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	Conformational diversity and protein evolution--a 60-year-old hypothesis revisited. [My Copy] Trends Biochem Sci, Vol. 28, No. 7. (July 2003), pp. 361-368. by L. C. James, D. S. Tawfik posted to protein_structure protein_function protein_evolution protein_dynamics by ana on 2007-01-24 03:21:40 as along with 2 people and 2 groups dfdong barry structural_bioinformatics Bioinformatics
	Evolution of protein fold in the presence of functional constraints [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. 399-408. by Antonina Andreeva, Alexey G. Murzin posted to structure_classification protein_structure protein_function protein_evolution by ana on 2007-01-24 03:21:02 as along with 5 people and 2 groups dfdong barry Einat tny cjeans structural_bioinformatics Bioinformatics
	Protein molecular function prediction by Bayesian phylogenomics. [My Copy] PLoS computational biology, Vol. 1, No. 5. (7 October 2005) by B. E. Engelhardt, M. I. Jordan, K. E. Muratore, S. E. Brenner posted to function_prediction gene_duplication hgt orthology phylogenomics protein_evolution protein_function protein_sequence by ana on 2005-11-22 19:15:19 as along with 9 people and 4 groups sgoetz engelhardt kentsis eoghanharr Einat dlr marcius sriram_s bootsy structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
	Highways of gene sharing in prokaryotes [My Copy] PNAS, Vol. 102, No. 40. (4 October 2005), pp. 14332-14337. by Robert G. Beiko, Timothy J. Harlow, Mark A. Ragan posted to hgt phylogeny protein_evolution protein_sequence by ana on 2005-11-22 00:44:19 as along with 3 people and 2 groups AaronDarling treangen Minty structural_bioinformatics Bioinformatics
	Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. [My Copy] Nature, Vol. 399, No. 6734. (27 May 1999), pp. 323-329. by K. E. Nelson, R. A. Clayton, S. R. Gill, et al.M. L. Gwinn, R. J. Dodson, D. H. Haft, E. K. Hickey, J. D. Peterson, W. C. Nelson, K. A. Ketchum, L. McDonald, T. R. Utterback, J. A. Malek, K. D. Linher, M. M. Garrett, A. M. Stewart, M. D. Cotton, M. S. Pratt, C. A. Phillips, D. Richardson, J. Heidelberg, G. G. Sutton, R. D. Fleischmann, J. A. Eisen, O. White, S. L. Salzberg, H. O. Smith, J. C. Venter, C. M. Fraser posted to hgt protein_evolution by ana on 2005-11-19 21:39:08 as along with 2 people and 2 groups jmeppley karfunkel structural_bioinformatics Bioinformatics
	Convergent evolution: the need to be explicit. [My Copy] Trends Biochem Sci, Vol. 19, No. 1. (January 1994), pp. 15-18. by R. F. Doolittle posted to protein_evolution by ana on 2005-11-19 21:36:51 as along with 1 person and 2 groups barry structural_bioinformatics Bioinformatics
	The multiplicity of domains in proteins. [My Copy] Annu Rev Biochem, Vol. 64 (1995), pp. 287-314. by R. F. Doolittle posted to protein_evolution by ana on 2005-11-19 21:35:02 as along with 3 people and 2 groups swp09 barry dlr structural_bioinformatics Bioinformatics
	Distinguishing homologous from analogous proteins. [My Copy] Syst Zool, Vol. 19, No. 2. (June 1970), pp. 99-113. by W. M. Fitch posted to protein_evolution by ana on 2005-11-19 21:32:52 as along with 3 people and 2 groups sgoetz cgaugain barry structural_bioinformatics Bioinformatics
	Evolution of the Protein Repertoire [My Copy] Science, Vol. 300, No. 5626. (13 June 2003), pp. 1701-1703. by Cyrus Chothia, Julian Gough, Christine Vogel, Sarah A. Teichmann posted to protein_evolution by ana on 2005-11-19 21:30:23 as along with 3 people and 2 groups karbak barry tny structural_bioinformatics Bioinformatics
