Tag fold [142 articles] Export

Recent papers classified by the tag fold.

	Fold space unlimited [My Copy] Current Opinion in Structural Biology, Vol. 19, No. 3. (08 June 2009), pp. 312-320. by Manfred J. Sippl posted to structure review protein fold by pansapiens on 2009-11-09 07:27:12 as along with 2 people and 1 group skywalkerus02 davidalee Orengo Group Journal Picks
	Backtracking iterators [My Copy] In ML '06: Proceedings of the 2006 workshop on ML (2006), pp. 55-62. by Jean C. Filliâtre posted to structural-induction iterators induction fold backtrack by robertjohnsimmons on 2009-10-11 18:51:07 as
	Three-Dimensional Structural View of the Central Metabolic Network of Thermotoga maritima [My Copy] Science, Vol. 325, No. 5947. (18 September 2009), pp. 1544-1549. by Ying Zhang, Ines Thiele, Dana Weekes, et al.Zhanwen Li, Lukasz Jaroszewski, Krzysztof Ginalski, Ashley M. Deacon, John Wooley, Scott A. Lesley, Ian A. Wilson, Bernhard Palsson, Andrei Osterman, Adam Godzik posted to viz structure protrel networks metabolic_pathways fold embedding biochemical by riffraff on 2009-10-01 09:55:42 as along with 13 people michaelbarton venancio schwartzjmc apocapoc eehsanipour reyez TRHvidsten flbarroso daveGerrard zwang pablocarb phoenixzxl roys
	Inactive Enzyme-homologues Find New Function in Regulatory Processes [My Copy] Journal of Molecular Biology, Vol. 340, No. 3. (09 July 2004), pp. 399-404. by Birgit Pils, Jörg Schultz posted to protein inactive fold evolution enzyme by robfsouza on 2009-09-30 00:55:50 as along with 3 people tny jwm Jporci
	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 protein interaction fold evolution correlation contact compensatory coevolution by robfsouza on 2009-09-23 19:49:40 as along with 10 people and 1 group yyfwuhan cmzmasek dgront pansapiens pablocarb vvoorr biomcgary dayjm jwm jbhiatt Marcotte_Lab
	Assembly reflects evolution of protein complexes. [My Copy] Nature, Vol. 453, No. 7199. (26 June 2008), pp. 1262-1265. by E. D. Levy, E. Boeri Erba, C. V. Robinson, S. A. Teichmann posted to topology structure quaternary protein oligomer mass_spectometry interaction inactive homomer fold experimental evolution complex assembly by robfsouza on 2009-09-23 19:27:54 as along with 11 people and 1 group chica noraziz chad_davis psique marck paulschlesinger neils jwm zwang faion phoenixzxl KeatingJClub
	The catalytic domains of thiamine triphosphatase and CyaB-like adenylyl cyclase define a novel superfamily of domains that bind organic phosphates [My Copy] BMC Genomics, Vol. 3, No. 1. (2002), 33. by Lakshminarayan Iyer, L. Aravind posted to superfamily protein inactive fold enzyme domain aravind by robfsouza on 2009-09-18 23:09:50 as
	Diversification of Catalytic Activities and Ligand Interactions in the Protein Fold Shared by the Sugar Isomerases, eIF2B, DeoR Transcription Factors, Acyl-CoA Transferases and Methenyltetrahydrofolate Synthetase [My Copy] Journal of Molecular Biology, Vol. 356, No. 3. (24 February 2006), pp. 823-842. by Vivek Anantharaman, L. Aravind posted to protein inactive fold enzyme carbohydrate aravind by robfsouza on 2009-09-18 23:04:56 as along with 1 person tny
	Anatomy of the E2 ligase fold: Implications for enzymology and evolution of ubiquitin/Ub-like protein conjugation [My Copy] Journal of Structural Biology, Vol. 162, No. 2. (May 2008), pp. 205-218. by A. Burroughs, M. Jaffee, L. Iyer, L. Aravind posted to ubiquitin inactive fold enzyme aravind by robfsouza on 2009-09-18 22:58:34 as
	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 superfamily protein inactive fold evolution enzyme aravind by robfsouza on 2009-09-18 22:54:02 as along with 3 people martainn tny christiw
