Structural Genomics @CNAG · CRG


The view of RNA as simple information transfer molecule has been continuously challenged since the discovery of ribozymes. Moreover, the recent discovery of tiny RNA molecules such as µRNAs and small interfering RNA, are transforming our thinking about how gene expression is regulated.

Functional RNA molecules fold into their native three-dimensional conformations essential for performing their biological activity. Despite advances in understanding the folding and unfolding of RNA molecules, our knowledge of the atomic mechanism by which RNA molecules adopt their biological active structures is still limited. Moreover, we have limited knowledge on how non-coding RNA molecules regulate gene expression in health and disease.

Fortunately, there has been a recent burst of interest in RNA at all levels of resolution, including sequence, structure and function. Many new methods are appearing for characterizing how RNA sequences fold and perform their functions. However, to our knowledge, very few (if any) of such new methods are systematically exploiting the evolutionary record of RNA structures. Over the past years, we have established a line of research dedicated to RNA. We have been making use of structural data in the Protein Data Bank to develop new methods for aligning RNA structures, assigning function to new RNA structures, and determining the limits of automatic RNA comparative structure prediction.

Selected articles

Dufour, D. and Marti-Renom, M.A.
"Software for predicting the 3D structure of RNA molecules."
WIREs Comput Mol Sci (2014) 5 (1) 56–61  
Kemena, C.,  Bussotti, G.,  Capriotti, E.,  Marti-Renom, M.A. and Notredame, C
"Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package"
Bioinformatics (2013) 29 1112-1119  
Capriotti, E.,  Norambuena, T,  Marti-Renom, M.A. and Melo, F.
"All-atom knowledge-based potential for RNA structure prediction and assessment"
Bioinformatics (2011) 27 1086-1093  
Capriotti, E. and Marti-Renom, M.A.
"Quantifying the relationship between sequence and three-dimensional structure conservation in RNA"
BMC Bioinformatics (2010) 11 322  
Capriotti, E. and Marti-Renom, M.A.
"SARA: a server for function annotation of RNA structures"
Nucleic Acids Research (2009) 37 W260-5  


Spain. MINECO. Plan Nacional. 2014-2016 [BFU2013-47736].
Determining the three-dimensional structure of genomes and genomic domains.
Spain. MICINN. Plan Nacional. 2011-2014 [BFU2010-19310].
Structural bioinformatics for drug discovery against organisms causing neglected tropical diseases.
Valencia. Complementary Grant. 2011-2011 [ACOMP/2011/048].
Structural bioinformatics for drug discovery against organisms causing neglected tropical diseases.
European Union. Marie Curie Action. 2006-2009 [IRG39722].
Comparative Modeling of RNA structures at atomic resolution.
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