ZikaVR: An Integrated Zika Virus Resource for Genomics, Proteomics, Phylogenetic and Therapeutic Analysis

Scientific Reports

Volumn 6, Issue , 2016, Pages

  Gupta, Amit Kumar ^a   Kaur, Karambir ^a   Rajput, Akanksha ^a   Dhanda, Sandeep Kumar ^a   Sehgal, Manika ^a   Khan, Md Shoaib ^a   Monga, Isha ^a   Dar, Showkat Ahmad ^a   Singh, Sandeep ^a   Nagpal, Gandharva ^a   Usmani, Salman Sadullah ^a   Thakur, Anamika ^a   Kaur, Gazaldeep ^a   Sharma, Shivangi ^a   Bhardwaj, Aman ^a   Qureshi, Abid ^a   Raghava, Gajendra Pal Singh ^a   Kumar, Manoj ^a  

^a INSTITUTE OF MICROBIAL TECHNOLOGY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

VIRAL PROTEIN; VIRUS RNA;

ANIMAL; CLASSIFICATION; CODON; GENETICS; GLYCOSYLATION; HUMAN; METABOLISM; MOLECULAR DIAGNOSIS; MOLECULAR GENETICS; PHYLOGENY; PROTEOMICS; SOFTWARE; VIROLOGY; VIRUS GENOME; ZIKA FEVER; ZIKA VIRUS;

ANIMALS; CODON; GENOME, VIRAL; GLYCOSYLATION; HUMANS; MOLECULAR DIAGNOSTIC TECHNIQUES; MOLECULAR SEQUENCE ANNOTATION; PHYLOGENY; PROTEOMICS; RNA, VIRAL; SOFTWARE; VIRAL PROTEINS; ZIKA VIRUS; ZIKA VIRUS INFECTION;

EID: 84988442219     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep32713     Document Type: Article

References (111)

1. Hayes, E. B. Zika virus outside Africa. Emerg Infect Dis 15, 1347-1350, doi: 10. 3201/eid1509. 090442 (2009).
2. Dick, G. W., Kitchen, S. F., Haddow, A. J. Zika virus. I. Isolations and serological specificity. Trans R Soc Trop Med Hyg 46, 509-520 (1952).
3. Musso, D., Nilles, E. J., Cao-Lormeau, V. M. Rapid spread of emerging Zika virus in the Pacific area. Clin Microbiol Infect 20, O595-O596, doi: 10. 1111/1469-0691. 12707 (2014).
4. Oehler, E. et al. Zika virus infection complicated by Guillain-Barre syndrome-case report, French Polynesia, December 2013. Euro Surveill 19 (2014).
5. Tetro, J. A. Zika and microcephaly: causation, correlation, or coincidence? Microbes Infect 18, 167-168, doi: 10. 1016/j. micinf. 2015. 12. 010 (2016).
6. Schuler-Faccini, L. et al. Possible Association Between Zika Virus Infection and Microcephaly-Brazil, 2015. MMWR Morb Mortal Wkly Rep 65, 59-62, doi: 10. 15585/mmwr. mm6503e2 (2016).
7. Musso, D. et al. Potential sexual transmission of Zika virus. Emerg Infect Dis 21, 359-361, doi: 10. 3201/eid2102. 141363 (2015).
8. Foy, B. D. et al. Probable non-vector-borne transmission of Zika virus, Colorado, USA. Emerg Infect Dis 17, 880-882, doi: 10. 3201/eid1705. 101939 (2011).
9. McCrae, A. W., Kirya, B. G. Yellow fever and Zika virus epizootics and enzootics in Uganda. Trans R Soc Trop Med Hyg 76, 552-562 (1982).
10. Fagbami, A. H. Zika virus infections in Nigeria: virological and seroepidemiological investigations in Oyo State. J Hyg (Lond) 83, 213-219 (1979).
11. Robin, Y., Mouchet, J. Serological and entomological study on yellow fever in Sierra Leone. Bull Soc Pathol Exot Filiales 68, 249-258 (1975).
12. Jan, C., Languillat, G., Renaudet, J., Robin, Y. [A serological survey of arboviruses in Gabon]. Bull Soc Pathol Exot Filiales 71, 140-146 (1978).