	The prokaryotic antecedents of the ubiquitin-signaling system and the early evolution of ubiquitin-like beta-grasp domains [My Copy] Genome Biology, Vol. 7, No. 7. (19 July 2006), R60. by Lakshminarayan Iyer, A. Maxwell Burroughs, L. Aravind posted to ubiquitin protein prokaryotes inactive fold evolution enzyme aravind by robfsouza on 2009-09-18 22:43:56 as
	Novel Families of Putative Protein Kinases in Bacteria and Archaea: Evolution of the âEukaryoticâ Protein Kinase Superfamily [My Copy] Genome Research, Vol. 8, No. 10. (1 October 1998), pp. 1038-1047. by Christopher J. Leonard, L. Aravind, Eugene V. Koonin posted to superfamily protein kinase inactive fold enzyme aravind by robfsouza on 2009-09-18 22:42:18 as along with 3 people and 1 group anuragsethi thegoose2 tharris C. elegans / WormBase
	The many faces of the helix-turn-helix domain: Transcription regulation and beyond⋆ [My Copy] FEMS Microbiology Reviews, Vol. 29, No. 2. (2005), pp. 231-262. by L. Aravind, Vivek Anantharaman, Santhanam Balaji, Mohan M. Babu, Lakshminarayan M. Iyer posted to transcription protein inactive fold evolution enzyme domain aravind by robfsouza on 2009-09-18 22:22:35 as
	Evolution and Classification of P-loop Kinases and Related Proteins☆ [My Copy] Journal of Molecular Biology, Vol. 333, No. 4. (31 October 2003), pp. 781-815. by Detlef D. Leipe, Eugene V. Koonin, L. Aravind posted to protein kinase inactive fold evolution enzyme aravind by robfsouza on 2009-09-18 22:17:14 as along with 1 person tny
	Detection of novel members, structure-function analysis and evolutionary classification of the 2H phosphoesterase superfamily [My Copy] Nucl. Acids Res., Vol. 30, No. 23. (1 December 2002), pp. 5229-5243. by Raja Mazumder, Lakshminarayan M. Iyer, Sona Vasudevan, L. Aravind posted to protein inactive fold evolution enzyme aravind by robfsouza on 2009-09-18 22:09:37 as along with 1 person and 1 group lilith 8_01
	The RAGNYA fold: a novel fold with multiple topological variants found in functionally diverse nucleic acid, nucleotide and peptide-binding proteins [My Copy] Nucl. Acids Res., Vol. 35, No. 17. (27 September 2007), pp. 5658-5671. by S. Balaji, L. Aravind posted to peptide_binding nucleotide inactive fold enzyme binding aravind by robfsouza on 2009-09-18 22:07:19 as
	Themis is a member of a new metazoan gene family and is required for the completion of thymocyte positive selection [My Copy] Nature Immunology, Vol. 10, No. 8. (13 July 2009), pp. 831-839. by Andy L. Johnson, L. Aravind, Natalia Shulzhenko, et al.Andre Morgun, See-Young Choi, Tanya L. Crockford, Teresa Lambe, Heather Domaschenz, Edyta M. Kucharska, Lixin Zheng, Carola G. Vinuesa, Michael J. Lenardo, Christopher C. Goodnow, Richard J. Cornall, Ronald H. Schwartz posted to protein inactive fold evolution enzyme domain aravind by robfsouza on 2009-09-18 22:05:45 as along with 1 person leliavski
	Small but versatile: the extraordinary functional and structural diversity of the beta-grasp fold [My Copy] Biology Direct, Vol. 2, No. 1. (02 July 2007), 18. by A. Maxwell Burroughs, S. Balaji, Lakshminarayan Iyer, L. Aravind posted to protein inactive fold evolution enzyme domain aravind by robfsouza on 2009-09-18 22:00:49 as
	The signaling helix: a common functional theme in diverse signaling proteins [My Copy] Biology Direct, Vol. 1, No. 1. (05 September 2006), 25. by Vivek Anantharaman, S. Balaji, L. Aravind posted to signaling protein inactive fold evolution enzyme aravind by robfsouza on 2009-09-18 21:58:51 as along with 1 person choonpeng
	Analysis of DBC1 and its homologs suggests a potential mechanism for regulation of sirtuin domain deacetylases by NAD metabolites. [My Copy] Cell cycle (Georgetown, Tex.), Vol. 7, No. 10. (15 May 2008), pp. 1467-1472. by Vivek Anantharaman, L. Aravind posted to protein inactive fold evolution enzyme domain aravind acetylation by robfsouza on 2009-09-18 21:38:46 as
