martainn's fold-evolution [109 articles] Export

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	Morphological aspects of oligomeric protein structures. [My Copy] Progress in biophysics and molecular biology, Vol. 89, No. 1. (September 2005), pp. 9-35. by Hannes Ponstingl, Thomas Kabir, Denise Gorse, Janet M. Thornton posted to theory structure fold-evolution assembly by martainn on 2009-12-10 13:08:28 as along with 1 person bicko
	Hidden alternative structures of proline isomerase essential for catalysis [My Copy] Nature In Nature, Vol. 462, No. 7273. (03 December 2009), pp. 669-673. by James S. Fraser, Michael W. Clarkson, Sheena C. Degnan, Renske Erion, Dorothee Kern, Tom Alber posted to structure kinetics heterogeneity fold-evolution dynamics crystallography by martainn on 2009-12-04 17:57:14 as along with 1 person and 1 group robertrentzsch Orengo Group Journal Picks
	The selection of acceptable protein mutations. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 24. (12 June 2007), pp. 10080-10085. by Rajkumar Sasidharan, Cyrus Chothia posted to structure fold-evolution alignment 1barrel by martainn on 2009-11-12 15:52:05 as along with 3 people aalibes gpalidwor zwang
	The relation between the divergence of sequence and structure in proteins. [My Copy] The EMBO journal, Vol. 5, No. 4. (April 1986), pp. 823-826. by C. Chothia, A. M. Lesk posted to structure fold-evolution evolution alignment 1barrel by martainn on 2009-11-12 14:50:55 as along with 15 people and 6 groups parnell dfdong ucbcjbm bertelsen semin sgoetz cen4ik ana pansapiens jwm Einat marcius xdeupi ffranca insectopalo structural_bioinformatics Radiation_Damage Stressosome Bioinformatics BioinfoCIPF SGU-CIPF
	The effect of sequence evolution on protein structural divergence. [My Copy] Molecular biology and evolution, Vol. 26, No. 5. (1 May 2009), pp. 1055-1065. by Simon G. Williams, Simon C. Lovell posted to structure fold-evolution alignment 1barrel by martainn on 2009-11-12 14:27:05 as along with 3 people robfsouza djkt bpcusack
	Evolutionary genomics of the HAD superfamily: understanding the structural adaptations and catalytic diversity in a superfamily of phosphoesterases and allied enzymes. [My Copy] Journal of molecular biology, Vol. 361, No. 5. (1 September 2006), pp. 1003-1034. by A. Maxwell Burroughs, Karen N. Allen, Debra Dunaway-Mariano, L. Aravind posted to superfolds structure rna fold-evolution exosome evolution by martainn on 2009-11-11 12:26:30 as along with 3 people robfsouza tny christiw
	DOM-fold: a structure with crossing loops found in DmpA, ornithine acetyltransferase, and molybdenum cofactor-binding domain. [My Copy] Protein science : a publication of the Protein Society, Vol. 14, No. 7. (July 2005), pp. 1902-1910. by Hua Cheng, Nick V. Grishin posted to structure fold-evolution evolution duplication 1barrel by martainn on 2009-11-11 12:09:39 as
	Characterization of SCaMC-3-like/slc25a41, a novel calcium-independent mitochondrial ATP-Mg/Pi carrier. [My Copy] The Biochemical journal, Vol. 418, No. 1. (15 February 2009), pp. 125-133. by Javier Traba, Jorgina Satrústegui, Araceli del Arco posted to mitochondrial fold-evolution comparative_genomics carriers by martainn on 2009-11-10 16:07:49 as
	Mimicking the evolution of a thermally stable monomeric four-helix bundle by fusion of four identical single-helix peptides. [My Copy] Journal of biochemistry (4 November 2009) by Satoshi Akanuma, Taku Matsuba, Emi Ueno, Naoki Umeda, Akihiko Yamagishi posted to structure fold-evolution evolution duplication carriers by martainn on 2009-11-10 16:01:11 as
	Assessment of the probabilities for evolutionary structural changes in protein folds. [My Copy] Bioinformatics (Oxford, England), Vol. 23, No. 7. (1 April 2007), pp. 832-841. by Juris Viksna, David Gilbert posted to structure fold-evolution duplication comparative_genomics by martainn on 2009-11-10 15:56:35 as along with 1 person kluck