13. Saluzzo, J. F., Gonzalez, J. P., Herve, J. P., Georges, A. J. Serological survey for the prevalence of certain arboviruses in the human population of the south-east area of Central African Republic (author's transl). Bull Soc Pathol Exot Filiales 74, 490-499 (1981).
14. Cao-Lormeau, V. M. et al. Zika virus, French polynesia, South pacific, 2013. Emerg Infect Dis 20, 1085-1086, doi: 10. 3201/eid2006. 140138 (2014).
15. Campos, G. S., Bandeira, A. C., Sardi, S. I. Zika Virus Outbreak, Bahia, Brazil. Emerg Infect Dis 21, 1885-1886, doi: 10. 3201/eid2110. 150847 (2015).
16. Kilbourn, A. M. et al. Health evaluation of free-ranging and semi-captive orangutans (Pongo pygmaeus pygmaeus) in Sabah, Malaysia. J Wildl Dis 39, 73-83, doi: 10. 7589/0090-3558-39. 1. 73 (2003).
17. Lanciotti, R. S. et al. Genetic and serologic properties of Zika virus associated with an epidemic, Yap State, Micronesia, 2007. Emerg Infect Dis 14, 1232-1239, doi: 10. 3201/eid1408. 080287 (2008).
18. Darwish, M. A., Hoogstraal, H., Roberts, T. J., Ahmed, I. P., Omar, F. A sero-epidemiological survey for certain arboviruses (Togaviridae) in Pakistan. Trans R Soc Trop Med Hyg 77, 442-445 (1983).
19. Heang, V. et al. Zika virus infection, Cambodia, 2010. Emerg Infect Dis 18, 349-351, doi: 10. 3201/eid1802. 111224 (2012).
20. Kuno, G., Chang, G. J. Full-length sequencing and genomic characterization of Bagaza, Kedougou, Zika viruses. Arch Virol 152, 687-696, doi: 10. 1007/s00705-006-0903-z (2007).
21. Centers for Disease Control and Prevention, http://www. cdc. gov/zika/symptoms/.
22. Chambers, T. J., Hahn, C. S., Galler, R., Rice, C. M. Flavivirus genome organization, expression, replication. Annu Rev Microbiol 44, 649-688, doi: 10. 1146/annurev. mi. 44. 100190. 003245 (1990).
23. Lindenbach, B. D., Rice, C. M. Molecular biology of flaviviruses. Adv Virus Res 59, 23-61 (2003).
24. Faye, O. et al. One-step RT-PCR for detection of Zika virus. J Clin Virol 43, 96-101, doi: 10. 1016/j. jcv. 2008. 05. 005 (2008).
25. Dyer, O. Zika vaccine could be in production by year's end, says maker. BMJ 352, i630, doi: 10. 1136/bmj. i630 (2016).
26. Cohen, J. INFECTIOUS DISEASE. The race for a Zika vaccine is on. Science 351, 543-544, doi: 10. 1126/science. 351. 6273. 543 (2016).
27. Fauci, A. S., Morens, D. M. Zika Virus in the Americas-Yet Another Arbovirus Threat. N Engl J Med 374, 601-604, doi: 10. 1056/NEJMp1600297 (2016).
28. Moriel, D. G. et al. Genome-based vaccine development: a short cut for the future. Hum Vaccin 4, 184-188 (2008).
29. Sette, A., Fikes, J. Epitope-based vaccines: an update on epitope identification, vaccine design and delivery. Curr Opin Immunol 15, 461-470 (2003).
30. Ben-Yedidia, T., Arnon, R. Epitope-based vaccine against influenza. Expert Rev Vaccines 6, 939-948, doi: 10. 1586/14760584. 6. 6. 939 (2007).
31. Koshy, R., Inchauspe, G. Evaluation of hepatitis C virus protein epitopes for vaccine development. Trends Biotechnol 14, 364-369, doi: 10. 1016/0167-7799(96)10049-4 (1996).
32. Sintchenko, V. Infectious disease informatics (Springer, 2010).
33. Efficacy and safety of RTS, S/AS01 malaria vaccine with or without a booster dose in infants and children in Africa: final results of a phase 3, individually randomised, controlled trial. Lancet 386, 31-45, doi: 10. 1016/s0140-6736(15)60721-8 (2015).
34. Oyarzun, P., Kobe, B. Recombinant and epitope-based vaccines on the road to the market and implications for vaccine design and production. Hum Vaccin Immunother 0, doi: 10. 1080/21645515. 2015. 1094595 (2015).
