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	Novel use of a genetic algorithm for protein structure prediction: searching template and sequence alignment space [My Copy] Proteins, Vol. 53 Suppl 6 (2003), 424-9. by B. Contreras-Moreira, P. W. Fitzjohn, M. Offman, G. R. Smith, P. A. Bates posted to tertiary structure sites-genetics sequence proteins-chemistry-genetics protein molecular models humans homology file-import-09-11-28 data computational biology-methods binding bacterial amino algorithms acid by brunocontreras on 2009-11-28 20:45:35 as
	Comparative footprinting of DNA-binding proteins [My Copy] Bioinformatics, Vol. 22, No. 14. (2006), e74-80. by B. Contreras-Moreira, J. Collado-Vides posted to sites simulation proteins-chemistry protein-methods protein models homology footprinting-methods dna-methods dna-chemistry dna-binding computer chemical binding analysis algorithms uracil transcription thymine sequence repressor regions proteins-genetics-metabolism operator mutation molecular genetics file-import-09-11-28 factors-metabolism dna-genetics-metabolism data amino acid by brunocontreras on 2009-11-28 20:26:49 as
	OPCML at 11q25 is epigenetically inactivated and has tumor-suppressor function in epithelial ovarian cancer [My Copy] Nat Genet, Vol. 34, No. 3. (2003), 337-43. by G. C. Sellar, K. P. Watt, G. J. Rabiasz, et al.E. A. Stronach, L. Li, E. P. Miller, C. E. Massie, J. Miller, B. Contreras-Moreira, D. Scott, I. Brown, A. R. Williams, P. A. Bates, J. F. Smyth, H. Gabra posted to tumor transfection transcriptase tissue suppressor-physiology studies site-directed rna reverse reaction proteins-genetics proteins-antagonists polymerase pair ovarian of nude nerve neoplasms-genetics neoplasms mutation-genetics mutagenesis molecules-antagonists mice methylation messenger-metabolism loss islands inhibitors-pharmacology inhibitors-genetics-metabolism humans human heterozygosity glandular genes female epithelial-genetics enzyme dna-genetics-metabolism dna cultured-transplantation cpg chromosomes chain cells case-control carrier breast azacitidine-pharmacology animals and adhesion 11-genetics zinc transcription surface-chemistry stereoisomerism sites simulation sequence receptors proteins-chemistry protein motifs molecular models hydrogen helix-loop-helix fingers file-import-09-11-28 factors-chemistry dna-chemistry dna-binding data computer chemical cell bonding binding base amino acid by brunocontreras on 2009-11-28 20:26:49 as
	In silico protein recombination: enhancing template and sequence alignment selection for comparative protein modelling [My Copy] J Mol Biol, Vol. 328, No. 3. (2003), 593-608. by B. Contreras-Moreira, P. W. Fitzjohn, P. A. Bates posted to tertiary results reproducibility proteins-chemistry-genetics of mutation models homology evolution directed alignment-methods algorithms zinc transcription tfiiia structure-activity structure sites sequences sequence secondary repressor relationship regulatory proteins-chemistry-metabolism proteins protein nucleic molecular fingers file-import-09-11-28 factors-chemistry-metabolism factor drosophila dna-chemistry-metabolism dna-binding data crystallization conformation binding arginine-metabolism amino acid by brunocontreras on 2009-11-28 20:26:49 as
	TFmodeller: comparative modelling of protein-DNA complexes [My Copy] Bioinformatics, Vol. 23, No. 13. (2007), 1694-6. by B. Contreras-Moreira, P. A. Branger, J. Collado-Vides posted to simulation proteins-chemistry protein-methods dna-chemistry dna-binding databases computer chemical analysis theoretical systems sites sequence receptor proteins-metabolism protein neoplasm molecular models information file-import-09-11-28 dna-metabolism data cyclic carrier binding base amp algorithms by brunocontreras on 2009-11-28 20:26:49 as
	An efficient conformational sampling method for homology modeling [My Copy] Proteins, Vol. 71, No. 1. (2008), 175-88. by R. Han, A. Leo-Macias, D. Zerbino, U. Bastolla, B. Contreras-Moreira, A. R. Ortiz posted to sequence proteins-chemistry-genetics protein molecular models methods homology evolution databases conformation computational biology-methods amino acid sites research-history proteins-history-metabolism history file-import-09-11-28 dna-binding dna-analysis-history century binding 20th by brunocontreras on 2009-11-28 20:26:49 as