	Convergent evolution of domain architectures (is rare). [My Copy] Bioinformatics (Oxford, England) (7 December 2004) by Julian Gough posted to structure fold-evolution duplication comparative_genomics by martainn on 2009-11-10 15:54:26 as along with 3 people and 2 groups matzke ana barry structural_bioinformatics Bioinformatics
	Domain tree-based analysis of protein architecture evolution. [My Copy] Molecular biology and evolution, Vol. 25, No. 2. (1 February 2008), pp. 254-264. by Kristoffer Forslund, Anna Henricson, Volker Hollich, Erik L. Sonnhammer posted to structure fold-evolution duplication comparative_genomics by martainn on 2009-11-10 15:47:01 as along with 5 people calderonv jameswasmuth cjeans vinithepooh gulkur
	Modeling the evolution of protein domain architectures using maximum parsimony. [My Copy] Journal of molecular biology, Vol. 366, No. 1. (9 February 2007), pp. 307-315. by Jessica H. Fong, Lewis Y. Geer, Anna R. Panchenko, Stephen H. Bryant posted to structure fold-evolution duplication comparative_genomics by martainn on 2009-11-10 15:45:08 as along with 10 people and 3 groups swp09 calderonv wiedenhoeft jameswasmuth icases marcius tny choonpeng redelings zwang BioinfoCIPF SGU-CIPF TNT
	Gene fusion/fission is a major contributor to evolution of multi-domain bacterial proteins. [My Copy] Bioinformatics (Oxford, England), Vol. 22, No. 12. (15 June 2006), pp. 1418-1423. by Sophie Pasek, Jean-Loup L. Risler, Pierre Brézellec posted to structure fold-evolution duplication 1barrel by martainn on 2009-11-10 15:31:21 as along with 1 person wiedenhoeft
	Evolution of gene fusions: horizontal transfer versus independent events. [My Copy] Genome biology, Vol. 3, No. 5. (2002) by Itai Yanai, Yuri I. Wolf, Eugene V. Koonin posted to structure fold-evolution duplication comparative_genomics 1barrel by martainn on 2009-11-10 15:28:39 as
	Evolution of antiparallel two-domain membrane proteins: tracing multiple gene duplication events in the DUF606 family. [My Copy] Journal of molecular biology, Vol. 378, No. 3. (2 May 2008), pp. 596-606. by Juke S. Lolkema, Adam Dobrowolski, Dirk-Jan J. Slotboom posted to structure membrane_proteins fold-evolution duplication by martainn on 2009-11-10 15:25:27 as
	Evolution based on domain combinations: the case of glutaredoxins. [My Copy] BMC evolutionary biology, Vol. 9, No. 1. (2009), 66. by Rui Alves, Ester Vilaprinyo, Albert Sorribas, Enrique Herrero posted to structure fold-evolution duplication by martainn on 2009-11-10 15:11:49 as along with 1 person druvus
	Transmembrane protein domains rarely use covalent domain recombination as an evolutionary mechanism. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 101, No. 10. (9 March 2004), pp. 3495-3497. by Yang Liu, Mark Gerstein, Donald M. Engelman posted to structure mitochondrial fold-evolution evolution comparative_genomics carriers by martainn on 2009-11-10 15:07:37 as
	MALIDUP: a database of manually constructed structure alignments for duplicated domain pairs. [My Copy] Proteins, Vol. 70, No. 4. (March 2008), pp. 1162-1166. by Hua Cheng, Bong-Hyun H. Kim, Nick V. Grishin posted to structure fold-evolution evolution duplication comparative_genomics 1barrel by martainn on 2009-11-10 14:40:39 as along with 1 person dimka
	Amino and carboxy-terminal regions in globular proteins. [My Copy] Journal of molecular biology, Vol. 167, No. 2. (25 June 1983), pp. 443-460. by J. M. Thornton, B. L. Sibanda posted to superfolds structure fold-evolution evolution by martainn on 2009-11-10 14:26:22 as
	Structural divergence and distant relationships in proteins: evolution of the globins. [My Copy] Current opinion in structural biology, Vol. 15, No. 3. (June 2005), pp. 290-301. by Juliette T. Lecomte, David A. Vuletich, Arthur M. Lesk posted to superfolds structure fold-evolution evolution by martainn on 2009-11-10 10:43:15 as along with 1 person cjeans