35. Davis, M. E. et al. Evidence of RNAi in humans from systemically administered siRNA via targeted nanoparticles. Nature 464, 1067-1070, doi: 10. 1038/nature08956 (2010).
36. Thakur, N., Qureshi, A., Kumar, M. VIRsiRNAdb: a curated database of experimentally validated viral siRNA/shRNA. Nucleic Acids Res 40, D230-D236, doi: 10. 1093/nar/gkr1147 (2012).
37. Ozcan, G., Ozpolat, B., Coleman, R. L., Sood, A. K., Lopez-Berestein, G. Preclinical and clinical development of siRNA-based therapeutics. Adv Drug Deliv Rev 87, 108-119, doi: 10. 1016/j. addr. 2015. 01. 007 (2015).
38. Burnett, J. C., Rossi, J. J., Tiemann, K. Current progress of siRNA/shRNA therapeutics in clinical trials. Biotechnol J 6, 1130-1146, doi: 10. 1002/biot. 201100054 (2011).
39. Haasnoot, P. C., Cupac, D., Berkhout, B. Inhibition of virus replication by RNA interference. J Biomed Sci 10, 607-616, doi: 73526 (2003).
40. Tiemann, K., Rossi, J. J. RNAi-based therapeutics-current status, challenges and prospects. EMBO Molecular Medicine 1, 142-151, doi: 10. 1002/emmm. 200900023 (2009).
41. Ashfaq, U. A. et al. siRNAs: Potential therapeutic agents against Hepatitis C Virus. Virology Journal 8, 276-276, doi: 10. 1186/1743-422x-8-276 (2011).
42. Geisbert, T. W. et al. Postexposure protection of non-human primates against a lethal Ebola virus challenge with RNA interference: a proof-of-concept study. Lancet 375, 1896-1905, doi: 10. 1016/s0140-6736(10)60357-1 (2010).
43. Dhanda, S. K., Chaudhary, K., Gupta, S., Brahmachari, S. K., Raghava, G. P. A web-based resource for designing therapeutics against Ebola Virus. Sci Rep 6, 24782, doi: 10. 1038/srep24782 (2016).
44. Lares, M. R., Rossi, J. J., Ouellet, D. L. RNAi and small interfering RNAs in human disease therapeutic applications. Trends Biotechnol 28, 570-579, doi: 10. 1016/j. tibtech. 2010. 07. 009 (2010).
45. Dar, S. A., Thakur, A., Qureshi, A., Kumar, M. siRNAmod: A database of experimentally validated chemically modified siRNAs. Sci Rep 6, 20031, doi: 10. 1038/srep20031 (2016).
46. Lodish, H. F., Zhou, B., Liu, G., Chen, C. Z. Micromanagement of the immune system by microRNAs. Nat Rev Immunol 8, 120-130, doi: 10. 1038/nri2252 (2008).
47. Shawan, M. M. A. K. et al. Design and Prediction of Potential RNAi (siRNA) Molecules for 3? UTR PTGS of Different Strains of Zika Virus: A Computational Approach. Nat. Sci 13, 37-50 (2015).
48. Shawan, M. M. A. et al. In Silico Modeling and Immunoinformatics Probing Disclose the Epitope Based PeptideVaccine Against Zika Virus Envelope Glycoprotein. Indian Journal of Pharmaceutical and Biological Research 2, 44 (2014).
49. Mali, P. et al. RNA-guided human genome engineering via Cas9. Science 339, 823-826, doi: 10. 1126/science. 1232033 (2013).
50. Price, A. A., Sampson, T. R., Ratner, H. K., Grakoui, A., Weiss, D. S. Cas9-mediated targeting of viral RNA in eukaryotic cells. Proc Natl Acad Sci USA 112, 6164-6169, doi: 10. 1073/pnas. 1422340112 (2015).
51. Kaur, K., Tandon, H., Gupta, A. K., Kumar, M. CrisprGE: a central hub of CRISPR/Cas-based genome editing. Database (Oxford) 2015, 55, doi: 10. 1093/database/bav055 (2015).
52. Dudley, J. T., Deshpande, T., Butte, A. J. Exploiting drug-disease relationships for computational drug repositioning. Brief Bioinform 12, 303-311, doi: 10. 1093/bib/bbr013 (2011).
