Structural Genomics @CNAG ˇ CRG


Proteins

We have been pioneers in applying computational methods within an open source framework. In 2004, while I was Assistant Adj. Professor at UCSF, I co-initiated the Tropical Disease Initiative (TDI) with the aim of finding cures for tropical diseases such as malaria, leishmaniasis, denge, or tuberculosis. The main idea behind TDI is to promote research in a decentralized, Web-based, community-wide effort where scientists from laboratories, universities, institutes, and corporations can work together for a common cause. TDI provides, in our opinion, a perfect venue where our research can be tested and applied with immediate repercussion and publicity. Our inmediate aim is to continue applying our protein structure prediction methods to study neglected diseases.

Selected articles

Baeza-Delgado, C.,  Von Heijne, G.,  Marti-Renom, M.A. and Mingarro, I.
"Biological insertion of computationally designed short transmembrane segments."
Scientific Reports (2016) 6 23397   
  
Martínez-Jiménez, F. and Marti-Renom, M.A.
"Ligand-target prediction by structural network biology using nAnnoLyze."
PLOS Computational Biology (2015) 11(3) e1004157  
  
Martínez-Jiménez, F.,  Papadatos, G.,  Yang, L.,  Wallace, I.M.,  Kumar, V.,  Pieper, U.,  Sali, A.,  Brown, J.R.,  Overington, J.P. and Marti-Renom, M.A.
"Target prediction for an open access set of compounds active against Mycobacterium tuberculosis"
PLOS Computational Biology (2013) 9(10) e1003253  
  
Köser, C.U.,  Bryant, J.M.,  Becq, J.,  Török, M.E.,  Ellington, M.J.,  Marti-Renom, M.A.,  Carmichael, A.J.,  Parkhill, J.,  Smith, G.P. and Peacock, S.J.
"Whole-genome sequencing for rapid susceptibility testing of M. tuberculosis"
NEJM (2013) 369 290-292  
  
Orti, L.,   Carbajo, R.J.,   Pieper, U.,  Eswar, N.,  Maurer, S.M.,  Rai, A.K.,  Taylor, G.,  Todd, M.H.,  Pineda-Lucena, A.,  Sali, A. and Marti-Renom, M.A.
"A kernel for open source drug discovery in tropical diseases"
PLoS Neglected Tropical Diseases (2009) 3 e18  
  

Grants

European Union. ERA-NET Pathogenomics. 2011-2014 [PIM2010EPA-00719].
A genome-wide approach for characterizing the mode of action of novel compounds against Tuberculosis (GeMoA).
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.
Valencia. Complementary Grant. 2009-2009 [ACOMP/2009/007].
Comparative docking of proteins and small molecules.
European Union. 6th Framework Programme. 2007-2010 [STREP018830].
Chemical Genomics by Activity Monitoring of Proteases.
Spain. MEC. Plan Nacional. 2007-2010 [BIO2007-66670].
Comparative docking of proteins and small molecules.
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