	Prediction of functional specificity determinants from protein sequences using log-likelihood ratios [My Copy] Bioinformatics (8 August 2005) by J. Pei, W. Cai, L. N. Kinch, N. V. Grishin posted to classification function_prediction protein_evolution protein_function by ana on 2005-11-09 18:56:06 as along with 2 people and 2 groups barry Einat structural_bioinformatics Bioinformatics
	A class of eukaryotic GTPase with a punctate distribution suggesting multiple functional replacements of translation elongation factor 1alpha. [My Copy] Proc Natl Acad Sci U S A, Vol. 101, No. 43. (26 October 2004), pp. 15380-15385. by P. J. Keeling, Y. Inagaki posted to evolution hgt protein_evolution taxonomy by ana on 2005-10-29 18:56:22 as along with 1 person and 3 groups vwchan structural_bioinformatics Bioinformatics beta
	The cobweb of life revealed by genome-scale estimates of horizontal gene transfer. [My Copy] PLoS Biol, Vol. 3, No. 10. (October 2005) by F. Ge, L. S. Wang, J. Kim posted to evolution hgt protein_evolution taxonomy tree_of_life by ana on 2005-10-29 18:51:34 as along with 4 people and 2 groups sriesenfeld operon jmeppley AaronDarling structural_bioinformatics Bioinformatics
	Structural Features can be Unconserved in Proteins with Similar Folds : An Analysis of Side-chain to Side-chain Contacts Secondary Structure and Accessibility [My Copy] Journal of Molecular Biology, Vol. 244, No. 3. (1 December 1994), pp. 332-350. by Robert B. Russell, Geoffrey J. Barton posted to contact_prediction protein_evolution protein_structure structure_comparison by ana on 2005-10-05 22:30:59 as along with 2 people and 2 groups dfdong rabio structural_bioinformatics Bioinformatics
	The C-type lectin fold as an evolutionary solution for massive sequence variation [My Copy] Nature Structural & Molecular Biology In Nat Struct Mol Biol, Vol. 12, No. 10. (18 September 2005), pp. 886-892. by Stephen A. McMahon, Jason L. Miller, Jeffrey A. Lawton, et al.Donald E. Kerkow, Asher Hodes, Marc A. Marti-Renom, Sergei Doulatov, Eswar Narayanan, Andrej Sali, Jeff F. Miller, Partho Ghosh posted to protein_evolution protein_sequence protein_structure by ana on 2005-10-05 19:51:48 as along with 3 people and 4 groups taenneken stevanspringer marcius structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
	Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function. [My Copy] J Mol Biol, Vol. 291, No. 1. (6 August 1999), pp. 177-196. by L. A. Mirny, E. I. Shakhnovich posted to protein_evolution protein_folding protein_function protein_structure sequence_comparison structure_comparison by ana on 2005-09-28 01:09:51 as along with 4 people and 4 groups dfdong barry Einat marcius structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
	On Evolutionary Conservation of Thermodynamic Coupling in Proteins [My Copy] Journal of Biological Chemistry, Vol. 279, No. 18. (30 April 2004), pp. 19046-19050. by Anthony A. Fodor, Richard W. Aldrich posted to correlated_mutations protein_evolution protein_folding protein_function protein_structure statistical_coupling_analysis by ana on 2005-09-27 22:12:45 as along with 8 people and 2 groups dfdong barry gbart cjeans tale friendpine ca3295 Lombardo_7 structural_bioinformatics Bioinformatics
	Influence of conservation on calculations of amino acid covariance in multiple sequence alignments. [My Copy] Proteins, Vol. 56, No. 2. (1 August 2004), pp. 211-221. by Anthony A. Fodor, Richard W. Aldrich posted to correlated_mutations multiple_sequence_alignment protein_evolution protein_sequence protein_structure statistical_coupling_analysis by ana on 2005-09-27 22:05:54 as along with 10 people and 2 groups dfdong mgomes qluo RebeccaHamer gbart cjeans jlh64 mingzhi dgront Lombardo_7 structural_bioinformatics Bioinformatics