53. Ashburn, T. T., Thor, K. B. Drug repositioning: identifying and developing new uses for existing drugs. Nat Rev Drug Discov 3, 673-683, doi: 10. 1038/nrd1468 (2004).
54. Khan, M. S., Gupta, A. K., Kumar, M. ViralEpi v1. 0: a high-throughput spectrum of viral epigenomic methylation profiles from diverse diseases. Epigenomics 8, 67-75, doi: 10. 2217/epi. 15. 95 (2016).
55. Kumar Gupta, A., Kumar, M. HPVbase-a knowledgebase of viral integrations, methylation patterns and microRNAs aberrant expression: As potential biomarkers for Human papillomaviruses mediated carcinomas. Sci Rep 5, 12522, doi: 10. 1038/srep12522 (2015).
56. Kostyuchenko, V. A. et al. Structure of the thermally stable Zika virus. Nature 533, 425-428, doi: 10. 1038/nature17994 (2016).
57. Sirohi, D. et al. The 3. 8 A resolution cryo-EM structure of Zika virus. Science 352, 467-470, doi: 10. 1126/science. aaf5316 (2016).
58. Song, H., Qi, J., Haywood, J., Shi, Y., Gao, G. F. Zika virus NS1 structure reveals diversity of electrostatic surfaces among flaviviruses. Nat Struct Mol Biol 23, 456-458, doi: 10. 1038/nsmb. 3213 (2016).
59. Dai, L. et al. Structures of the Zika Virus Envelope Protein and Its Complex with a Flavivirus Broadly Protective Antibody. Cell Host Microbe 19, 696-704, doi: 10. 1016/j. chom. 2016. 04. 013 (2016).
60. Tian, H. et al. The crystal structure of Zika virus helicase: basis for antiviral drug design. Protein Cell 7, 450-454, doi: 10. 1007/s13238-016-0275-4 (2016).
61. Roy, A., Kucukural, A., Zhang, Y. I-TASSER: a unified platform for automated protein structure and function prediction. Nat Protoc 5, 725-738, doi: 10. 1038/nprot. 2010. 5 (2010).
62. Ye, Q. et al. Genomic characterization and phylogenetic analysis of Zika virus circulating in the Americas. Infect Genet Evol 43, 43-49, doi: 10. 1016/j. meegid. 2016. 05. 004 (2016).
63. Shen, S. et al. Phylogenetic analysis revealed the central roles of two African countries in the evolution and worldwide spread of Zika virus. Virol Sin 31, 118-130, doi: 10. 1007/s12250-016-3774-9 (2016).
64. Lednicky, J. et al. Zika Virus Outbreak in Haiti in 2014: Molecular and Clinical Data. PLoS Negl Trop Dis 10, e0004687, doi: 10. 1371/journal. pntd. 0004687 (2016).
65. Lanciotti, R. S., Lambert, A. J., Holodniy, M., Saavedra, S., Signor Ldel, C. Phylogeny of Zika Virus in Western Hemisphere, 2015. Emerg Infect Dis 22, 933-935, doi: 10. 3201/eid2205. 160065 (2016).
66. Haddow, A. D. et al. Genetic characterization of Zika virus strains: geographic expansion of the Asian lineage. PLoS Negl Trop Dis 6, e1477, doi: 10. 1371/journal. pntd. 0001477 (2012).
67. Vigerust, D. J., Shepherd, V. L. Virus glycosylation: role in virulence and immune interactions. Trends Microbiol 15, 211-218, doi: 10. 1016/j. tim. 2007. 03. 003 (2007).
68. Chambers, T. J., Halevy, M., Nestorowicz, A., Rice, C. M., Lustig, S. West Nile virus envelope proteins: nucleotide sequence analysis of strains differing in mouse neuroinvasiveness. J Gen Virol 79 (Pt 10), 2375-2380, doi: 10. 1099/0022-1317-79-10-2375 (1998).
69. Faye, O. et al. Molecular evolution of Zika virus during its emergence in the 20(th) century. PLoS Negl Trop Dis 8, e2636, doi: 10. 1371/journal. pntd. 0002636 (2014).
70. Van den Steen, P., Rudd, P. M., Dwek, R. A., Opdenakker, G. Concepts and principles of O-linked glycosylation. Crit Rev Biochem Mol Biol 33, 151-208, doi: 10. 1080/10409239891204198 (1998).
