robfsouza's library 247 articles Export

	MUSTANG: A multiple structural alignment algorithm [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 64, No. 3. (2006), pp. 559-574. by Arun S. Konagurthu, James C. Whisstock, Peter J. Stuckey, Arthur M. Lesk posted to structure bioinformatics alignment by robfsouza on 2009-11-20 23:52:04 as along with 5 people and 3 groups karbak ana jwm rabio Thaverkamp structural_bioinformatics Bioinformatics Microbial-Ecology
	Comparative genomics and structural biology of the molecular innovations of eukaryotes [My Copy] Current Opinion in Structural Biology In Nucleic acids/Sequences and topology - Anna Marie Pyle and Jonathan Widom/Nick V Grishin and Sarah A Teichmann, Vol. 16, No. 3. (June 2006), pp. 409-419. by L. Aravind, L. Iyer, E. Koonin posted to protein ph fold evolution eukaryote domain architecture by robfsouza on 2009-11-19 20:53:54 as
	uDENN, DENN, and dDENN: Indissociable Domains in Rab and MAP Kinases Signaling Pathways [My Copy] Biochemical and Biophysical Research Communications, Vol. 287, No. 3. (28 September 2001), pp. 688-695. by E. Levivier posted to ubiquitination ubiquitin uba1 mvb12 by robfsouza on 2009-11-18 19:47:09 as
	Comprehensive Multigene Phylogenies of Excavate Protists Reveal the Evolutionary Positions of "Primitive" Eukaryotes [My Copy] Mol Biol Evol, Vol. 23, No. 3. (1 March 2006), pp. 615-625. by Alastair G. B. Simpson, Yuji Inagaki, Andrew J. Roger posted to protozoa phylogeny phylogenomics evolution eukaryote by robfsouza on 2009-10-17 02:24:53 as
	The human disease network [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 21. (22 May 2007), pp. 8685-8690. by Kwang-Il Goh, Michael E. Cusick, David Valle, Barton Childs, Marc Vidal, Albert-LÃ¡szlÃ³ BarabÃ¡si posted to scale neurobiology network large interaction gene disease development by robfsouza on 2009-10-09 01:28:31 as along with 39 people and 9 groups bertelsen smichan biomcgary pawelsobko CurAbility Scis0000002 qluo cbforrest daforerog nedwards Dulcinea saket kaarsinogen roys Yanno guhjy aalibes cannin kuhn jfr yas balicea neveaire bundschu raiyar grahamc joepickrell leSyl henning dejori xingxu winterschlaefer naegele shoshin shikin nolodie mingzhi carlk yaredo Network Analysis of Genes Regulated in Renal Diseases Biostatistics Computational-Genomics Bioinformatics Neuroscience steinmetzlab ic4 generif_paper GomezLab
	Is protein classification necessary? Toward alternative approaches to function annotation. [My Copy] Current opinion in structural biology, Vol. 19, No. 3. (5 June 2009), pp. 363-368. by Donald Petrey, Barry Honig posted to structure protein inactive enzyme classification by robfsouza on 2009-10-07 17:07:31 as along with 7 people and 4 groups sconlan davidalee sobolevnrm janasont idoerg fgibson barry Orengo Group Journal Picks baker-group structural_bioinformatics Bioinformatics
	SCOPEC: a database of protein catalytic domains [My Copy] Bioinformatics, Vol. 20, No. suppl_1. (4 August 2004), pp. i130-136. by Richard A. George, Ruth V. Spriggs, Janet M. Thornton, Bissan Al-Lazikani, Mark B. Swindells posted to structure site protein inactive enzyme catalytic by robfsouza on 2009-10-07 17:00:53 as along with 5 people ucbcjbm pablocarb shung gbart tny
	The 10,000 Year Explosion: How Civilization Accelerated Human Evolution [My Copy] (26 January 2009) by Gregory Cochran, Henry Harpending posted to human evolution by robfsouza on 2009-10-05 03:57:17 as
	The Man Who Mistook His Wife For A Hat: And Other Clinical Tales [My Copy] (02 April 1998) by Oliver Sacks posted to neurology disease brain by robfsouza on 2009-10-05 03:37:03 as along with 4 people and 1 group STUDENT09 haveuheard NitinCR majak FAL
	TED: Ideas worth spreading [My Copy] posted to videos links ideas by robfsouza on 2009-10-03 21:11:02 as
	'God vs. Science - A debate between Richard Dawkins and Francis Collins' by TIME Magazine - RichardDawkins.net [My Copy] by Richard Dawkins, Francis Collins posted to religion phylosophy evolution debate by robfsouza on 2009-10-01 16:37:23 as
	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
	Resurrecting the Ancestral Enzymatic Role of a Modulatory Subunit [My Copy] Journal of Biological Chemistry, Vol. 280, No. 11. (18 March 2005), pp. 10189-10195. by Miguel A. Ballicora, Jennifer R. Dubay, Claire H. Devillers, Jack Preiss posted to reconstruction inactive evolution enzyme domain character ancestral by robfsouza on 2009-09-21 16:50:34 as along with 2 people and 1 group matzke nknii TCR_Signaling
