Skip to main content

Role of Bioinformatics in Drug Design and Discovery

  • Chapter
  • First Online:
CADD and Informatics in Drug Discovery

Abstract

Bioinformatics can speed up the identification of therapeutic targets, screening drug candidates, and refinement of those candidates. It can also make it easier to characterise side effects and anticipate drug resistance. Data from transcriptomic, proteomic, transcriptomic architecture, ribosome profiling, epigenetic, cistromic, and genomic sources, among other high-throughput data, have all contributed significantly to the development of mechanism-based drugs and pharmacological repurposing. Large-scale databases of tiny chemicals’ structures and metabolites, along with the building up of RNA and protein structures, predictions of protein structure and homology mapping, provided the ground for much accurate docking of protein and compound investigations and much insightful virtual refining. The outlined conceptual framework underpins the high-throughput data storage, summarises the value and mining potential for these data for drugs, and points out some underlying restrictions inside the data and the programs used to mine them, indicating novel approaches to improve examination of these different information formats, highlighting popular libraries, and software that are pertinent to drugs.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 189.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 249.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Free shipping worldwide - see info
Hardcover Book
USD 249.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  • Abdel-Hameed EA, Ji H, Shata MT (2016) HIV-induced epigenetic alterations in host cells. Adv Exp Med Biol 879:27–38. https://doi.org/10.1007/978-3-319-24738-0_2

    Article  CAS  PubMed  Google Scholar 

  • Abraham EP, Chain E (1940) An enzyme from bacteria able to destroy penicillin. Rev Infect Dis 10(3):677–678. https://doi.org/10.1038/146837a0

    Article  Google Scholar 

  • Abraham EP, Chain E, Fletcher CM, Florey HW, Gardner AD, Heatley NG, Jennings MA (1941) Further observations on penicillin. Lancet 238:177–189. https://doi.org/10.1016/S0140-6736(00)72122-2

    Article  Google Scholar 

  • Alderwick LJ, Seidel M, Sahm H, Besra GS, Eggeling L (2006) Identification of a novel arabinofuranosyltransferase (AftA) involved in cell wall arabinan biosynthesis in Mycobacterium tuberculosis. J Biol Chem 281(23):15653–15661. https://doi.org/10.1074/jbc.M600045200

    Article  CAS  PubMed  Google Scholar 

  • Anisimova M (2015) Darwin and Fisher meet at biotech: on the potential of computational molecular evolution in industry. BMC Evol Biol 15(1):76. https://doi.org/10.1186/s12862-015-0352-y

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Arava Y, Wang Y, Storey JD, Liu CL, Brown PO, Herschlag D (2003) Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 100(7):3889–3894. https://doi.org/10.1073/pnas.0635171100

    Article  CAS  PubMed Central  Google Scholar 

  • Arbibe L, Sansonetti PJ (2007) Epigenetic regulation of host response to LPS: causing tolerance while avoiding toll errancy. Cell Host Microbe 1(4):244–246. https://doi.org/10.1016/j.chom.2007.05.011

    Article  CAS  PubMed  Google Scholar 

  • Arvaniti E, Moulos P, Vakrakou A, Chatziantoniou C, Chadjichristos C, Kavvadas P, Charonis A, Politis PK (2016) Whole transcriptome analysis of UUO mouse model of renal fibrosis reveals new molecular players in kidney diseases. Sci Rep 6:26235. https://doi.org/10.1038/srep26235

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Averof M, Rokas A, Wolfe KH, Sharp PM (2000) Evidence for a high frequency of simultaneous double-nucleotide substitutions. Science 287(5456):1283–1286. https://doi.org/10.1126/science.287.5456.1283

    Article  CAS  PubMed  Google Scholar 

  • Baird AL, Westwood S, Lovestone S (2015) Blood-based proteomic biomarkers of Alzheimer’s disease pathology. Front Neurol 6:236. https://doi.org/10.3389/fneur.2015.00236

