| ||
| 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. et.al. (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] |