ramiro2k's library 71 articles Export

	Sequence divergence, functional constraint, and selection in protein evolution. [My Copy] Annual review of genomics and human genetics, Vol. 4, No. 1. (2003), pp. 213-235. by Justin C. Fay, Chung-I I. Wu posted to evolution protein selection by ramiro2k on 2009-07-31 22:26:17 as along with 3 people and 1 group renewang operon dmc Durbin group
	Vernier zone residue 4 of mouse subgroup II kappa light chains is a critical determinant for antigen recognition [My Copy] Immunotechnology, Vol. 4, No. 3. (March 1999), pp. 203-215. by H. de Haard, B. Kazemier, A. van der Bent, et al.P. Oudshoorn, P. Boender, J. W. Arends, B. van Gemen posted to vernier by ramiro2k on 2009-07-12 23:27:17 as
	Correlated Cleavage of Damaged DNA by Bacterial and Human 8-Oxoguanine-DNA Glycosylases† [My Copy] Biochemistry, Vol. 47, No. 34. (1 August 2008), pp. 8970-8976. by Viktoriya S. Sidorenko, Dmitry O. Zharkov posted to fpg mutagenesis nei by ramiro2k on 2009-06-19 20:01:33 as
	Computational Analysis of the Mode of Binding of 8-Oxoguanine to Formamidopyrimidine-DNA Glycosylase† [My Copy] Biochemistry, Vol. 45, No. 36. (1 September 2006), pp. 10886-10894. by Kun Song, Viktor Hornak, de Los, Arthur P. Grollman, Carlos Simmerling posted to fpg mutagenesis nei by ramiro2k on 2009-06-19 18:42:23 as
	Substrate discrimination by formamidopyrimidine-DNA glycosylase: a mutational analysis. [My Copy] The Journal of biological chemistry, Vol. 279, No. 6. (6 February 2004), pp. 4849-4861. by E. I. Zaika, R. A. Perlow, E. Matz, et al.S. Broyde, R. Gilboa, A. P. Grollman, D. O. Zharkov posted to fpg mutagenesis nei by ramiro2k on 2009-06-17 20:44:12 as
	Mechanism of action of base release by Escherichia coli Fpg protein: role of lysine 155 in catalysis. [My Copy] Biochemistry, Vol. 36, No. 16. (22 April 1997), pp. 5084-5096. by L. E. Rabow, Y. W. Kow posted to fpg mutagenesis nei by ramiro2k on 2009-06-16 20:10:11 as
	Mechanism of action of Escherichia coli formamidopyrimidine N-glycosylase: role of K155 in substrate binding and product release. [My Copy] Progress in nucleic acid research and molecular biology, Vol. 68 (2001), pp. 223-234. by L. Rabow, R. Venkataraman, Y. W. Kow posted to fpg mutagenesis nei by ramiro2k on 2009-06-16 20:08:12 as
	Base excision repair of oxidative DNA damage and association with cancer and aging. [My Copy] Carcinogenesis, Vol. 30, No. 1. (January 2009), pp. 2-10. by S. Maynard, S. H. Schurman, C. Harboe, N. C. de Souza-Pinto, V. A. Bohr posted to disease dnarepair by ramiro2k on 2009-06-15 20:31:56 as along with 1 person guhjy
	Base-excision repair of oxidative DNA damage [My Copy] Nature, Vol. 447, No. 7147. (20 June 2007), pp. 941-950. by Sheila S. David, Valerie L. O'Shea, Sucharita Kundu posted to baseexcisionrepair dnarepair by ramiro2k on 2009-06-15 20:20:35 as along with 3 people and 2 groups merpublic guhjy dchughes G4ID Genetics-of-Gambling
	Plant and fungal Fpg homologs are formamidopyrimidine DNA glycosylases but not 8-oxoguanine DNA glycosylases. [My Copy] DNA repair, Vol. 8, No. 5. (1 May 2009), pp. 643-653. by S. D. Kathe, R. Barrantes-Reynolds, P. Jaruga, et al.M. R. Newton, C. J. Burrows, V. Bandaru, M. Dizdaroglu, J. P. Bond, S. S. Wallace posted to fpg nei by ramiro2k on 2009-06-15 20:05:38 as
	Heterotachy, an important process of protein evolution. [My Copy] Molecular biology and evolution, Vol. 19, No. 1. (January 2002), pp. 1-7. by P. Lopez, D. Casane, H. Philippe posted to divergence evolution heterotachy by ramiro2k on 2009-06-15 18:37:08 as along with 1 person and 1 group michaelbarton BergmanLab