	Evolutionary information for specifying a protein fold [My Copy] Nature, Vol. 437, No. 7058., pp. 512-518. by Michael Socolich, Steve W. Lockless, William P. Russ, Heather Lee, Kevin H. Gardner, Rama Ranganathan posted to correlated_mutations protein_evolution protein_sequence protein_structure statistical_coupling_analysis by ana on 2005-09-22 23:02:40 as along with 18 people and 5 groups edvin krapnik dfdong ucbcjbm barry lna bpb Einat balajis marcius gbart analogAI nirfriedman caporaso massivemayhem mingzhi bethbromley ca3295 structural_bioinformatics Bioinformatics biomedical-nlp BioinfoCIPF SGU-CIPF
	Detection of hydrogen-bond signature patterns in protein families. [My Copy] Bioinformatics, Vol. 19, No. 1. (January 2003), pp. 167-168. by T. Prasad, M. N. Prathima, N. Chandra posted to hydrogen-bond protein_evolution protein_stability protein_structure structure_comparison web_server by ana on 2005-09-07 20:01:20 as along with 2 groups structural_bioinformatics Bioinformatics
	Small libraries of protein fragments model native protein structures accurately. [My Copy] J Mol Biol, Vol. 323, No. 2. (18 October 2002), pp. 297-307. by R. Kolodny, P. Koehl, L. Guibas, M. Levitt posted to comparative_modeling protein_design protein_evolution protein_structure structure_comparison structure_fragments by ana on 2005-09-07 17:58:32 as along with 3 people and 2 groups barry eckart_bindewald j3xucite structural_bioinformatics Bioinformatics
	Protein families and their evolution-a structural perspective. [My Copy] Annu Rev Biochem, Vol. 74 (2005), pp. 867-900. by C. A. Orengo, J. M. Thornton posted to protein_evolution protein_function protein_structure by ana on 2005-09-01 23:12:18 as along with 20 people and 6 groups krapnik dfdong ucbcjbm flbarroso kumar_physics yuslinaz ssgong barry tjimenez jwm chad_davis Einat Schmidtc marcius sriram_s ezotenko redelings medic0747 nigham sim82 structural_bioinformatics Radiation_Damage Stressosome Bioinformatics BioinfoCIPF SGU-CIPF
	How old is your fold? [My Copy] Bioinformatics, Vol. 21 Suppl 1 (1 June 2005) by H. F. Winstanley, S. Abeln, C. M. Deane posted to protein_evolution protein_sequence protein_structure by ana on 2005-08-12 21:03:50 as along with 2 people and 2 groups pansapiens cdeane structural_bioinformatics Bioinformatics
	The relationship between domain duplication and recombination. [My Copy] Journal of molecular biology, Vol. 346, No. 1. (11 February 2005), pp. 355-365. by Christine Vogel, Sarah A. Teichmann, Jose Pereira-Leal posted to gene_duplication genome_evolution power-law protein_evolution protein_interaction protein_universe selection stochastic_process by ana on 2005-06-27 18:10:37 as along with 5 people and 4 groups marcius tny cjeans martainn mdimon structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
	Evolutionary lines of cysteine peptidases. [My Copy] Biol Chem, Vol. 382, No. 5. (May 2001), pp. 727-733. by A. J. Barrett, N. D. Rawlings posted to molecular_mimicry protein_evolution protein_sequence protein_structure virulence_factor by ana on 2005-06-20 19:06:44 as along with 2 groups structural_bioinformatics Bioinformatics