	Classification of the caspase-hemoglobinase fold: Detection of new families and implications for the origin of the eukaryotic separins [My Copy] Proteins: Structure, Function, and Genetics, Vol. 46, No. 4. (2002), pp. 355-367. by L. Aravind, Eugene V. Koonin posted to protease inactive fold evolution enzyme aravind by robfsouza on 2009-09-18 21:36:22 as
	Peptide-N-glycanases and DNA repair proteins, Xp-C/Rad4, are, respectively, active and inactivated enzymes sharing a common transglutaminase fold [My Copy] Hum. Mol. Genet., Vol. 10, No. 16. (1 August 2001), pp. 1627-1630. by Vivek Anantharaman, Eugene V. Koonin, L. Aravind posted to repair inactive fold evolution enzyme aravind by robfsouza on 2009-09-18 21:34:14 as
	The relationship between protein structure and function: a comprehensive survey with application to the yeast genome. [My Copy] Journal of molecular biology, Vol. 288, No. 1. (23 April 1999), pp. 147-164. by H. Hegyi, M. Gerstein posted to function fold enzyme by pablocarb on 2009-09-17 14:20:22 as along with 5 people and 1 group MarcoAlvarez Einat eweaver tny siebertm structural_bioinformatics
	Virus evolution: how far does the double \|[beta]\|-barrel viral lineage extend? [My Copy] Nat Rev Micro, Vol. 6, No. 12. (01 December 2008), pp. 941-948. by Mart Krupovic, Dennis H. Bamford posted to virus structure fold evolution capsid by robfsouza on 2009-09-15 20:26:47 as along with 1 person Terkko
	A tutorial on the universality and expressiveness of fold [My Copy] J. Funct. Program., Vol. 9, No. 4. (July 1999), pp. 355-372. by Graham Hutton posted to possible-concertrg-paper iterators functional-programming fold by robertjohnsimmons to the group ConcertRG on 2009-09-07 19:21:58 as along with 4 people and 1 group pedagand draganigajic mcclurmc jimburton functional programming
	Organizing Functional Code for Parallel Execution or, foldl and foldr Considered Slightly Harmful [My Copy] In ICFP '09: Proceedings of the 14th ACM SIGPLAN international conference on Functional programming (2009), pp. 1-2. by Guy L. Steele posted to parallel-programming monoids functional-programming fold by spl on 2009-09-07 11:47:58 as
	The NYN domains: novel predicted RNAses with a PIN domain-like fold. [My Copy] RNA biology, Vol. 3, No. 1. (r 2006), pp. 18-27. by Vivek Anantharaman, L. Aravind posted to superfamily rnase rna replication recombination fold family evolution domain aravind by robfsouza on 2009-09-04 17:08:43 as
	Trends in protein evolution inferred from sequence and structure analysis [My Copy] Current Opinion in Structural Biology, Vol. 12, No. 3. (1 June 2002), pp. 392-399. by L. Aravind posted to structure protein inactive fold family evolution enzyme aravind by robfsouza on 2009-09-03 03:17:37 as
	The continuity of protein structure space is an intrinsic property of proteins [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 37. (15 September 2009), pp. 15690-15695. by Jeffrey Skolnick, Adrian K. Arakaki, Seung Y. Lee, Michal Brylinski posted to structure space protein fold by philomorph on 2009-09-02 18:37:55 as along with 3 people docv zwang TRHvidsten
	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 space protein fold by philomorph on 2009-09-02 18:36:07 as along with 4 people and 1 group skywalkerus02 martainn davidalee paulschlesinger Orengo Group Journal Picks
	An Evolutionary Classification of the Metallo-ß-Lactamase Fold Proteins [My Copy] In Silico Biology, Vol. 1, No. 2. (1 January 1999), pp. 69-91. by L. Aravind posted to superfamily protein inactive fold evolutionary evolution enzyme classification carbohydrate binding aravind by robfsouza on 2009-08-20 22:29:53 as
	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 protein phylogenetics fold evolution by yuslinaz on 2009-08-13 04:07:29 as along with 6 people and 4 groups martainn cmura ana barry dlr caporaso structural_bioinformatics Bioinformatics biomedical-nlp McCammon
