by Wanjun Gu, Wanjun Gu, Tong Zhou, et al.Tong Zhou, Jianmin Ma, Jianmin Ma, Xiao Sun, Zuhong Lu posted to usage structure secondary codon by saunders on 2009-10-23 10:58:09 as along with 1 person msafi
	Non-random usage of 'degenerate' codons is related to protein three-dimensional structure [My Copy] pp. 78-82. by A. A. Adzhubei posted to usage structure protein link codon by saunders on 2009-10-23 10:56:09 as along with 1 person msafi
	The equilibrium partition function and base pair binding probabilities for RNA secondary structure. [My Copy] Biopolymers, Vol. 29, No. 6-7. (n 1990), pp. 1105-1119. by J. S. McCaskill posted to vienna rna folding by saunders on 2009-10-12 10:45:48 as along with 9 people and 3 groups NicholasErho rb_india ellarond evaf marcius arcticrasta condon Hosna Kiarostami beta BioinfoCIPF SGU-CIPF
	Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information. [My Copy] Nucleic acids research, Vol. 9, No. 1. (10 January 1981), pp. 133-148. by M. Zuker, P. Stiegler posted to vienna rna minimum free folding energy by saunders on 2009-10-12 10:43:02 as along with 11 people and 2 groups rb_india NicholasErho agrobledo gzm55 heliopais evaf marcius arcticrasta mtagaya Hosna guxiyou BioinfoCIPF SGU-CIPF

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bibtex-import	153
protein	68
folding	52
structure	43
codon	41
usage	38
prediction	29
co-translation	24
mrna	18
secondary	17
model	13
ribosome	13
review	10
sse	9
experiment	7
bias	6
cotranslation	6
hp	6
trna	6
boundaries	5
crowding	5
evolution	5
stability	5
translation	5
vivo	5
casp	4
database	4
function	4
lattice	4
molecular	4
mutation	4
synonymous	4
translocation	4
2d	3
3d	3
chaperones	3
domains	3
exon	3
expression	3
fragments	3
global	3
grail	3
holy	3
kinetics	3
nmr	3
progress	3
rosetta	3
sequence	3
signal	3
slow	3
speed	3
uniprot	3
vectorial	3
assessment	2
cai	2
carlo	2
casp7	2
chaperone	2
codons	2
concentration	2
contact	2
cooperativity	2
domain	2
eva	2
evidence	2
fragment	2
funnel	2
gdt_ts	2
gene	2
gtop	2
levinthal	2
link	2
measure	2
monte	2
nonrandom	2
n-terminal	2
nucleotide	2
pause	2
pdb	2
rna	2
scoring	2
sec	2
server	2
tertiary	2
third	2
time	2
vienna	2
x-ray	2
abcb1	1
acetylation	1
adaption	1
addition	1
algorithm	1
alignment	1
alignments	1
alphabet	1
amino	1
analysis	1
angstrom	1
astral	1
attenuation	1
background	1
bacteria	1
binding	1
biology	1
bond	1
breast	1
buried	1
calculate	1
cancer	1
casp4	1
casp6	1
casp8	1
cg	1
chain	1
chemistry	1
chimera	1
classification	1
cluster	1
clustering	1
comparison	1
computational	1
conserved	1
constraints	1
contacts	1
conversion	1
cotranslational	1
co-translational	1
cross-reference	1
cut-off	1
degenerate	1
degradation	1
deoptimised	1
dfire	1
difference	1
directionality	1
distribution	1
dope	1
dssp	1
dynamics	1
dyson	1
ecoli	1
effects	1
electron	1
embl	1
endoplasmic	1
energy	1
evaluation	1
experimental	1
formation	1
free	1
fret	1
gfp	1
glycan	1
groel	1
groes	1
helices	1
hepatitis	1
human	1
hydrophobicity	1
hypothesis	1
in	1
index	1
infection	1
initiation	1
i-tasser	1
jpred	1
kinetic	1
learning	1
local	1
loop	1
lysozyme	1
machine	1
mapping	1
mdr1	1
mediated	1
microscopy	1
minimum	1
minmax	1
modeling	1
modelling	1
multiple	1
myoglobin	1
nascent	1
network	1
nuclei	1
order	1
organisms	1
p22	1
peptide	1
peptides	1
phd	1
phdpsi	1
physics	1
picr	1
position	1
prion	1
processing	1
prof_king	1
proline	1
psipred	1
pyrimidines	1
rate	1
reference	1
relationship	1
residues	1
restriction	1
reticulum	1
rmsd	1
role	1
rrna	1
sam-t99	1
samt_99	1
scop	1
secretion	1
selection	1
semliki	1
sensing	1
sensitive	1
signalling	1
simplified	1
simulation	1
space	1
srp	1
sspro2	1
tasser	1
techniques	1
terminal	1
termini	1
thermodynamic	1
time-scale	1
timing	1
tmscore	1
transition	1
trembl	1
tructure	1
unstructured	1
virus	1
visualisation	1
vitro	1
water	1
yeast	1
zhang	1

saunders's library 323 articles Export

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