    Article  PubMed  PubMed Central  Google Scholar 

  • Bao J, Bedford MT (2016) Epigenetic regulation of the histone-toprotamine transition during spermiogenesis. Reproduction 151(5):R55–R70. https://doi.org/10.1530/REP-15-0562

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bastianelli G, Bouillon A, Nguyen C, Crublet E, Petres S, Gorgette O, Le-Nguyen D, Barale JC, Nilges M (2011) Computational reverse-engineering of a spider-venom derived peptide active against Plasmodium falciparum SUB1. PLoS One 6(7):e21812. https://doi.org/10.1371/journal.pone.0021812

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bauer RA, Gunther S, Jansen D, Heeger C, Thaben PF, Preissner R (2009) SuperSite: dictionary of metabolite and drug binding sites in proteins. Nucleic Acids Res 37(Database issue):D195–D200. https://doi.org/10.1093/nar/gkn618

    Article  CAS  Google Scholar 

  • Belanger AE, Lai A, Brackman MA, LeBlanc DJ (2002) PCR based ordered genomic libraries: a new approach to drug target identification for Streptococcus pneumoniae. Antimicrob Agents Chemother 46(8):2507–2512. https://doi.org/10.1128/AAC.46.8.2507-2512.2002

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bell D, Bell AH, Bondaruk J, Hanna EY, Weber RS (2016) In-depth characterization of the salivary adenoid cystic carcinoma transcriptome with emphasis on dominant cell type. Cancer 122(10):1513–1522. https://doi.org/10.1002/cncr.29959

    Article  CAS  PubMed  Google Scholar 

  • Berger MF, Levin JZ, Vijayendran K, Sivachenko A, Adiconis X, Maguire J, Johnson LA, Robinson J, Verhaak RG, Sougnez C, Onofrio RC, Ziaugra L, Cibulskis K, Laine E, Barretina J, Winckler W, Fisher DE, Getz G, Meyerson M, Jaffe DB, Gabriel SB, Lander ES, Dummer R, Gnirke A, Nusbaum C, Garraway LA (2010) Integrative analysis of the melanoma transcriptome. Genome Res 20(4):413–427. https://doi.org/10.1101/gr.103697.109

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bergsten E, Uutela M, Li X, Pietras K, Ostman A, Heldin CH, Alitalo K, Eriksson U (2001) PDGF-D is a specific, protease activated ligand for the PDGF beta-receptor. Nat Cell Biol 3(5):512–516. https://doi.org/10.1038/35074588

    Article  CAS  PubMed  Google Scholar 

  • Beverley SM, Owens KL, Showalter M, Griffith CL, Doering TL, Jones VC, McNeil MR (2005) Eukaryotic UDP-galactopyranose mutase (GLF gene) in microbial and metazoal pathogens. Eukaryot Cell 4(6):1147–1154. https://doi.org/10.1128/EC.4.6.1147-1154.2005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bhatia B, Ponia SS, Solanki AK, Dixit A, Garg LC (2014) Identification of glutamate ABC-Transporter component in Clostridium perfringens as a putative drug target. Bioinformation 10(7):401–405. https://doi.org/10.6026/97320630010401

    Article  PubMed  PubMed Central  Google Scholar 

  • Biasini M, Bienert S, Waterhouse A, Arnold K, Studer G, Schmidt T, Kiefer F, Gallo Cassarino T, Bertoni M, Bordoli L, Schwede T (2014) SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res 42(Web Server issue):W252–W258. https://doi.org/10.1093/nar/gku340

    Article  CAS  Google Scholar 

  • Bibikova M, Barnes B, Tsan C, Ho V, Klotzle B, Le JM, Delano D, Zhang L, Schroth GP, Gunderson KL, Fan JB, Shen R (2011) High density DNA methylation array with single CpG site resolution. Genomics 98(4):288–295. https://doi.org/10.1016/j.ygeno.2011.07.007

    Article  CAS  PubMed  Google Scholar 

  • Bierne H, Hamon M, Cossart P (2012) Epigenetics and bacterial infections. Cold Spring Harb Perspect Med 2(12):a010272. https://doi.org/10.1101/cshperspect.a010272