	The origin of new genes: glimpses from the young and old. [My Copy] Nat Rev Genet, Vol. 4, No. 11. (November 2003), pp. 865-875. by M. Long, E. Betrán, K. Thornton, W. Wang posted to divergence evolution by ramiro2k on 2009-06-15 18:15:26 as along with 5 people wangbo jbsaltz ushishir timflutre shoshin
	Involvement of Phylogenetically Conserved Acidic Amino Acid Residues in Catalysis by an Oxidative DNA Damage Enzyme Formamidopyrimidine Glycosylase† [My Copy] Biochemistry, Vol. 39, No. 49. (1 December 2000), pp. 15266-15271. by Oleg V. Lavrukhin, Stephen R. Lloyd posted to fpg mutagenesis nei by ramiro2k on 2009-06-09 18:32:30 as
	Combining structural and bioinformatics methods for the analysis of functionally important residues in DNA glycosylases. [My Copy] Free radical biology & medicine, Vol. 32, No. 12. (15 June 2002), pp. 1254-1263. by D. O. Zharkov, A. P. Grollman posted to fpg mutagenesis nei by ramiro2k on 2009-06-09 16:43:41 as
	Function of the zinc finger in Escherichia coli Fpg protein [My Copy] J. Biol. Chem., Vol. 268, No. 35. (15 December 1993), pp. 26738-26744. by J. Tchou, M. L. Michaels, J. H. Miller, A. P. Grollman posted to fpg mutagenesis nei by ramiro2k on 2009-06-09 16:08:19 as along with 1 person msuarezdiez
	Fpg protein of Escherichia coli is a zinc finger protein whose cysteine residues have a structural and/or functional role [My Copy] J. Biol. Chem., Vol. 268, No. 12. (25 April 1993), pp. 9063-9070. by T. R. O'Connor, R. J. Graves, G. de Murcia, B. Castaing, J. Laval posted to fpg mutagenesis nei by ramiro2k on 2009-06-09 16:04:48 as
	Catalytic Mechanism of Escherichia coli Endonuclease VIII: Roles of the Intercalation Loop and the Zinc Finger† [My Copy] Biochemistry, Vol. 45, No. 39. (1 October 2006), pp. 12039-12049. by Konstantin Y. Kropachev, Dmitry O. Zharkov, Arthur P. Grollman posted to fpg nei by ramiro2k on 2009-06-09 15:53:42 as
	Towards a phylogeny of the actinomycetes and related organisms [My Copy] Current Microbiology, Vol. 5, No. 4. (1 July 1981), pp. 197-202. by Erko Stackebrandt, Carl R. Woese posted to actinomycetes evolution phylogenetics by ramiro2k on 2009-06-02 20:31:33 as
	Genomic evidence for antibiotic resistance genes of actinomycetes as origins of antibiotic resistance genes in pathogenic bacteria simply because actinomycetes are more ancestral than pathogenic bacteria [My Copy] Medical Hypotheses, Vol. 67, No. 6. (2006), pp. 1297-1304. by P. Woo, S. Lau, Y. Huang, K. Yuen posted to actinomycetes antibiotics evolution phylogenetics by ramiro2k on 2009-06-02 20:24:13 as
	Structure of the uncomplexed DNA repair enzyme endonuclease VIII indicates significant interdomain flexibility. [My Copy] Nucleic acids research, Vol. 33, No. 15. (2005), pp. 5006-5016. by G. Golan, D. O. Zharkov, H. Feinberg, et al.A. S. Fernandes, E. I. Zaika, J. H. Kycia, A. P. Grollman, G. Shoham posted to apoform nei structure by ramiro2k on 2009-05-18 21:12:56 as
	Human Genome Ultraconserved Elements Are Ultraselected [My Copy] Science, Vol. 317, No. 5840. (17 August 2007), 915. by Sol Katzman, Andrew D. Kern, Gill Bejerano, et al.Ginger Fewell, Lucinda Fulton, Richard K. Wilson, Sofie R. Salama, David Haussler posted to ultraconserved by ramiro2k on 2009-05-07 18:43:50 as along with 12 people and 1 group clearbluespring galka8_diploma aprasad balicea djkt lp2 cabbagezs cisevol Minty fpattyn gjuggler bpcusack cis-regulatory-evolution
