Contreras-Moreira B - Search Results

1

Empirical limits for template-based protein structure prediction: the CASP5 example.

Contreras-Moreira B, Ezkurdia I, Tress ML, Valencia A. Contreras-Moreira B, et al. FEBS Lett. 2005 Feb 14;579(5):1203-7. doi: 10.1016/j.febslet.2005.01.014. FEBS Lett. 2005. PMID: 15710414 Free article.

2

Comparative footprinting of DNA-binding proteins.

Contreras-Moreira B, Collado-Vides J. Contreras-Moreira B, et al. Bioinformatics. 2006 Jul 15;22(14):e74-80. doi: 10.1093/bioinformatics/btl215. Bioinformatics. 2006. PMID: 16873524

3

An efficient conformational sampling method for homology modeling.

Han R, Leo-Macias A, Zerbino D, Bastolla U, Contreras-Moreira B, Ortiz AR. Han R, et al. Proteins. 2008 Apr;71(1):175-88. doi: 10.1002/prot.21672. Proteins. 2008. PMID: 17985353

4

TFmodeller: comparative modelling of protein-DNA complexes.

Contreras-Moreira B, Branger PA, Collado-Vides J. Contreras-Moreira B, et al. Bioinformatics. 2007 Jul 1;23(13):1694-6. doi: 10.1093/bioinformatics/btm148. Epub 2007 Apr 25. Bioinformatics. 2007. PMID: 17459960

5

Novel use of a genetic algorithm for protein structure prediction: searching template and sequence alignment space.

Contreras-Moreira B, Fitzjohn PW, Offman M, Smith GR, Bates PA. Contreras-Moreira B, et al. Proteins. 2003;53 Suppl 6:424-9. doi: 10.1002/prot.10549. Proteins. 2003. PMID: 14579331

6

In silico protein recombination: enhancing template and sequence alignment selection for comparative protein modelling.

Contreras-Moreira B, Fitzjohn PW, Bates PA. Contreras-Moreira B, et al. J Mol Biol. 2003 May 2;328(3):593-608. doi: 10.1016/s0022-2836(03)00309-7. J Mol Biol. 2003. PMID: 12706719

7

Robust identification of orthologues and paralogues for microbial pan-genomics using GET_HOMOLOGUES: a case study of pIncA/C plasmids.

Vinuesa P, Contreras-Moreira B. Vinuesa P, et al. Methods Mol Biol. 2015;1231:203-32. doi: 10.1007/978-1-4939-1720-4_14. Methods Mol Biol. 2015. PMID: 25343868 Free article.

8

Prediction of TF target sites based on atomistic models of protein-DNA complexes.

Angarica VE, Pérez AG, Vasconcelos AT, Collado-Vides J, Contreras-Moreira B. Angarica VE, et al. BMC Bioinformatics. 2008 Oct 16;9:436. doi: 10.1186/1471-2105-9-436. BMC Bioinformatics. 2008. PMID: 18922190 Free PMC article.

9

Comparative modelling: an essential methodology for protein structure prediction in the post-genomic era.

Contreras-Moreira B, Fitzjohn PW, Bates PA. Contreras-Moreira B, et al. Appl Bioinformatics. 2002;1(4):177-90. Appl Bioinformatics. 2002. PMID: 15130836 Review.

10

Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli.

Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juárez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E. Mendoza-Vargas A, et al. PLoS One. 2009 Oct 19;4(10):e7526. doi: 10.1371/journal.pone.0007526. PLoS One. 2009. PMID: 19838305 Free PMC article.

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