	Detecting coevolution in and among protein domains. [My Copy] PLoS computational biology, Vol. 3, No. 11. (1 November 2007), e211. by Chen-Hsiang H. Yeang, David Haussler posted to structure fold-evolution evolution alignment by martainn on 2009-11-10 10:41:43 as along with 13 people and 1 group dfdong balicea skhadar zwang sobolevnrm niallhaslam hpaces mingzhi Ema phoenixzxl penpen926 friendpine pradiptaray baker-group
	COMPASS server for remote homology inference. [My Copy] Nucleic acids research, Vol. 35, No. Web Server issue. (July 2007) by Ruslan I. Sadreyev, Ming Tang, Bong-Hyun H. Kim, Nick V. Grishin posted to structure fold-evolution evolution alignment by martainn on 2009-11-10 09:56:14 as along with 1 person sebk
	Discrimination between distant homologs and structural analogs: lessons from manually constructed, reliable data sets. [My Copy] Journal of molecular biology, Vol. 377, No. 4. (4 April 2008), pp. 1265-1278. by Hua Cheng, Bong-Hyun H. Kim, Nick V. Grishin posted to structure fold-evolution alignment by martainn on 2009-11-10 09:51:37 as along with 2 people and 1 group barry cdeane structural_bioinformatics
	The subunit interfaces of oligomeric enzymes are conserved to a similar extent to the overall protein sequences. [My Copy] Protein science : a publication of the Protein Society, Vol. 3, No. 12. (December 1994), pp. 2455-2458. by N. V. Grishin, M. A. Phillips posted to structure fold-evolution duplication assembly by martainn on 2009-11-10 09:44:45 as
	Multiple structural alignment for distantly related all beta structures using TOPS pattern discovery and simulated annealing. [My Copy] Protein engineering, Vol. 16, No. 12. (December 2003), pp. 913-923. by A. Williams, D. R. Gilbert, D. R. Westhead posted to structure fold-evolution alignment by martainn on 2009-11-06 18:50:16 as
	One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions. [My Copy] Journal of molecular biology, Vol. 321, No. 5. (30 August 2002), pp. 741-765. by Nozomi Nagano, Christine A. Orengo, Janet M. Thornton posted to superfolds structure fold-evolution evolution by martainn on 2009-11-06 15:41:56 as along with 2 people tjimenez jwm
	Divergent evolution within protein superfolds inferred from profile-based phylogenetics. [My Copy] Journal of molecular biology, Vol. 354, No. 3. (2 December 2005), pp. 722-737. by Douglas L. Theobald, Deborah S. Wuttke posted to superfolds small-motifs fold-evolution by martainn on 2009-11-06 14:52:50 as along with 7 people and 4 groups dfdong cmura yuslinaz ana barry dlr caporaso structural_bioinformatics Bioinformatics biomedical-nlp McCammon
	Supersites within superfolds. Binding site similarity in the absence of homology. [My Copy] Journal of molecular biology, Vol. 282, No. 4. (2 October 1998), pp. 903-918. by R. B. Russell, P. D. Sasieni, M. J. Sternberg posted to superfolds structure small-motifs fold-evolution by martainn on 2009-11-06 14:50:38 as along with 2 people chad_davis nickolay
	Correlation of observed fold frequency with the occurrence of local structural motifs. [My Copy] Journal of molecular biology, Vol. 287, No. 5. (16 April 1999), pp. 969-981. by G. M. Salem, E. G. Hutchinson, C. A. Orengo, J. M. Thornton posted to superfolds structure fold-evolution by martainn on 2009-11-06 14:48:52 as
	Functional proteins from a random-sequence library. [My Copy] Nature, Vol. 410, No. 6829. (5 April 2001), pp. 715-718. by A. D. Keefe, J. W. Szostak posted to small-motifs non-biological fold-evolution atp-binding by martainn on 2009-11-06 12:49:23 as
	Evolutionary optimization of a nonbiological ATP binding protein for improved folding stability. [My Copy] Chemistry & biology, Vol. 11, No. 6. (June 2004), pp. 865-874. by John C. Chaput, Jack W. Szostak posted to non-biological fold-evolution atp-binding by martainn on 2009-11-06 12:40:40 as
	A case of convergent evolution of nucleic acid binding modules. [My Copy] BioEssays : news and reviews in molecular, cellular and developmental biology, Vol. 18, No. 4. (April 1996), pp. 309-315. by P. Graumann, M. A. Marahiel posted to small-motifs rna_binding rna fold-evolution by martainn on 2009-11-06 12:07:57 as