	A link between sequence conservation and domain motion within the AAA+ family [My Copy] J Struct Biol, Vol. 146, No. 1-2. (2004), 189-204. by G. R. Smith, B. Contreras-Moreira, X. Zhang, P. A. Bates posted to triphosphatases-chemistry-classification tertiary-drug structure structural simulation quaternary protein pliability nucleotides-chemistry-pharmacology motion homology effects conserved computer adenosine viral tryptophan-genetics t-phages-genetics statistics sites serine sequence rna ribosomes-metabolism repressor regions proteins-genetics proteins polymerases-genetics operon operator lac genetics file-import-09-11-28 escherichia endopeptidases dna-directed dna-binding dna coli-genetics-metabolism binding base bacterial-genetics-metabolism bacterial by brunocontreras on 2009-11-28 20:26:49 as
	Functional recycling of C2 domains throughout evolution: a comparative study of synaptotagmin, protein kinase C and phospholipase C by sequence, structural and modelling approaches [My Copy] J Mol Biol, Vol. 333, No. 3. (2003), 621-39. by J. L. Jimenez, G. R. Smith, B. Contreras-Moreira, et al.J. G. Sgouros, F. A. Meunier, P. A. Bates, G. Schiavo posted to type tissue tertiary synaptotagmins structure proteomics proteins-chemistry proteins protein phospholipases-chemistry nerve molecular models membrane kinase humans homology glycoproteins-chemistry evolution data conserved calcium-binding c-chemistry c animals amino acid software sites sequence regions promoter genetics genes file-import-09-11-28 escherichia dna-metabolism dna composition coli binding base bacterial-metabolism bacterial by brunocontreras on 2009-11-28 20:26:48 as
	3D-footprint: a database for the structural analysis of protein-DNA complexes [My Copy] Nucleic Acids Res, Vol. 64, No. 3. (2009), 908-10. by B. Contreras-Moreira posted to sites sequence models humans genetic fragility-genetics fragile file-import-09-11-28 factual dna databases chromosome banding analysis by brunocontreras on 2009-11-28 20:26:48 as
	primers4clades: a web server that uses phylogenetic trees to design lineage-specific PCR primers for metagenomic and diversity studies [My Copy] Nucleic Acids Res, Vol. 37, No. Web Server issue. (2009), W95-W100. by B. Contreras-Moreira, B. Sachman-Ruiz, I. Figueroa-Palacios, P. Vinuesa posted to variation user-computer software results reproducibility reaction primers-chemistry polymerase phylogeny of microbiology internet interface genomics genetic environmental dna chain algorithms x-ray proteins-chemistry molecular models hydrogen file-import-09-11-28 electrostatics dna-chemistry dna-binding crystallography composition bonding base by brunocontreras on 2009-11-28 20:26:48 as
	Comparison of DNA binding across protein superfamilies [My Copy] Proteins, Vol. 26, No. 10. (2009), 2306-12. by B. Contreras-Moreira, J. Sancho, V. E. Angarica posted to zinc x-ray sites simulation proteins-chemistry likelihood hydrogen functions fingers file-import-09-11-28 dna-chemistry dna-binding crystallography computer bonding binding amino acids-chemistry by brunocontreras on 2009-11-28 20:26:48 as
	Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli [My Copy] PLoS One, Vol. 4, No. 10. (2009), e7526. by A. Mendoza-Vargas, L. Olvera, M. Olvera, et al.R. Grande, L. Vega-Alvarado, B. Taboada, V. Jimenez-Jacinto, H. Salgado, K. Juarez, B. Contreras-Moreira, A. M. Huerta, J. Collado-Vides, E. Morett posted to sites-genetics sequence regions receptor proteins-metabolism proteins protein-metabolism promoter models genetics file-import-09-11-28 escherichia dna-genetics-metabolism dna-binding cyclic crystallography coli-genetics-metabolism chemical carrier binding base amp algorithms by brunocontreras on 2009-11-28 20:26:48 as
	The role of DNA-binding specificity in the evolution of bacterial regulatory networks [My Copy] Journal of molecular biology, Vol. 379, No. 3. (2008), 627-43. by I. Lozada-Chavez, V. E. Angarica, J. Collado-Vides, B. Contreras-Moreira posted to transcription theoretical subtilis-genetics-metabolism regulatory regulation random proteins-chemistry-genetics-metabolism protein networks molecular models microarray genetic gene file-import-09-11-28 factors-chemistry-genetics-metabolism expression evolution escherichia duplication conformation coli-genetics-metabolism bacterial bacillus analysis allocation by brunocontreras on 2009-11-28 20:26:47 as