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bigaud E, Corrales FJ (2016) Methylthioadenosine (MTA) regulates liver cells proteome and methylproteome: implications in liver biology and disease. Mol Cell Proteomics 15(5):1498–1510. https://doi.org/10.1074/mcp.M115.055772

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Birney E, Stamatoyannopoulos JA et al (2007) Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 447(7146):799–816. https://doi.org/10.1038/nature05874

    Article  CAS  PubMed  Google Scholar 

  • Boehringer D, Thermann R, Ostareck-Lederer A, Lewis JD, Stark H (2005) Structure of the hepatitis C virus IRES bound to the human 80S ribosome: remodeling of the HCV IRES. Structure 13(11):1695–1706. https://doi.org/10.1016/j.str.2005.08.008

    Article  CAS  PubMed  Google Scholar 

  • Bolden JE, Peart MJ, Johnstone RW (2006) Anticancer activities of histone deacetylase inhibitors. Nat Rev Drug Discov 5(9):769–784. https://doi.org/10.1038/nrd2133

    Article  CAS  PubMed  Google Scholar 

  • Boxall AB, Rudd MA, Brooks BW, Caldwell DJ, Choi K, Hickmann S, Innes E, Ostapyk K, Staveley JP et al (2012) Pharmaceuticals and personal care products in the environment: what are the big questions? Environ Health Perspect 120(9):1221–1229. https://doi.org/10.1289/ehp.1104477

    Article  PubMed  PubMed Central  Google Scholar 

  • Broglia R, Levy Y, Tiana G (2008) HIV-1 protease folding and the design of drugs which do not create resistance. Curr Opin Struct Biol 18(1):60–66. https://doi.org/10.1016/j.sbi.2007.10.004

    Article  CAS  PubMed  Google Scholar 

  • Brooks BR, Brooks CL 3rd, Mackerell AD Jr, Nilsson L, Petrella RJ, Roux B, Won Y, Archontis G, Bartels C, Boresch S, Caflisch A, Caves L, Cui Q, Dinner AR, Feig M, Fischer S, Gao J, Hodoscek M, Im W, Kuczera K, Lazaridis T, Ma J, Ovchinnikov V, Paci E, Pastor RW, Post CB, Pu JZ, Schaefer M, Tidor B, Venable RM, Woodcock HL, Wu X, Yang W, York DM, Karplus M (2009) CHARMM: the biomolecular simulation program. J Comput Chem 30(10):1545–1614. https://doi.org/10.1002/jcc.21287

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Brucher BL, Jamall IS (2016) Somatic mutation theory - why it’s wrong for most cancers. Cell Physiol Biochem 38(5):1663–1680. https://doi.org/10.1159/000443106

    Article  CAS  PubMed  Google Scholar 

  • Cardon LR, Burge C, Clayton DA, Karlin S (1994) Pervasive CpG suppression in animal mitochondrial genomes. Proc Natl Acad Sci U S A 91(9):3799–3803. https://doi.org/10.1073/pnas.91.9.3799

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chan WK, Zhang H, Yang J, Brender JR, Hur J, Ozgur A, Zhang Y (2015) GLASS: a comprehensive database for experimentally validated GPCR-ligand associations. Bioinformatics 31(18):3035–3042. https://doi.org/10.1093/bioinformatics/btv302

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen Q, Yan M, Cao Z, Li X, Zhang Y, Shi J, Feng GH, Peng H, Zhang X, Qian J, Duan E, Zhai Q, Zhou Q (2016) Sperm tsRNAs contribute to intergenerational inheritance of an acquired metabolic disorder. Science 351(6271):397–400. https://doi.org/10.1126/science.aad7977

    Article  CAS  PubMed  Google Scholar 

  • Chithambaram S, Prabhakaran R, Xia X (2014a) Differential codon adaptation between dsDNA and ssDNA Phages in Escherichia coli. Mol Biol Evol 31(6):1606–1617. https://doi.org/10.1093/molbev/msu087