	Structure and evolutionary analysis of a non-biological ATP-binding protein. [My Copy] Journal of molecular biology, Vol. 371, No. 2. (10 August 2007), pp. 501-513. by Sheref S. Mansy, Jinglei Zhang, Rainer Kümmerle, et al.Mikael Nilsson, James J. Chou, Jack W. Szostak, John C. Chaput posted to non-biological fold-evolution evolution atp-binding by martainn on 2009-11-06 11:58:29 as
	Structure of a genetically engineered molecular motor. [My Copy] The EMBO journal, Vol. 20, No. 1-2. (15 January 2001), pp. 40-46. by W. Kliche, S. Fujita-Becker, M. Kollmar, D. J. Manstein, F. J. Kull posted to theory fold-evolution by martainn on 2009-11-06 11:52:54 as
	Interactions of the QacR multidrug-binding protein with structurally diverse ligands: implications for the evolution of the binding pocket. [My Copy] Biochemistry, Vol. 42, No. 51. (30 December 2003), pp. 15226-15236. by Steve Grkovic, Kate M. Hardie, Melissa H. Brown, Ronald A. Skurray posted to fold-evolution drug-efflux by martainn on 2009-11-06 11:50:45 as
	Discrete–continuous duality of protein structure space [My Copy] Current Opinion in Structural Biology, Vol. 19, No. 3. (29 June 2009), pp. 321-328. by Ruslan I. Sadreyev, Bong-Hyun Kim, Nick V. Grishin posted to structure fold-evolution evolution 1barrel by martainn on 2009-09-08 17:27:49 as along with 4 people and 1 group skywalkerus02 philomorph davidalee paulschlesinger Orengo Group Journal Picks
	Revised structure of the AbrB N-terminal domain unifies a diverse superfamily of putative DNA-binding proteins. [My Copy] FEBS letters, Vol. 579, No. 25. (24 October 2005), pp. 5669-5674. by Benjamin G. Bobay, Antonina Andreeva, Geoffrey A. Mueller, John Cavanagh, Alexey G. Murzin posted to structure fold-evolution evolution beta-sheets 1barrel by martainn on 2009-09-08 16:15:24 as
	Evolution of circular permutations in multidomain proteins. [My Copy] Mol Biol Evol, Vol. 23, No. 4. (April 2006), pp. 734-743. by J. Weiner, E. Bornberg-Bauer posted to duplication fold-evolution by martainn on 2009-03-12 18:37:14 as along with 2 people pansapiens tny
	Protein domain organisation: adding order [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009) by Sarah Kummerfeld, Sarah Teichmann posted to beta-barrel comparative_genomics duplication fold-evolution structure by martainn on 2009-03-12 18:35:35 as along with 6 people wiedenhoeft gulkur nlapalu kshameer druvus svozil
	Supra-domains: evolutionary units larger than single protein domains. [My Copy] J Mol Biol, Vol. 336, No. 3. (20 February 2004), pp. 809-823. by C. Vogel, C. Berzuini, M. Bashton, J. Gough, S. A. Teichmann posted to beta-barrel comparative_genomics fold-evolution structure by martainn on 2009-03-12 18:34:25 as along with 4 people tjimenez Schmidtc tny choonpeng
	The geometry of domain combination in proteins. [My Copy] J Mol Biol, Vol. 315, No. 4. (25 January 2002), pp. 927-939. by M. Bashton, C. Chothia posted to beta-barrel comparative_genomics fold-evolution by martainn on 2009-03-12 18:20:36 as along with 4 people jameswasmuth Schmidtc tny choonpeng
	Mimicking enzyme evolution by generating new (betaalpha)8-barrels from (betaalpha)4-half-barrels. [My Copy] Proc Natl Acad Sci U S A, Vol. 101, No. 47. (23 November 2004), pp. 16448-16453. by B. Höcker, J. Claren, R. Sterner posted to beta-barrel fold-evolution structure by martainn on 2009-03-12 18:00:28 as along with 1 person echinotrix
	Structural specificity in coiled-coil interactions [My Copy] Current Opinion in Structural Biology, Vol. In Press, Corrected Proof by Gevorg Grigoryan, Amy E. Keating posted to coiled-coils fold-evolution structure by martainn on 2009-03-12 17:47:29 as along with 7 people and 1 group kgutwin oteri markchen phoenixzxl marck zwang viktor21614 LOX-1 Receptor