	Protein Dynamism and Evolvability [My Copy] Science, Vol. 324, No. 5924. (10 April 2009), pp. 203-207. by Nobuhiko Tokuriki, Dan S. Tawfik posted to evolution protein structure by ramiro2k on 2009-05-05 21:35:32 as along with 20 people and 3 groups dfdong tomhebbron anuragsethi ahmetbakan kevinchannon klexa lauresultan dbikard ibuch barry pablocarb ramanuja sobolevnrm biomcgary hsekiguc VGreiff phoenixzxl zwang jdoconnell paulschlesinger structural_bioinformatics McCammon baker-group
	An automated phylogenetic key for classifying homeoboxes. [My Copy] Molecular phylogenetics and evolution, Vol. 24, No. 3. (September 2002), pp. 388-399. by I. N. Sarkar, J. W. Thornton, P. J. Planet, D. H. Figurski, B. Schierwater, R. DeSalle posted to evolution phylogenetics symplesiomorphy by ramiro2k on 2009-05-05 19:05:09 as
	Prediction of functional sites by analysis of sequence and structure conservation. [My Copy] Protein Sci, Vol. 13, No. 4. (April 2004), pp. 884-892. by A. R. Panchenko, F. Kondrashov, S. Bryant posted to functionalsites structure by ramiro2k on 2009-05-04 20:53:34 as along with 5 people chrn skhadar sriram_s tanuja_rastogi Jporci
	Determination of protein function, evolution and interactions by structural genomics [My Copy] Current Opinion in Structural Biology, Vol. 11, No. 3. (1 June 2001), pp. 354-363. by Sarah A. Teichmann, Alexey G. Murzin, Cyrus Chothia posted to structure by ramiro2k on 2009-05-04 20:37:06 as along with 1 person cjeans
	Base excision DNA repair [My Copy] Cellular and Molecular Life Sciences CMLS, Vol. 65, No. 10. (May 2008), pp. 1544-1565. by Zharkov, D. posted to ber by ramiro2k on 2009-04-20 15:01:48 as along with 1 person guhjy
	Evaluation of features for catalytic residue prediction in novel folds. [My Copy] Protein science : a publication of the Protein Society, Vol. 16, No. 2. (February 2007), pp. 216-226. by E. Youn, B. Peters, P. Radivojac, S. D. Mooney posted to functionalsites by ramiro2k on 2009-04-13 21:32:13 as along with 1 person esyoun
	Reliabilities of identifying positive selection by the branch-site and the site-prediction methods [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 16. (21 April 2009), pp. 6700-6705. by Masafumi Nozawa, Yoshiyuki Suzuki, Masatoshi Nei posted to functionalsites positiveselection by ramiro2k on 2009-04-11 15:16:45 as along with 8 people and 1 group ckenaley sameersoi djkt rvosa gjuggler bpcusack atphan gulsacan FAB-lab
	Helix capping. [My Copy] Protein science : a publication of the Protein Society, Vol. 7, No. 1. (January 1998), pp. 21-38. by R. Aurora, G. D. Rose posted to helix-capping structure by ramiro2k on 2009-04-05 18:42:58 as
	Structural analysis of an Escherichia coli endonuclease VIII covalent reaction intermediate. [My Copy] The EMBO journal, Vol. 21, No. 4. (15 February 2002), pp. 789-800. by D. O. Zharkov, G. Golan, R. Gilboa, et al.A. S. Fernandes, S. E. Gerchman, J. H. Kycia, R. A. Rieger, A. P. Grollman, G. Shoham posted to fpg nei structure by ramiro2k on 2009-04-02 03:47:51 as
	Structural basis for the recognition of the FapydG lesion (2,6-diamino-4-hydroxy-5-formamidopyrimidine) by formamidopyrimidine-DNA glycosylase. [My Copy] The Journal of biological chemistry, Vol. 279, No. 42. (15 October 2004), pp. 44074-44083. by F. Coste, M. Ober, T. Carell, S. Boiteux, C. Zelwer, B. Castaing posted to fapy fpg nei structure by ramiro2k on 2009-04-02 03:43:50 as
	Using a neural network and spatial clustering to predict the location of active sites in enzymes. [My Copy] J Mol Biol, Vol. 330, No. 4. (18 July 2003), pp. 719-734. by A. Gutteridge, G. J. Bartlett, J. M. Thornton posted to functional sites functionalsites by ramiro2k on 2009-03-22 18:18:13 as along with 7 people and 1 group chrn Einat alexg gbart eweaver sriram_s tjimenez structural_bioinformatics