	Protein content of minimal and ancestral ribosome [My Copy] RNA, Vol. 11, No. 9. (September 2005), pp. 1400-1406. by Arcady Mushegian posted to ribosome protein evolution ancestral by robfsouza on 2009-09-18 23:49:45 as
	AAA+: A Class of Chaperone-Like ATPases Associated with the Assembly, Operation, and Disassembly of Protein Complexes [My Copy] Genome Research, Vol. 9, No. 1. (1 January 1999), pp. 27-43. by Andrew F. Neuwald, L. Aravind, John L. Spouge, Eugene V. Koonin posted to superfamily inactive enzyme chaperone atpase aravind by robfsouza on 2009-09-18 23:31:18 as along with 1 person leemary4
	Apoptotic Molecular Machinery: Vastly Increased Complexity in Vertebrates Revealed by Genome Comparisons [My Copy] Science, Vol. 291, No. 5507. (16 February 2001), pp. 1279-1284. by L. Aravind, Vishva M. Dixit, Eugene V. Koonin posted to vertebrates inactive evolution enzyme aravind apoptosis by robfsouza on 2009-09-18 23:28:19 as along with 2 people and 1 group thegoose2 tharris C. elegans / WormBase
	Phosphoesterase domains associated with DNA polymerases of diverse origins [My Copy] Nucl. Acids Res., Vol. 26, No. 16. (15 August 1998), pp. 3746-3752. by L. Aravind, E. V. Koonin posted to polymerase inactive evolution enzyme dna aravind by robfsouza on 2009-09-18 23:27:35 as
	Genome of the Extremely Radiation-Resistant Bacterium Deinococcus radiodurans Viewed from the Perspective of Comparative Genomics [My Copy] Microbiol. Mol. Biol. Rev., Vol. 65, No. 1. (1 March 2001), pp. 44-79. by Kira S. Makarova, L. Aravind, Yuri I. Wolf, et al.Roman L. Tatusov, Kenneth W. Minton, Eugene V. Koonin, Michael J. Daly posted to sequence inactive genome enzyme aravind by robfsouza on 2009-09-18 23:23:24 as along with 2 people and 1 group operon beatrizfernandez Microbial-Ecology
	Complete genome sequence of the apicomplexan, Cryptosporidium parvum. [My Copy] Science (New York, N.Y.), Vol. 304, No. 5669. (16 April 2004), pp. 441-445. by Mitchell S. Abrahamsen, Thomas J. Templeton, Shinichiro Enomoto, et al.Juan E. Abrahante, Guan Zhu, Cheryl A. Lancto, Mingqi Deng, Chang Liu, Giovanni Widmer, Saul Tzipori, Gregory A. Buck, Ping Xu, Alan T. Bankier, Paul H. Dear, Bernard A. Konfortov, Helen F. Spriggs, Lakshminarayan Iyer, Vivek Anantharaman, L. Aravind, Vivek Kapur posted to sequence inactive genome enzyme aravind by robfsouza on 2009-09-18 23:21:49 as along with 3 people kaarsinogen Cortel shung
	Eukaryote-specific Domains in Translation Initiation Factors: Implications for Translation Regulation and Evolution of the Translation System [My Copy] Genome Research, Vol. 10, No. 8. (1 August 2000), pp. 1172-1184. by L. Aravind, Eugene V. Koonin posted to translation regulation inactive factor evolution eukaryote enzyme aravind by robfsouza on 2009-09-18 23:20:10 as
	Differential Action of Natural Selection on the N and C-terminal Domains of 2′-5′ Oligoadenylate Synthetases and the Potential Nuclease Function of the C-terminal Domain [My Copy] Journal of Molecular Biology, Vol. 326, No. 5. (07 March 2003), pp. 1449-1461. by Igor B. Rogozin, L. Aravind, Eugene V. Koonin posted to selection inactive evolution enzyme aravind by robfsouza on 2009-09-18 23:15:11 as
	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
	The domains of death: evolution of the apoptosis machinery [My Copy] Trends in Biochemical Sciences, Vol. 24, No. 2. (1 February 1999), pp. 47-53. by L. Aravind posted to inactive enzyme domain aravind apoptosis by robfsouza on 2009-09-18 23:06:14 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
	Comparative Genomics of Protists: New Insights into the Evolution of Eukaryotic Signal Transduction and Gene Regulation* [My Copy] Annual Review of Microbiology, Vol. 61, No. 1. (2007), pp. 453-475. by Vivek Anantharaman, Lakshminarayan M. Iyer, L. Aravind posted to transduction signal regulation inactive gene expression evolution enzyme aravind by robfsouza on 2009-09-18 22:56:09 as along with 1 person cmzmasek
	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
	DNA polymerase beta-like nucleotidyltransferase superfamily: identification of three new families, classification and evolutionary history [My Copy] Nucl. Acids Res., Vol. 27, No. 7. (1 April 1999), pp. 1609-1618. by L. Aravind, E. V. Koonin posted to superfamily polymerase inactive evolution enzyme dna aravind by robfsouza on 2009-09-18 22:48:32 as
	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 X-ray crystallographic structure and activity analysis of a <I>Pseudomonas-</I>specific subfamily of the HAD enzyme superfamily evidences a novel biochemical function [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 70, No. 1. (2008), pp. 197-207. by Ezra Peisach, Liangbing Wang, A. Maxwell Burroughs, L. Aravind, Debra Dunaway-Mariano, Karen N. Allen posted to structure protein inactive enzyme aravind by robfsouza on 2009-09-18 22:33:22 as
