TiPs: a database of therapeutic targets in pathogens and associated tools

Motivation: The need for new drugs and new targets is particularly compelling in an era that is witnessing an alarming increase of drug resistance in human pathogens. The identification of new targets of known drugs is a promising approach, which has proven successful in several cases. Here, we describe a database that includes information on 5153 putative drug–target pairs for 150 human pathogens derived from available drug–target crystallographic complexes. Availability and implementation: The TiPs database is freely available at http://biocomputing.it/tips. Contact: anna.tramontano@uniroma1.it or allegra.via@uniroma1.it

[1]  Torsten Schwede,et al.  Automated protein structure homology modeling: a progress report. , 2004, Pharmacogenomics.

[2]  Roman A. Laskowski,et al.  LigPlot+: Multiple Ligand-Protein Interaction Diagrams for Drug Discovery , 2011, J. Chem. Inf. Model..

[3]  Adam Zemla,et al.  LGA: a method for finding 3D similarities in protein structures , 2003, Nucleic Acids Res..

[4]  John P. Overington,et al.  Rapid Analysis of Pharmacology for Infectious Diseases , 2011, Current topics in medicinal chemistry.

[5]  G. V. Paolini,et al.  Global mapping of pharmacological space , 2006, Nature Biotechnology.

[6]  Ning Ma,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

[7]  Haruki Nakamura,et al.  The Protein Data Bank at 40: reflecting on the past to prepare for the future. , 2012, Structure.

[8]  Carsten Kemena,et al.  Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures , 2011, Nature Protocols.

[9]  Narayanan Eswar,et al.  A Kernel for Open Source Drug Discovery in Tropical Diseases , 2009, PLoS neglected tropical diseases.

[10]  John P. Overington,et al.  Genomic-scale prioritization of drug targets: the TDR Targets database , 2008, Nature Reviews Drug Discovery.

[11]  A. Biegert,et al.  HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment , 2011, Nature Methods.

[12]  Philip E. Bourne,et al.  The Mycobacterium tuberculosis Drugome and Its Polypharmacological Implications , 2010, PLoS Comput. Biol..

[13]  Anna Tramontano,et al.  Identification of the Schistosoma mansoni Molecular Target for the Antimalarial Drug Artemether , 2011, J. Chem. Inf. Model..