	Domain fishing: a first step in protein comparative modelling [My Copy] Bioinformatics, Vol. 18, No. 8. (2002), 1141-2. by B. Contreras-Moreira, P. A. Bates posted to storage software retrieval-methods proteins-chemistry-genetics protein-methods programming languages information databases and analysis alignment algorithms water-chemistry sites sequence regions proteins-metabolism protein promoter primers nucleic hydrogen genetics file-import-09-11-28 dna-chemistry-metabolism dna-binding dna conformation bonding binding base acid by brunocontreras on 2009-11-28 20:26:47 as
	Comparative modelling: an essential methodology for protein structure prediction in the post-genomic era [My Copy] Appl Bioinformatics, Vol. 1, No. 4. (2002), 177-90. by B. Contreras-Moreira, P. W. Fitzjohn, P. A. Bates posted to thermodynamics simulation quality proteomics-standards-statistics proteins-chemistry-genetics numerical models internet humans control computational biology x-ray transcription tata-box tata solvents-chemistry sites sequence proteins-chemistry protein nucleic molecular homology graphics file-import-09-11-28 factors-chemistry dna-chemistry dna-binding data crystallography conformation computer box binding base arabidopsis-chemistry amino acid by brunocontreras on 2009-11-28 20:26:47 as
	Multilocus sequence analysis for assessment of the biogeography and evolutionary genetics of four Bradyrhizobium species that nodulate soybeans on the asiatic continent [My Copy] Appl Environ Microbiol, Vol. 74, No. 22. (2008), 6987-96. by P. Vinuesa, K. Rojas-Jimenez, B. Contreras-Moreira, et al.S. K. Mahna, B. N. Prasad, H. Moe, S. B. Selvaraju, H. Thierfelder, D. Werner posted to typing techniques soybeans-microbiology roots-microbiology purification polymorphism plant phylogeny molecular geography genotype genetic cluster climate bradyrhizobium-classification-genetics-isolation bacterial-chemistry-genetics asia analysis software sites-genetics sequence receptor proteins-genetics-metabolism proteins-genetics proteins protein-genetics-metabolism numerical models linear file-import-09-11-28 escherichia dna-genetics dna data cyclic coli-genetics-metabolism carrier binding base bacterial-genetics bacterial amp alignment-methods-statistics algorithms by brunocontreras on 2009-11-28 20:26:47 as
	The role of DNA-binding specificity in the evolution of bacterial regulatory networks [My Copy] J Mol Biol, Vol. 379, No. 3. (2008), 627-43. by I. Lozada-Chavez, V. E. Angarica, J. Collado-Vides, B. Contreras-Moreira posted to transcription theoretical subtilis-genetics-metabolism regulatory regulation random proteins-chemistry-genetics-metabolism protein networks molecular models microarray genetic gene factors-chemistry-genetics-metabolism expression evolution duplication conformation coli-genetics-metabolism bacillus analysis allocation sequence regions promoter nucleic homology genetics genes file-import-09-11-28 escherichia dna consensus coli-genetics base bacterial-genetics bacterial alignment acid by brunocontreras on 2009-11-28 20:26:47 as
	RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation [My Copy] Nucleic Acids Res, Vol. 36, No. Database issue. (2008), D120-4. by S. Gama-Castro, V. Jimenez-Jacinto, M. Peralta-Gil, et al.A. Santos-Zavaleta, M. I. Penaloza-Spinola, B. Contreras-Moreira, J. Segura-Salazar, L. Muniz-Rascado, I. Martinez-Flores, H. Salgado, C. Bonavides-Martinez, C. Abreu-Goodger, C. Rodriguez-Penagos, J. Miranda-Rios, E. Morett, E. Merino, A. M. Huerta, L. Trevino-Quintanilla, J. Collado-Vides posted to transcription site sigma sequences ribonucleic regulon regulatory regulation regions promoter networks models k12-genetics internet initiation genetic gene factors-metabolism factor-metabolism expression databases computational coli biology acid software sites serine sequence recognition proteins-genetics pattern molecular genes file-import-09-11-28 escherichia endopeptidases dna data coli-genetics binding base bacterial-genetics bacterial automated algorithms by brunocontreras on 2009-11-28 20:26:47 as
	RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation [My Copy] Nucleic acids research, Vol. 36, No. Database issue. (2008), D120-4. by S. Gama-Castro, V. Jimenez-Jacinto, M. Peralta-Gil, et al.A. Santos-Zavaleta, M. I. Penaloza-Spinola, B. Contreras-Moreira, J. Segura-Salazar, L. Muniz-Rascado, I. Martinez-Flores, H. Salgado, C. Bonavides-Martinez, C. Abreu-Goodger, C. Rodriguez-Penagos, J. Miranda-Rios, E. Morett, E. Merino, A. M. Huerta, L. Trevino-Quintanilla, J. Collado-Vides posted to transcription software site sigma sequences ribonucleic regulon regulatory regulation regions promoter networks models k12-genetics internet initiation genetics genetic gene file-import-09-11-28 factors-metabolism factor-metabolism expression escherichia databases computational coli biology bacterial acid by brunocontreras on 2009-11-28 20:26:47 as
	Comparative footprinting of DNA-binding proteins [My Copy] Bioinformatics, Vol. 22, No. 14. (2006), e74-80. by B. Contreras-Moreira, J. Collado-Vides posted to sites simulation sequence proteins-chemistry protein-methods protein molecular models homology footprinting-methods file-import-09-11-28 dna-methods dna-chemistry dna-binding computer chemical binding analysis algorithms by brunocontreras on 2009-11-28 20:26:47 as
	TFmodeller: comparative modelling of protein-DNA complexes [My Copy] Bioinformatics (Oxford, England), Vol. 23, No. 13. (2007), 1694-6. by B. Contreras-Moreira, P. A. Branger, J. Collado-Vides posted to sites simulation sequence proteins-chemistry protein-methods protein models file-import-09-11-28 dna-chemistry dna-binding databases computer chemical binding analysis algorithms by brunocontreras on 2009-11-28 20:26:47 as
	Empirical limits for template-based protein structure prediction: the CASP5 example [My Copy] FEBS Lett, Vol. 579, No. 5. (2005), 1203-7. by B. Contreras-Moreira, I. Ezkurdia, M. L. Tress, A. Valencia posted to structural specificity sensitivity protein models homology computational chemical biology-methods and alignment algorithms zinc transcription structure-activity sites sequence relationship recombinant proteins-chemistry proteins oligodeoxyribonucleotides-chemistry molecular kinetics fingers file-import-09-11-28 factors-chemistry dna-binding data binding base amino acid by brunocontreras on 2009-11-28 20:26:47 as
	Structural context of exons in protein domains: implications for protein modelling and design [My Copy] J Mol Biol, Vol. 333, No. 5. (2003), 1045-59. by B. Contreras-Moreira, P. F. Jonsson, P. A. Bates posted to trypsin-metabolism transcription tertiary structure simulation regulatory protein myogenic molecular models mice humans factors-metabolism factors exons-physiology engineering computer animals sites regulation proteins-metabolism gene file-import-09-11-28 expression dna-metabolism dna-binding binding by brunocontreras on 2009-11-28 20:26:46 as
	Prediction of TF target sites based on atomistic models of protein-DNA complexes [My Copy] BMC Bioinformatics, Vol. 9 (2008), 436. by V. E. Angarica, A. G. Perez, A. T. Vasconcelos, J. Collado-Vides, B. Contreras-Moreira posted to x-ray under transcription structure statistical sites-genetics sequence secondary roc regression proteins-metabolism proteins-chemistry-metabolism protein models file-import-09-11-28 factors-metabolism dna-metabolism dna-binding curve crystallography computational biology-methods biological binding-genetics binding base area analysis amino algorithms acid by brunocontreras on 2009-11-28 20:26:46 as
	3D-footprint: a database for the structural analysis of protein-DNA complexes [My Copy] Nucl. Acids Res., Vol. 38, No. suppl_1. (1 January 2010), pp. D91-97. by Bruno Contreras-Moreira posted to protein pdb footprint dna database by brunocontreras on 2009-11-08 21:39:08 as along with 1 person flbarroso

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drift	1
cooperation	1
neoplasm	1
linear	1
protein-chemistry-metabolism	1
automated	1
introns	1
uracil	1
typing	1
i-chemistry-genetics-metabolism	1
coli-chemistry-metabolism	1
replication	1
molecules-antagonists	1
population-methods-statistics	1
alignment-methods-statistics	1
hydrogen-chemistry	1
restriction	1
host	1
trans-activators-chemistry-genetics-metabolism	1
antennapedia	1
phospholipases-chemistry	1
pliability	1
environment	1

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