	THEMATICS: A simple computational predictor of enzyme function from structure [My Copy] PNAS, Vol. 98, No. 22. (23 October 2001), pp. 12473-12478. by Mary J. Ondrechen, James G. Clifton, Dagmar Ringe posted to functional sites functionalsites by ramiro2k on 2009-03-21 20:25:44 as along with 3 people and 3 groups Einat sangeetha sriram_s structural_bioinformatics Bioinformatics insilicodrug
	Prediction of active sites for protein structures from computed chemical properties [My Copy] Bioinformatics, Vol. 21, No. suppl_1. (1 June 2005), pp. i258-265. by Jaeju Ko, Leonel F. Murga, Ying Wei, Mary J. Ondrechen posted to no-tag by ramiro2k on 2009-03-21 20:23:22 as along with 3 people barmak7282 chrn sriram_s
	Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins. [My Copy] J Mol Biol, Vol. 307, No. 5. (13 April 2001), pp. 1487-1502. by R. Landgraf, I. Xenarios, D. Eisenberg posted to functional sites functionalsites by ramiro2k on 2009-03-21 20:20:41 as along with 7 people and 2 groups barry pansapiens sriram_s cjeans mingzhi Pao-Yang marti structural_bioinformatics Bioinformatics
	Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites [My Copy] Bioinformatics, Vol. 21, No. 9. (1 May 2005), pp. 1908-1916. by Alasdair T. Laurie, Richard M. Jackson posted to energy functional sites functionalsites by ramiro2k on 2009-03-21 20:16:42 as along with 3 people tomjad sriram_s nickolay
	Prediction of functionally important residues based solely on the computed energetics of protein structure. [My Copy] J Mol Biol, Vol. 312, No. 4. (28 September 2001), pp. 885-896. by A. H. Elcock posted to functional sites functionalsites by ramiro2k on 2009-03-21 20:14:43 as along with 1 person sriram_s
	The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria. [My Copy] J Mol Biol, Vol. 256, No. 1. (16 February 1996), pp. 201-213. by K. P. Peters, J. Fauck, C. Frömmel posted to functional sites structure functionalsites by ramiro2k on 2009-03-21 20:12:29 as along with 3 people tjimenez nickolay sriram_s
	A family of evolution-entropy hybrid methods for ranking protein residues by importance. [My Copy] J Mol Biol, Vol. 336, No. 5. (5 March 2004), pp. 1265-1282. by I. Mihalek, I. Res, O. Lichtarge posted to functional sites functionalsites by ramiro2k on 2009-03-21 20:00:38 as along with 5 people omc11 kirasato feenstra sriram_s mingzhi
	Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking. [My Copy] J Mol Biol, Vol. 311, No. 2. (10 August 2001), pp. 395-408. by P. Aloy, E. Querol, F. X. Aviles, M. J. Sternberg posted to no-tag by ramiro2k on 2009-03-21 19:34:17 as along with 6 people kaarsinogen chrn bicko chad_davis sriram_s cjeans
	ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures. [My Copy] Nucleic acids research, Vol. 33, No. Web Server issue. (1 July 2005) by Meytal Landau, Itay Mayrose, Yossi Rosenberg, et al.Fabian Glaser, Eric Martz, Tal Pupko, Nir Ben-Tal posted to divergence functional sites functionalsites by ramiro2k on 2009-03-21 19:32:10 as along with 8 people and 1 group pablocarb tomjad klexa shacko oteri chrn sriram_s bicko Structural Biology Group TorVergata
	An evolutionary trace method defines binding surfaces common to protein families. [My Copy] J Mol Biol, Vol. 257, No. 2. (29 March 1996), pp. 342-358. by O. Lichtarge, H. R. Bourne, F. E. Cohen posted to divergence functional functionalsites by ramiro2k on 2009-03-21 19:29:16 as along with 4 people and 1 group lna nickolay sriram_s cat_worth structural_bioinformatics
