BIBLIOGRAFIA Y LINKS DE WEBS

Contar con bibliografía y softwares libres (Web), es de vital importancia, por lo cual, les compartimos los siguientes links.

https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html

https://www.cgl.ucsf.edu/chimera/

https://www.cgl.ucsf.edu/chimera/pdf/UsersGuide1.10.pdf

https://pymol.org/2/

http://pymol.sourceforge.net/newman/userman.pdf

http://www.pitt.edu/~epolinko/IntroPyMOL.pdf

https://www.rcsb.org/

https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/introduction

https://www.cell.com/action/showPdf?pii=S0969-2126%2821%2900126-X

https://swissmodel.expasy.org/

https://swissmodel.expasy.org/docs/help

https://swissmodel.expasy.org/course

http://www.hiv.lanl.gov/content/sequence/ FORMAT_CONVERSION/form.html

https://www.benchling.com/

www.ncbi.nlm.nih.gov.

https://benchling.com/

https://www.idtdna.com/calc/analyzer.

https://www.ncbi.nlm.nih.gov/tools/primer-blast/index.cgi,

Cañedo Andalia, Rubén, Rodríguez Labrada, Roberto, & Vázquez Mojena, Yaimeé. (2009). Centro Nacional para la Información Biotecnológica de los Estados Unidos: un palacio de la información para la medicina molecular. ACIMED, 19(4) http://scielo.sld.cu/scielo.php?script=sci_arttext&pid=S1024 94352009000400003&lng=es&tlng=es.

Sayers EW, Cavanaugh M, Clark K, Ostell J, Pruitt KD, Karsch-Mizrachi I. GenBank. Nucleic Acids Res. 2019 Jan 8;47(D1):D94-D99. doi: 10.1093/nar/gky989. PMID: 30365038; PMCID: PMC6323954.

Sayers, E. W., Beck, J., Bolton, E. E., Bourexis, D., Brister, J. R., Canese, K., Comeau, D. C., Funk, K., Kim, S., Klimke, W., Marchler-Bauer, A., Landrum, M., Lathrop, S., Lu, Z., Madden, T. L., O'Leary, N., Phan, L., Rangwala, S. H., Schneider, V. A., Skripchenko, Y., … Sherry, S. T. (2021). Database resources of the National Center for Biotechnology Information. Nucleic acids research, 49(D1), D10–D17. https://doi.org/10.1093/nar/gkaa892

Wassmann, P., Chan, C., Paul, R., Beck, A., Heerklotz, H., Jenal, U., SchirmeT. Structure of Bef3--Modified Response Regulator Pled: Implications for Diguanylate Cyclase Activation, Catalysis, and Feedback Inhibition. Structure volume15, ISSUE 8, P915-927, august 14, 2007 DOI: https://doi.org/10.1016/j.str.2007.06.016

Protein Data Bank. Nat. New Biol.1971; 233:223.

BermanH., Henrick K., Nakamura H. Announcing the worldwide Protein Data Bank. Nat. Struc. Niol. 2003;10:980-980.

Berman H.M.,Westbook J., FengZ., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. The protein Data Bank. Nucleic Acids Res. 2000; 28:235-242.

Mir S., Alhroub  Y., Anyango S.,  Armstrong D.R., Berrisford J.M., Clark A.R.,  Conroy M.J.,  Dana J.M.,  Deshpande M., Gupta D. et al.   PDBe: towards reusable data delivery infrastructure at protein data bank in Europe.  Nucleic Acids Res. 2017; 46:D486–D492.

Kinjo A.R.,  Bekker G.-J.,  Suzuki H., Tsuchiya Y.,  Kawabata T., IkegawaY.,  Nakamura H. Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures. Nucleic Acids Res. 2017; 45:D282–D288.

NIH. (2019). Secuenciación del ADN. National Human Genome Research Institute. Recuperado de www.genome.gov/es/about-genomics/fact-sheets/Secuenciacion-del-ADN.

Marquez V. L. M. (s/f). Secuenciación de fragmentos de ADN. Herramientas Moleculares Aplicadas en Ecología.

NIH. (2019). SnapGene. Recuperado de ostr.ccr.cancer.gov/bioinformatics/software/snapgene/.

De Castro E, Sigrist CJA, Gattiker A, Bulliard V, Langendijk-Genevaux PS, Gasteiger E, Bairoch A, Hulo N (2006). "ScanProsite: detección de coincidencias de firma PROSITE y residuos estructurales y funcionales asociados a ProRule en proteínas". Ácidos nucleicos Res. 34 (Problema del servidor web): W362–365. doi: 10.1093 / nar / gkl124. PMC 1538847. PMID 16845026.