	Quod erat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences [My Copy] Genome Biology, Vol. 2, No. 12. (2001) by Lakshminarayan Iyer, L. Aravind, Peer Bork, et al.Kay Hofmann, Arcady Mushegian, Igor Zhulin, Eugene Koonin posted to sequence science inactive enzyme bioinformatics aravind analysis by robfsouza on 2009-09-18 22:31:39 as along with 2 people bpcusack eweaver
	Adhesion Molecules and Other Secreted Host‐Interaction Determinants in Apicomplexa: Insights from Comparative Genomics [My Copy] International Review of Cytology, Vol. 262 (2007), pp. 1-74. by V. Anantharaman, L. Iyer, S. Balaji, L. Aravind posted to inactive genomics evolution enzyme comparative aravind adhesion by robfsouza on 2009-09-18 22:28:41 as
	Plasmodium BiologyGenomic Gleanings [My Copy] Cell, Vol. 115, No. 7. (26 December 2003), pp. 771-785. by L. Aravind, Lakshminarayan M. Iyer, Thomas E. Wellems, Louis H. Miller posted to inactive enzyme aravind by robfsouza on 2009-09-18 22:25:55 as
	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
	Anabaena Sensory Rhodopsin: A Photochromic Color Sensor at 2.0 A [My Copy] Science, Vol. 306, No. 5700. (19 November 2004), pp. 1390-1393. by Lutz Vogeley, Oleg A. Sineshchekov, Vishwa D. Trivedi, Jun Sasaki, John L. Spudich, Hartmut Luecke posted to rhodopsin bacteria by robfsouza on 2009-09-17 17:24:20 as
	Crystal Structure of the Anabaena Sensory Rhodopsin Transducer [My Copy] Journal of Molecular Biology, Vol. 367, No. 3. (30 March 2007), pp. 741-751. by Lutz Vogeley, Vishwa D. Trivedi, Oleg A. Sineshchekov, Elena N. Spudich, John L. Spudich, Hartmut Luecke posted to structure rhodopsin by robfsouza on 2009-09-17 17:22:43 as
	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
	Review: Chromatin Structural Features and Targets That Regulate Transcription [My Copy] Journal of Structural Biology, Vol. 129, No. 2-3. (April 2000), pp. 102-122. by A. Wolffe posted to transcription regulation chromosome chromatin by robfsouza on 2009-09-15 17:33:59 as

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protein	134
evolution	117
aravind	64
enzyme	53
inactive	51
structure	40
fold	39
sequence	37
indel	35
gene	33
length	33
network	32
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domain	28
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low	24
biological	23
superfamily	23
transcription	22
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genome	20
regulation	18
virus	18
classification	16
binding	14
alignment	13
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homopeptide	11
prokaryotes	11
recombination	11
atpase	10
codon	10
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family	9
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development	7
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division	6
duplication	6
mobile	6
ntpase	6
selection	6
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rate	4
repair	4
review	4
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signaling	4
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genetic	3
human	3
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rhodopsin	3
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science	3
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transduction	3
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mcmc	2
meiosis	2
methylation	2
neurobiology	2
ontology	2
p-loop	2
proteomics	2
receptor	2
ribosome	2
shuffling	2
substitution	2
tol	2
transfer	2
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ubiquitination	2
aaa	1
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adaptation	1
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alternative	1
average	1
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breakpoint	1
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dns	1
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reconstruction	1
religion	1
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rnase	1
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self-organization	1
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single	1
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stoichiometry	1
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stress	1
suchard	1
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technology	1
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topology	1
transglutaminase	1
transport	1
tree	1
tutorial	1
uba1	1
vertebrates	1
videos	1
yeast	1
zinc-finger	1

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