	The properties of protein family space depend on experimental design [My Copy] Bioinformatics, Vol. 21, No. 11. (1 June 2005), pp. 2618-2622. by Victor Kunin, Sarah A. Teichmann, Martijn A. Huynen, Christos A. Ouzounis posted to power-law protein_evolution protein_function protein_universe by ana on 2005-06-15 20:20:37 as along with 2 people and 2 groups barry cjeans structural_bioinformatics Bioinformatics
	In search of the limits of evolution [My Copy] Nature Genetics, Vol. 37, No. 1. (January 2005), pp. 9-10. by Fyodor A. Kondrashov posted to directed_evolution neofunctionalization protein_evolution protein_function protein_moonlighting by ana on 2005-06-06 21:14:46 as along with 2 people and 2 groups dfdong LeightonP structural_bioinformatics Bioinformatics
	The 'evolvability' of promiscuous protein functions [My Copy] Nature Genetics, Vol. 37, No. 1. (January 2005), pp. 73-76. by Amir Aharoni, Leonid Gaidukov, Olga Khershonsky, Stephen M. Gould, Cintia Roodveldt, Dan S. Tawfik posted to directed_evolution neofunctionalization protein_evolution protein_function protein_moonlighting by ana on 2005-06-06 21:12:37 as along with 1 person and 2 groups LeightonP structural_bioinformatics Bioinformatics
	Evolution of protein structures and functions [My Copy] Current Opinion in Structural Biology, Vol. 12, No. 3. (1 June 2002), pp. 400-408. by L. Kinch posted to protein_evolution protein_structure structure_comparison by ana on 2005-06-06 19:09:49 as along with 2 people and 2 groups dfdong barry structural_bioinformatics Bioinformatics
	The evolutionary capacity of protein structures [My Copy] In RECOMB '04: Proceedings of the eighth annual international conference on Computational molecular biology (2004), pp. 290-297. by Leonid Meyerguz, David Kempe, Jon Kleinberg, Ron Elber posted to protein_evolution protein_structure by ana on 2005-05-25 19:02:32 as along with 2 people and 2 groups dfdong apaydin structural_bioinformatics Bioinformatics
	Convergent evolution of domain architectures (is rare). [My Copy] Bioinformatics (Oxford, England) (7 December 2004) by Julian Gough posted to protein_evolution structure_classification structure_comparison by ana on 2005-05-06 21:54:23 as along with 3 people and 2 groups martainn matzke barry structural_bioinformatics Bioinformatics
	Underlying hydrophobic sequence periodicity of protein tertiary structure. [My Copy] J Biomol Struct Dyn, Vol. 22, No. 4. (February 2005), pp. 411-423. by B. D. Silverman posted to protein_evolution protein_structure by ana on 2005-05-06 21:52:32 as along with 1 person and 2 groups barry structural_bioinformatics Bioinformatics
	Understanding protein folding via free-energy surfaces from theory and experiment. [My Copy] Trends Biochem Sci, Vol. 25, No. 7. (July 2000), pp. 331-339. by A. R. Dinner, A. Sali, L. J. Smith, C. M. Dobson, M. Karplus posted to protein_evolution protein_folding protein_structure by ana on 2005-05-03 03:49:29 as along with 1 person and 2 groups rabio structural_bioinformatics Bioinformatics
	Finding local structural similarities among families of unrelated protein structures: a generic non-linear alignment algorithm. [My Copy] Proteins, Vol. 34, No. 3. (15 February 1999), pp. 341-355. by J. V. Lehtonen, K. Denessiouk, A. C. May, M. S. Johnson posted to local_structure_similarity protein_evolution protein_function by ana on 2005-05-03 03:45:04 as along with 2 groups structural_bioinformatics Bioinformatics
	Protein Differentiation: Emergence of Novel Proteins during Evolution [My Copy] Angewandte Chemie International Edition in English, Vol. 20, No. 2. (22 December 2003), pp. 143-151. by Georg E. Schulz posted to protein_evolution protein_structure by ana on 2005-05-03 03:38:34 as along with 2 groups structural_bioinformatics Bioinformatics