	A method to predict functional residues in proteins. [My Copy] Nat Struct Biol, Vol. 2, No. 2. (February 1995), pp. 171-178. by G. Casari, C. Sander, A. Valencia posted to functional sites functionalsites by ramiro2k on 2009-03-21 19:10:35 as along with 2 people and 2 groups barry sriram_s structural_bioinformatics Bioinformatics
	Evolutionary Analysis for Functional Divergence of the Toll-Like Receptor Gene Family and Altered Functional Constraints [My Copy] Journal of Molecular Evolution, Vol. 65, No. 2. (August 2007), pp. 119-123. by Zhou, Huaijun, Gu, et al. Jianying, Lamont, Susan, Gu, Xun posted to divergence functional gu functionalsites by ramiro2k on 2009-03-18 14:43:22 as
	Effect of site-specific heterogeneous evolution on phylogenetic reconstruction: a simple evaluation. [My Copy] Gene, Vol. 441, No. 1-2. (15 July 2009), pp. 156-162. by Qiqun Cheng, Zhixi Su, Yang Zhong, Xun Gu posted to divergence functional phylogenetics functionalsites by ramiro2k on 2009-03-18 14:26:29 as
	Horizontal gene transfer, genome innovation and evolution [My Copy] Nature Reviews Microbiology, Vol. 3, No. 9. (01 September 2005), pp. 679-687. by Peter J. Gogarten, Jeffrey P. Townsend posted to evolution gene hgt lateral lgt transfer by ramiro2k on 2009-03-16 21:13:35 as along with 7 people and 1 group matzke jwortman imouthesmp ryang dbikard kinestetika karfunkel microbiology_nijmegen
	Prokaryotic evolution in light of gene transfer. [My Copy] Mol Biol Evol, Vol. 19, No. 12. (December 2002), pp. 2226-2238. by J. P. Gogarten, W. F. Doolittle, J. G. Lawrence posted to evolution gene hgt lateral lgt transfer by ramiro2k on 2009-03-16 21:11:40 as along with 4 people johanviklund jmeppley AaronDarling Tingting
	Crystal structure of a repair enzyme of oxidatively damaged DNA, MutM (Fpg), from an extreme thermophile, Thermus thermophilus HB8. [My Copy] The EMBO journal, Vol. 19, No. 15. (1 August 2000), pp. 3857-3869. by M. Sugahara, T. Mikawa, T. Kumasaka, et al.M. Yamamoto, R. Kato, K. Fukuyama, Y. Inoue, S. Kuramitsu posted to fpg nei structure by ramiro2k on 2009-03-13 19:33:02 as
	Structural insights into abasic site for Fpg specific binding and catalysis: comparative high-resolution crystallographic studies of Fpg bound to various models of abasic site analogues-containing DNA. [My Copy] Nucleic acids research, Vol. 33, No. 18. (2005), pp. 5936-5944. by K. Pereira de Jésus, L. Serre, C. Zelwer, B. Castaing posted to fpg nei structure by ramiro2k on 2009-03-13 19:30:42 as
	The crystal structure of human endonuclease VIII-like 1 (NEIL1) reveals a zincless finger motif required for glycosylase activity. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 101, No. 28. (13 July 2004), pp. 10284-10289. by S. Doublié, V. Bandaru, J. P. Bond, S. S. Wallace posted to fpg nei neil1 structure by ramiro2k on 2009-03-13 19:27:57 as

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fpg	19
nei	19
functionalsites	18
functional	15
structure	15
evolution	14
sites	11
divergence	9
mutagenesis	9
protein	5
gu	4
phylogenetics	4
actinomycetes	2
dnarepair	2
gene	2
glycosylase	2
hgt	2
lateral	2
lgt	2
selection	2
transfer	2
antibiotics	1
apoform	1
baseexcisionrepair	1
ber	1
cdd	1
cdtree	1
complex	1
disease	1
dna	1
energy	1
fapy	1
group	1
helix-capping	1
heterotachy	1
life	1
mvnei	1
neil1	1
neil3	1
networks	1
of	1
origin	1
planctomycetes	1
positiveselection	1
sociobiology	1
specificity	1
symplesiomorphy	1
systems	1
typeii	1
ultraconserved	1
vernier	1

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