71. Goto, Y. et al. C-mannosylation of human hyaluronidase 1: possible roles for secretion and enzymatic activity. Int J Oncol 45, 344-350, doi: 10. 3892/ijo. 2014. 2438 (2014).
72. Stowell, S. R., Ju, T., Cummings, R. D. Protein glycosylation in cancer. Annu Rev Pathol 10, 473-510, doi: 10. 1146/annurevpathol-012414-040438 (2015).
73. Li, X., Wang, X., Tan, Z., Chen, S., Guan, F. Role of Glycans in Cancer Cells Undergoing Epithelial-Mesenchymal Transition. Front Oncol 6, 33, doi: 10. 3389/fonc. 2016. 00033 (2016).
74. Faye, O. et al. Quantitative real-time PCR detection of Zika virus and evaluation with field-caught mosquitoes. Virol J 10, 311, doi: 10. 1186/1743-422x-10-311 (2013).
75. Qureshi, A., Thakur, N., Kumar, M. VIRsiRNApred: a web server for predicting inhibition efficacy of siRNAs targeting human viruses. J Transl Med 11, 305, doi: 10. 1186/1479-5876-11-305 (2013).
76. Crotty, S., Cameron, C., Andino, R. Ribavirin's antiviral mechanism of action: lethal mutagenesis? J Mol Med (Berl) 80, 86-95, doi: 10. 1007/s00109-001-0308-0 (2002).
77. Balzarini, J., De Clercq, E., Serafinowski, P., Dorland, E., Harrap, K. R. Synthesis and antiviral activity of some new S-adenosyl-Lhomocysteine derivatives. J Med Chem 35, 4576-4583 (1992).
78. Castresana, J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17, 540-552 (2000).
79. Krumsiek, J., Arnold, R., Rattei, T. Gepard: a rapid and sensitive tool for creating dotplots on genome scale. Bioinformatics 23, 1026-1028, doi: 10. 1093/bioinformatics/btm039 (2007).
80. Rajput, A., Gupta, A. K., Kumar, M. Prediction and analysis of quorum sensing peptides based on sequence features. PLoS One 10, e0120066, doi: 10. 1371/journal. pone. 0120066 (2015).
81. Thakur, N., Qureshi, A., Kumar, M. AVPpred: collection and prediction of highly effective antiviral peptides. Nucleic Acids Res 40, W199-W204, doi: 10. 1093/nar/gks450 (2012).
82. Webb, B., Sali, A. Comparative Protein Structure Modeling Using MODELLER. Curr Protoc Bioinformatics 47, 561-32, doi: 10. 1002/0471250953. bi0506s47 (2014).
83. Fu, L., Niu, B., Zhu, Z., Wu, S., Li, W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28, 3150-3152, doi: 10. 1093/bioinformatics/bts565 (2012).
84. Yang, J. et al. The I-TASSER Suite: protein structure and function prediction. Nat Methods 12, 7-8, doi: 10. 1038/nmeth. 3213 (2015).
85. Tamura, K., Stecher, G., Peterson, D., Filipski, A., Kumar, S. MEGA6: Molecular Evolutionary Genetics Analysis version 6. 0. Mol Biol Evol 30, 2725-2729, doi: 10. 1093/molbev/mst197 (2013).
86. Chenna, R. et al. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 31, 3497-3500 (2003).
87. Behura, S. K., Severson, D. W. Comparative analysis of codon usage bias and codon context patterns between dipteran and hymenopteran sequenced genomes. PLoS One 7, e43111, doi: 10. 1371/journal. pone. 0043111 (2012).
88. Moura, G. et al. Comparative context analysis of codon pairs on an ORFeome scale. Genome Biol 6, R28, doi: 10. 1186/gb-2005-6-3-r28 (2005).
89. Julenius, K. NetCGlyc 1. 0: prediction of mammalian C-mannosylation sites. Glycobiology 17, 868-876, doi: 10. 1093/glycob/cwm050 (2007).
90. Julenius, K., Molgaard, A., Gupta, R., Brunak, S. Prediction, conservation analysis, structural characterization of mammalian mucin-type O-glycosylation sites. Glycobiology 15, 153-164, doi: 10. 1093/glycob/cwh151 (2005).
91. Gupta, R., Brunak, S. Prediction of glycosylation across the human proteome and the correlation to protein function. Pac Symp Biocomput 310-322 (2002).