	Recognition of phylogenetic relationships from polypeptide chain fold similarities. [My Copy] J Mol Evol, Vol. 9, No. 4. (5 August 1977), pp. 339-342. by G. E. Schulz posted to protein_evolution protein_structure structure_comparison by ana on 2005-05-03 02:51:06 as along with 2 groups structural_bioinformatics Bioinformatics
	Evolution of protein structures and functions. [My Copy] Curr Opin Struct Biol, Vol. 12, No. 3. (June 2002), pp. 400-408. by L. N. Kinch, N. V. Grishin posted to homology_analogy protein_evolution protein_function protein_structure sequence_structure structure_function by ana on 2005-04-26 05:12:27 as along with 6 people and 7 groups dfdong korakot karbak matzke barry joergkurtwegner Philosophy_of_Information Blog_and_Wiki_Research structural_bioinformatics Bioinformatics Molecular-Modelling Drug-Design Cheminformatics
	Evolution and similarity evaluation of protein structures in contact map space. [My Copy] Proteins, Vol. 59, No. 2. (1 May 2005), pp. 196-204. by N. Gupta, N. Mangal, S. Biswas posted to contact_maps protein_evolution protein_structure structure_prediction by ana on 2005-04-20 23:53:24 as along with 1 person and 2 groups vavi structural_bioinformatics Bioinformatics
	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 protein_evolution protein_structure structure_comparison by ana on 2005-03-08 06:47:03 as along with 16 people and 6 groups edvin parnell dfdong martainn ucbcjbm bertelsen semin sgoetz cen4ik pansapiens jwm Einat marcius xdeupi ffranca insectopalo structural_bioinformatics Radiation_Damage Stressosome Bioinformatics BioinfoCIPF SGU-CIPF
	Sequence variations within protein families are linearly related to structural variations. [My Copy] J Mol Biol, Vol. 323, No. 3. (25 October 2002), pp. 551-562. by P. Koehl, M. Levitt posted to protein_evolution protein_structure score structure_comparison by ana on 2005-03-08 06:44:23 as along with 4 people and 2 groups dfdong barry okarsligil insectopalo structural_bioinformatics Bioinformatics
	Understanding hierarchical protein evolution from first principles. [My Copy] J Mol Biol, Vol. 312, No. 1. (7 September 2001), pp. 289-307. by N. V. Dokholyan, E. I. Shakhnovich posted to protein_evolution protein_structure structure_classification by ana on 2005-03-03 19:56:39 as along with 3 people and 2 groups mdimmic barry pansapiens structural_bioinformatics Bioinformatics
	Imprint of evolution on protein structures. [My Copy] Proc Natl Acad Sci U S A, Vol. 101, No. 9. (2 March 2004), pp. 2846-2851. by G. Tiana, B. E. Shakhnovich, N. V. Dokholyan, E. I. Shakhnovich posted to fold_space protein_evolution protein_structure protein_universe by ana on 2005-03-03 19:52:37 as along with 3 people and 2 groups dfdong barry pansapiens structural_bioinformatics Bioinformatics
	Expanding protein universe and its origin from the biological Big Bang [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 22. (29 October 2002), pp. 14132-14136. by Nikolay V. Dokholyan, Boris Shakhnovich, Eugene I. Shakhnovich posted to protein_evolution protein_universe by ana on 2005-03-03 19:48:01 as along with 3 people and 2 groups sschurer barry lulab structural_bioinformatics Bioinformatics
	Simulating protein evolution in sequence and structure space. [My Copy] Curr Opin Struct Biol, Vol. 14, No. 2. (April 2004), pp. 202-207. by Y. Xia, M. Levitt posted to protein_evolution protein_universe by ana on 2005-03-02 22:36:26 as along with 14 people and 4 groups dfdong idoerg yuslinaz saunders betainverse korakot mdimmic karbak rmj001 barry aalibes gbart analogAI insectopalo Philosophy_of_Information Blog_and_Wiki_Research structural_bioinformatics Bioinformatics

