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Should network biology be used for drug discovery?
Martínez-Jiménez F, Marti-Renom MA. Martínez-Jiménez F, et al. Expert Opin Drug Discov. 2016 Dec;11(12):1135-1137. doi: 10.1080/17460441.2016.1236786. Epub 2016 Sep 23. Expert Opin Drug Discov. 2016. PMID: 27635856 No abstract available.
A kernel for open source drug discovery in tropical diseases.
Ortí L, Carbajo RJ, Pieper U, Eswar N, Maurer SM, Rai AK, Taylor G, Todd MH, Pineda-Lucena A, Sali A, Marti-Renom MA. Ortí L, et al. PLoS Negl Trop Dis. 2009;3(4):e418. doi: 10.1371/journal.pntd.0000418. Epub 2009 Apr 21. PLoS Negl Trop Dis. 2009. PMID: 19381286 Free PMC article.
Target prediction for an open access set of compounds active against Mycobacterium tuberculosis.
Martínez-Jiménez F, Papadatos G, Yang L, Wallace IM, Kumar V, Pieper U, Sali A, Brown JR, Overington JP, Marti-Renom MA. Martínez-Jiménez F, et al. PLoS Comput Biol. 2013;9(10):e1003253. doi: 10.1371/journal.pcbi.1003253. Epub 2013 Oct 3. PLoS Comput Biol. 2013. PMID: 24098102 Free PMC article.
Ligand-target prediction by structural network biology using nAnnoLyze.
Martínez-Jiménez F, Marti-Renom MA. Martínez-Jiménez F, et al. PLoS Comput Biol. 2015 Mar 27;11(3):e1004157. doi: 10.1371/journal.pcbi.1004157. eCollection 2015 Mar. PLoS Comput Biol. 2015. PMID: 25816344 Free PMC article.
Restraint-based three-dimensional modeling of genomes and genomic domains.
Serra F, Di Stefano M, Spill YG, Cuartero Y, Goodstadt M, Baù D, Marti-Renom MA. Serra F, et al. FEBS Lett. 2015 Oct 7;589(20 Pt A):2987-95. doi: 10.1016/j.febslet.2015.05.012. Epub 2015 May 14. FEBS Lett. 2015. PMID: 25980604 Review.
Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop.
Sali A, Berman HM, Schwede T, Trewhella J, Kleywegt G, Burley SK, Markley J, Nakamura H, Adams P, Bonvin AM, Chiu W, Peraro MD, Di Maio F, Ferrin TE, Grünewald K, Gutmanas A, Henderson R, Hummer G, Iwasaki K, Johnson G, Lawson CL, Meiler J, Marti-Renom MA, Montelione GT, Nilges M, Nussinov R, Patwardhan A, Rappsilber J, Read RJ, Saibil H, Schröder GF, Schwieters CD, Seidel CA, Svergun D, Topf M, Ulrich EL, Velankar S, Westbrook JD. Sali A, et al. Structure. 2015 Jul 7;23(7):1156-67. doi: 10.1016/j.str.2015.05.013. Epub 2015 Jun 18. Structure. 2015. PMID: 26095030 Free PMC article.
Release of 50 new, drug-like compounds and their computational target predictions for open source anti-tubercular drug discovery.
Rebollo-Lopez MJ, Lelièvre J, Alvarez-Gomez D, Castro-Pichel J, Martínez-Jiménez F, Papadatos G, Kumar V, Colmenarejo G, Mugumbate G, Hurle M, Barroso V, Young RJ, Martinez-Hoyos M, González del Río R, Bates RH, Lopez-Roman EM, Mendoza-Losana A, Brown JR, Alvarez-Ruiz E, Marti-Renom MA, Overington JP, Cammack N, Ballell L, Barros-Aguire D. Rebollo-Lopez MJ, et al. PLoS One. 2015 Dec 7;10(12):e0142293. doi: 10.1371/journal.pone.0142293. eCollection 2015. PLoS One. 2015. PMID: 26642067 Free PMC article.
Biological insertion of computationally designed short transmembrane segments.
Baeza-Delgado C, von Heijne G, Marti-Renom MA, Mingarro I. Baeza-Delgado C, et al. Sci Rep. 2016 Mar 18;6:23397. doi: 10.1038/srep23397. Sci Rep. 2016. PMID: 26987712 Free PMC article.
Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors.
Serra F, Baù D, Goodstadt M, Castillo D, Filion GJ, Marti-Renom MA. Serra F, et al. PLoS Comput Biol. 2017 Jul 19;13(7):e1005665. doi: 10.1371/journal.pcbi.1005665. eCollection 2017 Jul. PLoS Comput Biol. 2017. PMID: 28723903 Free PMC article.
OneD: increasing reproducibility of Hi-C samples with abnormal karyotypes.
Vidal E, le Dily F, Quilez J, Stadhouders R, Cuartero Y, Graf T, Marti-Renom MA, Beato M, Filion GJ. Vidal E, et al. Nucleic Acids Res. 2018 May 4;46(8):e49. doi: 10.1093/nar/gky064. Nucleic Acids Res. 2018. PMID: 29394371 Free PMC article.
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