 Hulo N, Bairoch A, Bulliard V, Cerutti L, Cuche B, De Castro E, Lachaize C, Langendijk-Genevaux PS, Sigrist CJA (2007). "Los 20 años de PROSITE". Ácidos nucleicos Res. 36 (Problema de la base de datos): D245–9. doi: 10.1093 / nar / gkm977. PMC 2238851. PMID 18003654.

Sigrist CJ, De Castro E, Langendijk-Genevaux PS, Le Saux V, Bairoch A, Hulo N (2005). "ProRule: una nueva base de datos que contiene información funcional y estructural de los perfiles de PROSITE". Bioinformática. 21 (21): 4060–4066. doi: 10.1093 / bioinformatics / bti614. PMID 16091411.

Sievers, F., Wilm, A., Dineen, D., Gibson, T. J., Karplus, K., Li, W., Lopez, R., McWilliam, H., Remmert, M., Söding, J., Thompson, J. D., & Higgins, D. G. (2011). Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular Systems Biology, 7(539). https://doi.org/10.1038/msb.2011.75

Gold, L., Polisky, B., Uhlenbeck, O., & Yarus, M. (1995). Diversity of oligonucleotide functions. Annual review of biochemistry, 64(1), 763-797.

SnapGene software (from Insightful Science; available at snapgene.com)

Hung, J. H., & Weng, Z. (2016). Designing polymerase chain reaction primers using Primer3Plus. Cold Spring Harbor Protocols, 2016(9), pdb-prot093096.

Bickle, T. A., & Kruger, D. H. (1993). Biology of DNA restriction. Microbiological Reviews, 57(2), 434–450. https://doi.org/10.1128/mmbr.57.2.434-450.1993

Boyer, H. W. (1971). DNA Restriction and Modification Mechanisms in Bacteria. Annual Review of Microbiology, 25(1), 153–176. https://doi.org/10.1146/annurev.mi.25.100171.001101

Lodish, H. F. (2016). Molecular cell biology. New York: W.H. Freeman and Co.

Roberts, R. J. (2005). How restriction enzymes became the workhorses of molecular biology. www.pnas.orgcgidoi10.1073pnas.0500923102

Yuan, R. (1981). Structure and Mechanism of Multifunctional Restriction Endonucleases. Annual Review of Biochemistry, 50(1), 285–315. https://doi.org/10.1146/annurev.bi.50.070181.001441

Ye, J., Coulouris, G., Zaretskaya, I., Cutcutache, I., Rozen, S., & Madden, T. L. (2012). Primer-BLAST: a tool to design target-specific primers for polymerase chain reaction. BMC bioinformatics, 13(1), 1-11.

Dieffenbach, C. W., Lowe, T. M., & Dveksler, G. S. (1993). General concepts for PCR primer design. PCR methods appl, 3(3), S30-S37.

Koressaar, T., & Remm, M. (2007). Enhancements and modifications of primer design program Primer3. Bioinformatics, 23(10), 1289-1291.

Singh, V. K., & Kumar, A. (2001). PCR primer design. Mol. Biol. Today, 2(2), 27-32.

Singh, V. K., Govindarajan, R., Naik, S., & Kumar, A. (2000). The effect of hairpin structure on PCR amplification efficiency. Mol Biol Today, 1(3), 67-69.

Gold, L., Polisky, B., Uhlenbeck, O., & Yarus, M. (1995). Diversity of oligonucleotide functions. Annual review of biochemistry, 64(1), 763-797

SnapGene software (from Insightful Science; available at snapgene.com)

Dieffenbach, C. W., Lowe, T. M., & Dveksler, G. S. (1993). General concepts for PCR primer design. PCR methods appl, 3(3), S30-S37.

Singh, V. K., & Kumar, A. (2001). PCR primer design. Mol. Biol. Today, 2(2), 27-32.

González-Ballester, D., De Montaigu, A., Galván, A., & Fernández, E. (2005). Restriction enzyme site-directed amplification PCR: a tool to identify regions flanking a marker DNA. Analytical biochemistry, 340(2), 330-335.