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protein_structure	195
structure_comparison	99
protein_sequence	44
jcsg	43
protein_evolution	43
structure_alignment	38
new	37
interaction_hierarchy	29
comparative_genomics	28
sequence_comparison	26
virulence_factor	24
structure_classification	23
structure_prediction	23
split-barrel	21
structure_flexible	20
protein_folding	20
contact_maps	19
protein_function	17
indels	17
streptococcus	16
hgt	16
project	16
web_server	15
structural_genomics	14
fold_space	13
minimal_genome	13
benchmark	13
protein_interaction	13
protein_universe	13
structure_superposition	12
scop-b-45-1-1	12
essential_genes	11
target_selection	11
sequence_alignment	10
malaria	10
molecular_mimicry	10
pca	10
sequence_structure	9
protein_dynamics	9
genome_evolution	9
phylogeny	9
algorithms	8
comparative_modeling	8
homology_analogy	8
metagenomics	7
function_prediction	6
orthology	6
core_genome	6
function_evolution	6
nma	6
bioinformatics	6
statistical_coupling_analysis	6
multiple_structure_comparison	6
structure_core	6
protein_stability	5
hydrogen-bond	5
correlated_mutations	5
book	5
molecular_dynamics	5
protein_design	5
power-law	5
packing_density	5
contact_order	5
statistics	4
gene_finding	4
score	4
r	4
model_refinement	4
promoter_identification	4
contact_prediction	4
flexible_structure_alignment	4
family-size	4
local_structure_similarity	4
multiple_sequence_alignment	4
scop-b-45-1-1-pre	4
stochastic_process	3
evolution	3
selection	3
multiple_structure_alignment	3
scop-b-45-1-2	3
gene_duplication	3
barrel	3
mine	3
neofunctionalization	3
hmm	2
microarray	2
taxonomy	2
crystalization	2
remote_homology	2
protein_expression	2
local_interaction	2
protein_moonlighting	2
genome_sequence	2
pathway-genome_annotation	2
neural_networks	2
graph_theory	2
protein_disorder	2
water-mediated_contacts	2
secondary_structure	2
directed_evolution	2
ubiquitination	2
multi-domain	2
flavoenzymes	2
scop-b-43-4	2
crohns_disease	2
celegans	2
classification	2
loop	2
structure_fragments	2
phylogenetics	2
pathogenicity_island	2
pdb-1g77	1
pdb-1t9m	1
weibull_function	1
pdb-1eje	1
pdb-1xxo	1
repeats	1
dataset	1
genome_size	1
pdb-1w3r	1
pdb-2aq6	1
ddm	1
software_development	1
pdb-1xhn	1
structure_determination	1
pdb-1ci0	1
visualization	1
ferredoxin-reductase-fad-binding	1
pdb-1rz0	1
family_analysis	1
orfan	1
promoter_finding	1
daf-16	1
pdb-1jnw	1
promoter	1
potential	1
dna_structure	1
glycerol_kinase	1
aging	1
low-complexity_regions	1
gene_ontology	1
structure_function	1
codon_bias	1
pdb-1y30	1
threading	1
base_composition	1
pdb-1w9a	1
phylogenomics	1
ferrodoxin-reductase-fad-binding	1
abeta1-42	1
pdb-2asf	1
adaptive_evolution	1
pdb-1rz1	1
active_site	1
pdb-1w3o	1
hsf-1	1
structure_complexes	1
structure_uncertainty	1
allosteric	1
alzheimers	1
pdb-1axj	1
pdb-1g79	1
pdb-1w3p	1
pdb-1qtj	1
scop-b-45-2	1
scop-b-45	1
tree_of_life	1
pdb-1ywu	1
modeling	1
pdb-1g78	1
pdb-1wv4	1
subfunctionalization	1
hydrophobic_effect	1
pes	1
data_mining	1
dynamic_programming	1
luca	1
pdb-1dnl	1
dna	1
delaunay	1
kogs	1
scoring_matrix	1
pdb-1i0s	1
daf-2	1
pdb-1g76	1
pdb-1ty9	1
afp	1
transcription_factor	1
pdb-2a2j	1
pdb-1w3q	1
nachr	1
pdb-1i0r	1
pseudogene	1
database	1
hinge_bend	1
structure_domain	1
pdb-1flm	1
mutagenisis	1
prion	1
structure_invariant	1
subcellular_localization	1
pdb-1nrg	1

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