	The AAA+ superfamily of functionally diverse proteins [My Copy] Genome Biology, Vol. 9, No. 4. (30 April 2008), 216. by Jamie Snider, Guillaume Thibault, Walid Houry posted to superfamily protein ntpase fold evolution enzyme atpase by robfsouza on 2009-08-11 21:02:39 as
	Efficient SCOP-fold classification and retrieval using index-based protein substructure alignments [My Copy] Bioinformatics, Vol. 25, No. 19. (1 October 2009), pp. 2559-2565. by Pin-Hao Chi, Bin Pang, Dmitry Korkin, Chi-Ren Shyu posted to superfamily structure protein methods method fold classification bioinformatics by robfsouza on 2009-08-11 16:55:01 as along with 2 people walshtp zwang
	Type II restriction endonuclease R.KpnI is a member of the HNH nuclease superfamily [My Copy] Nucl. Acids Res., Vol. 32, No. 20. (23 November 2004), pp. 6129-6135. by Matheshwaran Saravanan, Janusz M. Bujnicki, Iwona A. Cymerman, Desirazu N. Rao, Valakunja Nagaraja posted to endonuclease enzyme fold homology protein restriction structure superfamily by robfsouza on 2009-08-07 01:08:43 as
	Structural and evolutionary classification of Type II restriction enzymes based on theoretical and experimental analyses [My Copy] Nucl. Acids Res., Vol. 36, No. 11. (1 June 2008), pp. 3552-3569. by Jerzy Orlowski, Janusz M. Bujnicki posted to analysis chromatin classification endonuclease enzyme evolution fold prediction recombination restriction sequence superfamily by robfsouza on 2009-08-06 23:55:35 as
	A novel family of P-loop NTPases with an unusual phyletic distribution and transmembrane segments inserted within the NTPase domain. [My Copy] Genome Biol, Vol. 5, No. 5. (2004) by L. Aravind, L. M. Iyer, D. D. Leipe, E. V. Koonin posted to aravind domain evolution fold ntpase p-loop protein superfamily by robfsouza on 2009-07-21 16:23:01 as along with 4 people and 3 groups thegoose2 tharris barry tny C. elegans / WormBase structural_bioinformatics Bioinformatics
	Group IIC intron mobility into attC sites involves a bulged DNA stem-loop motif. [My Copy] RNA (New York, N.Y.) (9 June 2009) by Grégory Léon, Paul H. Roy posted to fold integron by cambray on 2009-06-16 10:56:55 as
	Effect of rotational stacking faults on the Raman spectra of folded graphene [My Copy] Physical Review B (Condensed Matter and Materials Physics), Vol. 79, No. 19. (2009), 195417. by P. Poncharal, A. Ayari, T. Michel, J. L. Sauvajol posted to experimental fold graphene raman by kas on 2009-05-20 11:04:59 as
	Exploring the structure and function paradigm [My Copy] Current Opinion in Structural Biology In Nucleic acids / Sequences and topology, Vol. 18, No. 3. (June 2008), pp. 394-402. by O. Redfern, B. Dessailly, C. Orengo posted to binding database evolution fold orengo protein site structure by robfsouza on 2009-05-16 07:29:14 as along with 7 people and 1 group yylin bdessailly guhjy paulschlesinger marck chad_davis janasont Orengo Group Journal Picks
	Fold change in evolution of protein structures. [My Copy] J Struct Biol, Vol. 134, No. 2-3. (n 2001), pp. 167-185. by N. V. Grishin posted to classification evolution fold structure superfamily by robfsouza on 2009-05-15 01:58:54 as along with 7 people and 2 groups tomhebbron matzke ana barry pansapiens krishnaJCSG martainn structural_bioinformatics Bioinformatics
	Nothing about protein structure classification makes sense except in the light of evolution [My Copy] Current Opinion in Structural Biology, Vol. 19, No. 3. (24 June 2009), pp. 329-334. by Ruben E. Valas, Song Yang, Philip E. Bourne posted to network biological classification evolution fold protein structure superfamily by robfsouza on 2009-05-15 01:57:40 as along with 12 people and 3 groups mkotlyar skywalkerus02 dgront nyyu apaydin barry coela Zephyrus sobolevnrm zwang friendpine paulschlesinger structural_bioinformatics R.E.A.D baker-group