Lodish, H., Berk, A., Kaiser, C. A., Monty, K., Scott, M. P., Bretscher, A., Ploegh, H., & Matsudaira, P. (2008). Molecular cell biology. In General Pharmacology:The Vascular System (Vol. 18, Issue 6, p. 672). https://doi.org/10.1016/0306-3623(87)90055-3

Can Kesmir. (2013). Bioinformatics. UU: Utrecht University

Gale Rhodes. (2009). Bioinformática y modelación de proteínas por homología: un tutorial para principiantes Exploración de los pigmentos visuales humanos. México: UNAM.

Engelhardt, B. E., Jordan, M. I., Repo, S. T., & Brenner, S. E. (2009). Phylogenetic molecular function annotation. Journal of Physics: Conference Series, 180(1), 1–7. https://doi.org/10.1088/1742-6596/180/1/012024

Semagn, K. (2014). Leaf Tissue Sampling and DNA Extraction Protocols. In: Molecular Plant Taxonomy Methods and Protocols. In Molecular Plant Taxonomy: Methods and Protocols (Vol. 1115).

Weiß, M., & Göker, M. (2011). Molecular phylogenetic reconstruction. The Yeasts, 1, 159–174. https://doi.org/10.1016/B978-0-444-52149-1.00012-4

Gale Rhodes. (2009). Bioinformática y modelación de proteínas por homología: un tutorial para principiantes Exploración de los pigmentos visuales humanos. México: UNAM.

Daniel H. Huson, Regula Rupp, Celine Scornavacca. (2011). Phylogenetic Nettworks. Concepts, Algorithms and Applications 2nd ed. Cambridge. University Press. New York

 SMART: recent updates, new developments and status in 2020, Nucleic Acids Res 2020; doi:10.1093/nar/gkaa937

SMART, a simple modular architecture research tool: Identification of signaling domains.PNAS 1998; 95: 5857-5864

Marchler-Bauer A et al. (2015), "CDD: NCBI's conserved domain database.", Nucleic Acids Res.43(D)222-6.

Marchler-Bauer A et al. (2011), "CDD: a Conserved Domain Database for the functional annotation of proteins.", Nucleic Acids Res.39(D)225-9.

Marchler-Bauer A, Bryant SH (2004), "CD-Search: protein domain annotations on the fly.", Nucleic Acids Res.32(W)327-331.

SMART: recent updates, new developments and status in 2020, Nucleic Acids Res 2020; doi:10.1093/nar/gkaa937

Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.

Gupta R, Brunak S. Prediction of glycosylation across the human proteome and the correlation to protein function. Pac Symp Biocomput. 2002; 310-22.PMID: 11928486y

Pan, Z., Wang, B., Zhang, Y., Wang, Y., Ullah, S., Jian, R., Liu, Z., & Xue, Y. (2015). dbPSP: a curated database for protein phosphorylation sites in prokaryotes. Database : the journal of biological databases and curation, 2015, bav031. https://doi.org/10.1093/database/bav031

Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology. Steentoft C, Vakhrushev SY, Joshi HJ, Kong Y, Vester-Christensen MB, Schjoldager KT, Lavrsen K, Dabelsteen S, Pedersen NB, Marcos-Silva L, Gupta R, Bennett EP, Mandel U, Brunak S, Wandall HH, Levery SB, Clausen H. EMBO J, 32(10):1478-88, May 15, 2013. (doi: 10.1038/emboj.2013.79. Epub 2013 Apr 12.

Sequence- and structure-based prediction of eukaryotic protein phosphorylation sites. Blom, N., Gammeltoft, S., and Brunak, S. Journal of Molecular Biology: 294(5): 1351-1362, 1999.

Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Blom N, Sicheritz-Ponten T, Gupta R, Gammeltoft S, Brunak S. Proteomics: Jun;4(6):1633-49, review 2004.

Mackenzie CO, Grigoryan G. 2017. Protein Structural Motifs in Prediction and Design. Curr Opin Struct Biol 44:161–167.

H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne .2000. The Protein Data Bank.  Nucleic Acids Research, 28: 235-242. doi:10.1093/nar/28.1.235

Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. 2004. UCSF Chimera visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612.

The PyMOL Molecular Graphics System, Version 1.2r3pre, Schrödinger, LLC.

Meng EC, Pettersen EF, Couch GS, Huang CC, Ferrin TE. Tools for integrated sequence-structure analysis with UCSF Chimera. BMC Bioinformatics. 2006 Jul 12;7:339. doi: 10.1186/1471-2105-7-339. PMID: 16836757; PMCID: PMC157015

 

Análisis de secuencias de biológicas por medio de plataformas digitales.

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 https://analisisdesecuenciasdednayprot.blogspot.com/