92. Blom, N., Sicheritz-Ponten, T., Gupta, R., Gammeltoft, S., Brunak, S. Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Proteomics 4, 1633-1649, doi: 10. 1002/pmic. 200300771 (2004).
93. Yoon, H., Leitner, T. PrimerDesign-M: a multiple-alignment based multiple-primer design tool for walking across variable genomes. Bioinformatics 31, 1472-1474, doi: 10. 1093/bioinformatics/btu832 (2015).
94. Abecasis, G. R. et al. An integrated map of genetic variation from 1, 092 human genomes. Nature 491, 56-65, doi: 10. 1038/nature11632 (2012).
95. Singh, H., Ansari, H. R., Raghava, G. P. Improved method for linear B-cell epitope prediction using antigen's primary sequence. PLoS One 8, e62216, doi: 10. 1371/journal. pone. 0062216 (2013).
96. Ansari, H. R., Raghava, G. P. Identification of conformational B-cell Epitopes in an antigen from its primary sequence. Immunome Res 6, 6, doi: 10. 1186/1745-7580-6-6 (2010).
97. Singh, H., Raghava, G. P. ProPred1: prediction of promiscuous MHC Class-I binding sites. Bioinformatics 19, 1009-1014 (2003).
98. Bhasin, M., Raghava, G. P. Prediction of CTL epitopes using QM, SVM and ANN techniques. Vaccine 22, 3195-3204, doi: 10. 1016/j. vaccine. 2004. 02. 005 (2004).
99. Singh, H., Raghava, G. P. ProPred: prediction of HLA-DR binding sites. Bioinformatics 17, 1236-1237 (2001).
100. Kim, Y. et al. Immune epitope database analysis resource. Nucleic Acids Res 40, W525-W530, doi: 10. 1093/nar/gks438 (2012).
101. Dhanda, S. K., Vir, P., Raghava, G. P. Designing of interferon-gamma inducing MHC class-II binders. Biol Direct 8, 30, doi: 10. 1186/1745-6150-8-30 (2013).
102. Dhanda, S. K., Gupta, S., Vir, P., Raghava, G. P. Prediction of IL4 inducing peptides. Clin Dev Immunol 2013, 263952, doi: 10. 1155/2013/263952 (2013).
103. Ahmed, F., Raghava, G. P. Designing of highly effective complementary and mismatch siRNAs for silencing a gene. PLoS One 6, e23443, doi: 10. 1371/journal. pone. 0023443 (2011).
104. Chaudhary, K., Nagpal, G., Dhanda, S. K., Raghava, G. P. Prediction of Immunomodulatory potential of an RNA sequence for designing non-toxic siRNAs and RNA-based vaccine adjuvants. Sci Rep 6, 20678, doi: 10. 1038/srep20678 (2016).
105. Sullivan, C. S., Grundhoff, A. Identification of viral microRNAs. Methods Enzymol 427, 3-23, doi: 10. 1016/s0076-6879(07)27001-6 (2007).
106. Gkirtzou, K., Tsamardinos, I., Tsakalides, P., Poirazi, P. MatureBayes: a probabilistic algorithm for identifying the mature miRNA within novel precursors. PLoS One 5, e11843, doi: 10. 1371/journal. pone. 0011843 (2010).
107. Qureshi, A., Thakur, N., Monga, I., Thakur, A., Kumar, M. VIRmiRNA: a comprehensive resource for experimentally validated viral miRNAs and their targets. Database (Oxford) 2014, doi: 10. 1093/database/bau103 (2014).
108. Hofacker, I. L., Stadler, P. F. Memory efficient folding algorithms for circular RNA secondary structures. Bioinformatics 22, 1172-1176, doi: 10. 1093/bioinformatics/btl023 (2006).
109. Law, V. et al. DrugBank 4. 0: shedding new light on drug metabolism. Nucleic Acids Res 42, D1091-D1097, doi: 10. 1093/nar/gkt1068 (2014).
110. Rajput, A., Kaur, K., Kumar, M. SigMol: repertoire of quorum sensing signaling molecules in prokaryotes. Nucleic Acids Res 44, D634-D639, doi: 10. 1093/nar/gkv1076 (2016).
111. Qureshi, A., Thakur, N., Tandon, H., Kumar, M. AVPdb: a database of experimentally validated antiviral peptides targeting medically important viruses. Nucleic Acids Res 42, D1147-D1153, doi: 10. 1093/nar/gkt1191 (2014).