CancerDR: Cancer Drug Resistance Database

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Acknowledgement Page

We are grateful to researchers for their direct and indirect help in the development of this database. In this database we used information from various resources/databases as well as we used number of software/web services for developing this database. We are grateful to the developers of these databases/software/resources that include following resources.

Name of Resource/Database/Software Reference or Publications
COSMIC: Data of 138 anti-cancer drugs tested across 714 cell lines has been taken from COSMIC database. We acknowledge the COSMIC database developers.

Garnetti, M.J. et. al., (2012), Systematic identification of genomic markers of drug sensitivity in cancer cells. 483: 570-575. [PMID: 22460902]

CCLE: Pharmacological data of 24 drugs tested against 503 cancer cell lines has been taken from CCLE along with the mutational data of drug targets. We acknowledge the developers of CCLE.

Barretina, J. et. al. (2012), The Cancer Cell Line Encyclopedia enables predictive modeling of anticancer drug sensitivity. 483: 603-607. [PMID: 22460905]

BWA: In this database, short reads are aligned to the reference human genome using BWA software, which finally gives contigs. We are thankful to the developers of BWA.

BWA (Burrows-Wheeler Aligner):The short read alignment component (bwa-short) has been published:Li H. and Durbin R. (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics, 25:1754-60. [PMID: 19451168]

Tablet Viewer: To view the aligned short reads and contigs, powerful visualization software Tablet viewer is used in CancerDR. We acknowledge the developers of Tablet viewer software.

Tablet -Next Generation Sequence Assembly Visualization: Milne, I, Bayer, M, Cardle, L, Shaw, P, Stephen, G, Wright, F and Marshall, D. 2010. Tablet - next generation sequence assembly visualization. Bioinformatics 26(3), 401-402. [PMID:19965881]

BLAST: For fast sequence comparison of drug targets with the user-defined sequence (protein/nucleotide), BLAST software has been used. We acknowledge the BLAST developers.

BLAST : Altschul S.F., Gish W., Miller W., Myers E.W. and Lipman D.J. (1990) Basic local alignment search tool. J. Mol. Biol. 215: 403-410. [PMID:2231712]

HHblits: This software is used to generate the alignment file (used as input for MODELLER) in a fast and more efficient mannner. We acknowledge the team of HHblits.

Remmert M, Biegert A, Hauser A, Soding J., (2011), Nat Methods., 9: 173-175. HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment.[PMID:22198341]

Jalview: In this database we visualize multiple alignment of target mutants and variants using Jalview. We are thankful to developers for providing applet version of Jalview which we have integrated in CancerDR

Jalview is a multiple alignment editor: Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)" Jalview Version 2 - a multiple sequence alignment editor and analysis workbench" Bioinformatics 25 (9) 1189-1191. [PMID:19151095 ]

Jmol: JmolApplet has been integrated in various modules to represent the structure of mutants/variants and drug targets in 3D interactively; where user can change the colour, style etc. of the structures being represented. We acknowledge the JmolApplet developers.

Jmol: an open-source Java viewer for chemical structures in 3D.[Jmol]

MODELLER: For comparative protein structure prediction of mutants of various drug targets, MODELLER software has been used. We are thankful to the developers of this software.

Eswar, N. (2006), Comparative Protein Structure Modeling With MODELLER. Current Protocols in Bioinformatics, John Wiley & Sons, Inc., Supplement 15, 5.6.1-5.6.30. [PMID:18428767]

MUSTANG: In CancerDR, structural alignment of targets with their mutants/variants is performed with MUSTANG software. We are thankful to the developers of this software.

Konagurthu, A.S., Whisstock, J.C., Stuckey, P.J. and Lesk, A.M. (2006), MUSTANG: a multiple structural alignment algorithm. Proteins, 64(3): 559-74. [PMID:16736488]

PubChem: PubChem database has been used to collect the information regarding anti-cancer drugs. We acknowledge the PubChem team.

Bolton E, W.Y., Thiessen PA, Bryant SH. (2008), PubChem: Integrated Platform of Small Molecules and Biological Activities. Annual Reports in Computational Chemistry, Volume 4. Link

PSIPRED: Protein secondary structure has been predicted by the PSIPRED software. We acknowledge the PSIPRED developers.

Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol., 292: 195-202.[PMID: 10493868]