	Strategies for RNA folding. [My Copy] Trends in biochemical sciences, Vol. 21, No. 4. (April 1996), pp. 145-149. by D. E. Draper posted to fold rna by nikkiwithers on 2009-05-05 15:49:10 as
	The Effect of Sequence Evolution on Protein Structural Divergence [My Copy] Mol Biol Evol, Vol. 26, No. 5. (1 May 2009), pp. 1055-1065. by Simon G. Williams, Simon C. Lovell posted to alignment compensatory correlation evolution fold mutation protein by robfsouza on 2009-05-02 08:56:20 as along with 2 people djkt bpcusack
	Regulatory potential, phyletic distribution and evolution of ancient, intracellular small-molecule-binding domains1☆ [My Copy] Journal of Molecular Biology, Vol. 307, No. 5. (13 April 2001), pp. 1271-1292. by Vivek Anantharaman, Eugene V. Koonin, L. Aravind posted to small site protein molecule inactive genome fold evolution enzyme domain binding aravind by robfsouza on 2009-04-30 02:39:27 as
	Carbohydrate-binding modules: fine-tuning polysaccharide recognition. [My Copy] The Biochemical journal, Vol. 382, No. Pt 3. (15 September 2004), pp. 769-781. by A. B. Boraston, D. N. Bolam, H. J. Gilbert, G. J. Davies posted to carbohydrate classification fold protein by robfsouza on 2009-04-28 20:03:19 as
	3D Complex: A Structural Classification of Protein Complexes [My Copy] PLoS Computational Biology, Vol. 2, No. 11. (1 November 2006), e155. by Emmanuel D. Levy, Jose B. Pereira-Leal, Cyrus Chothia, Sarah A. Teichmann posted to assembly complex contact database evolution fold by robfsouza on 2009-04-22 01:39:01 as along with 3 people aalibes krishnaJCSG jteyra
	An evolutionary treasure: unification of a broad set of amidohydrolases related to urease [My Copy] Proteins: Structure, Function, and Genetics, Vol. 28, No. 1. (1997), pp. 72-82. by Liisa Holm, Chris Sander posted to evolution fold protein structure superfamily by robfsouza on 2009-04-21 23:51:05 as
	The emergence of catalytic and structural diversity within the beta-clip fold [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 55, No. 4. (2004), pp. 977-991. by Lakshminarayan M. Iyer, L. Aravind posted to superfamily protein inactive fold evolution enzyme domain aravind by robfsouza on 2009-04-21 22:53:05 as
	Recent structural studies of carbohydrate-binding modules [My Copy] Cellular and Molecular Life Sciences CMLS, Vol. 63, No. 24. (December 2006), pp. 2954-2967. by Hashimoto, H. posted to carbohydrate fold protein structure by robfsouza on 2009-04-21 22:35:56 as

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protein	80
structure	44
evolution	33
recognition	30
prediction	27
enzyme	26
aravind	22
inactive	22
superfamily	15
domain	10
rna	10
function	8
unfold	8
classification	7
sequence	6
space	6
vocal	6
binding	5
difference	5
qpcr	5
carbohydrate	4
change	4
folding	4
functional-programming	4
alignment	3
anamorphism	3
bioinformatics	3
casp	3
casp6	3
ctbp	3
database	3
differential	3
expression	3
genome	3
genomics	3
haskell	3
iterators	3
limma	3
microarray	3
nodules	3
nucleotide	3
polyps	3
protein_structure	3
recursion	3
small	3
virus	3
ab	2
algebra-of-programming	2
assembly	2
bayes	2
catamorphism	2
comparative	2
comparison	2
compensatory	2
complex	2
contact	2
correlation	2
dali	2
dna	2
endonuclease	2
evolutionary	2
experimental	2
family	2
functors	2
genetic	2
hiv	2
homolog	2
homology	2
initio	2
interaction	2
kinase	2
methods	2
modeling	2
motif	2
nascent	2
native	2
network	2
noncoding	2
ntpase	2
nucleocapsid	2
primer	2
program-calculation	2
rdc	2
recombination	2
restriction	2
retroviral	2
ribosome	2
rnaprotein	2
selection	2
shape	2
similarity	2
site	2
size	2
statistics	2
structural	2
template	2
transcriptase	2
transcriptome	2
trna	2
ubiquitin	2

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