	A seven-helix coiled coil [My Copy] PNAS, Vol. 103, No. 42. (17 October 2006), pp. 15457-15462. by Jie Liu, Qi Zheng, Yiqun Deng, Chao-Sheng Cheng, Neville R. Kallenbach, Min Lu posted to coiled-coils fold-evolution structure by martainn on 2009-03-12 17:43:38 as along with 1 person namtonthat
	Multiple sequence alignments [My Copy] Current Opinion in Structural Biology, Vol. 15, No. 3. (June 2005), pp. 261-266. by Iain M. Wallace, Gordon Blackshields, Desmond G. Higgins posted to alignment evolution fold-evolution programs structure by martainn on 2009-03-12 17:19:01 as along with 5 people Thaverkamp BioNica mdimmic bpb nklee
	Sensitive methods for determining the relatedness of proteins with limited sequence homology. [My Copy] Current opinion in biotechnology, Vol. 5, No. 4. (August 1994), pp. 361-371. by P. Argos posted to alignment fold-evolution programs structure by martainn on 2009-03-12 17:18:06 as
	Sequence context-specific profiles for homology searching [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 10. (10 March 2009), pp. 3770-3775. by A. Biegert, J. Söding posted to alignment fold-evolution programs small-motifs by martainn on 2009-03-12 17:17:12 as along with 7 people yylin ikirmitz TRHvidsten operon dakelley phoenixzxl zwang
	EmrE, a model for studying evolution and mechanism of ion-coupled transporters. [My Copy] Biochimica et biophysica acta, Vol. 1794, No. 5. (03 May 2009), pp. 748-762. by Shimon Schuldiner posted to drug-efflux emre fold-evolution smr by martainn on 2009-02-03 12:38:58 as along with 3 people paulschlesinger girayenkavi viktor21614
	An emerging consensus for the structure of EmrE [My Copy] Acta Crystallographica Section D: Biological Crystallography, Vol. 65, No. 2. (01 February 2009), pp. 186-192. by V. M. Korkhov, C. G. Tate posted to drug-efflux fold-evolution structure by martainn on 2009-02-03 12:16:18 as along with 1 person viktor21614

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structure	237
virulence	151
fold-evolution	109
drug-efflux	101
tolc	74
3review	70
evolution	66
phage	63
acra	56
1paper	49
type-iii	46
assembly	45
type-i	45
crystallography	41
acrb	40
4grant	33
mutation	32
atpase	31
programs	31
hemolysin	30
inhibitor	29
pilus	29
adapter	28
comparative_genomics	27
vibrio	27
flagella	26
pseudomonas	25
mexa	24
export	24
toxin	24
duplication	23
expression	21
srna	21
coiled-coils	20
ctx	20
beta-sheets	19
secretion	19
hlyd	17
fluorescence	17
small-motifs	16
4preview	16
docking	16
fusion	15
hlyb	15
crystallization	15
carriers	15
software	14
periplasmic	14
alignment	14
theory	13
mitochondrial	13
yersinia	13
colicin	12
salmonella	12
strategy	12
type-iv	11
abc_transporter	11
1barrel	11
beta-barrel	11
fret	10
crosslinking	10
rna	10
colicinv	10
competence	10
dynamics	9
effector	9
membrane_proteins	9
2discussion	8
methods	8
quorum	8
gram-positive	8
heterogeneity	7
type-ii	7
detergents	7
virus	7
superfolds	7
indels	7
mfs	6
shigella	6
heat-stable-enterotoxinii	6
pro-isomerization	6
type_i	6
truncation	6
kinetics	6
hfq	5
outer_membrane	5
channels	5
asymmetry	5
dhfr	5
pseudopilus	5
esat-6	5
plasmid	4
clostridium	4
pnpase	4
import	4
cvaa	4
mtx	4
trp	4
secretin	4
tolq	4
normalmodes	4
history	4
sipb	4
c-di-gmp	3
beta-bulge	3
apoptosis	3
rnd	3
vaccine	3
emre	3
electrophysiology	3
energy_landscape	3
smr	3
c_difficile	3
adp-atp	3
oprm	3
lactis	3
conjugation	3
non-biological	3
crick	3
rna_binding	3
microcin	3
atp-binding	3
polar	3
semet	3
2paper	3
chaperone	3
lipoyl	3
mitochondria	2
mexb	2
dispersin	2
dna	2
polysaccharide	2
puld	2
building	2
enolase	2
flhb	2
sv5	2
h_influenzae	2
nmr	2
equatorial	2
pilz	2
single-molecule	2
quenching	2
mitochondrial_disorders	2
rhodopsin_family	2
neisseria	2
peptidoglycan	2
citrate	2
virg	2
cryo	1
phasing	1
cusb	1
insulin_secretion	1
staphylococcus	1
em	1
human	1
prgk	1
medawar	1
binding_mechanisms	1
7-transmembrane	1
macab	1
exosome	1
serratia	1
cys	1
flhf	1
chloride	1
f1fo	1
ros	1
nesseria	1
cusf	1
cycling	1
epr	1
traffic	1
phage_shock	1
fission	1
ethics	1
darpins	1
proteasome	1

martainn's fold-evolution [109 articles] Export

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