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chithambaram S, Prabhakaran R, Xia X (2014b) The effect of mutation and selection on codon adaptation in Escherichia coli bacteriophage. Genetics 197(1):301–315. https://doi.org/10.1534/genetics.114.162842

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chu C, Qu K, Zhong FL, Artandi SE, Chang HY (2011) Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol Cell 44(4):667–678. https://doi.org/10.1016/j.molcel.2011.08.027

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chu C, Quinn J, Chang HY (2012) Chromatin isolation by RNA purification (ChIRP). J Vis Exp 61:3912. https://doi.org/10.3791/3912

    Article  CAS  Google Scholar 

  • Clark AT (2015) DNA methylation remodeling in vitro and in vivo. Curr Opin Genet Dev 34:82–87

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Daily K, Patel VR, Rigor P, Xie X, Baldi P (2011) MotifMap: integrative genome-wide maps of regulatory motif sites for model species. BMC Bioinform 12:495

    Article  Google Scholar 

  • David E, Tramontin T, Zemmel R (2009) Pharmaceutical R & D: the road to positive returns. Nat Rev Drug Discov 8:609–610

    Article  CAS  PubMed  Google Scholar 

  • Davies J, Davies D (2010) Origins and evolution of antibiotic resistance. Microbiol Mol Biol Rev 74:417–433

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Deng W, Lee J, Wang H, Miller J, Reik A, Gregory PD, Dean A, Blobel GA (2012) Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor. Cell 149:233–1244

    Article  Google Scholar 

  • Deng Q, Ramskold D, Reinius B, Sandberg R (2014a) Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells. Science 343:193–196

    Article  CAS  PubMed  Google Scholar 

  • Deng W, Rupon JW, Krivega I, Breda L, Motta I, Jahn KS, Reik A, Gregory PD, Rivella S, Dean A, Blobel GA (2014b) Reactivation of developmentally silenced globin genes by forced chromatin looping. Cell 158:849–860

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ding H, Takigawa I, Mamitsuka H, Zhu S (2014) Similarity-based machine learning methods for predicting drug-target interactions: a brief review. Brief Bioinform 15:734–747

    Article  PubMed  Google Scholar 

  • Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR (2013) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29:15–21

    Article  CAS  PubMed  Google Scholar 

  • Doolittle RF, Hunkapiller MW, Hood LE, Devare SG, Robbins KC, Aaronson SA, Antoniades HN (1983) Simian sarcoma virus onc gene, v-sis, is derived from the gene (or genes) encoding a platelet-derived growth factor. Science 221:275–277

    Article  CAS  PubMed  Google Scholar 

  • Doudna JA, Sarnow P, Mathews MB, Sonenberg N, Hershey J (2007) Translation initiation by viral internal ribosome entry sites. In: Translational control in biology and medicine. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, pp 129–154

    Google Scholar 

  • Drake JW (1964) Studies on the induction of mutations in bacteriophage t4 by ultraviolet irradiation and by proflavin. J Cell Physiol 64(SUPPL 1):19–31

    Article  CAS  Google Scholar 

  • Drake JW (1966) Spontaneous mutations accumulating in bacteriophage T4 in the complete absence of DNA replication. Proc Natl Acad Sci U S A 55:738–743

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Drake JW (2007a) Mutations in clusters and showers. Proc Natl Acad Sci U S A 104:8203–8204

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Drake JW (2007b) Too many mutants with multiple mutations. Crit Rev Biochem Mol Biol 42:247–258

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Drake JW, Bebenek A, Kissling GE, Peddada S (2005) Clusters of mutations from transient hypermutability. Proc Natl Acad Sci U S A 102:12849–12854

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Drews J, Ryser S (1997) The role of innovation in drug development. Nat Biotechnol 15:1318–1319

    Article  CAS  PubMed  Google Scholar 

  • Dykeman EC, Stockley PG, Twarock R (2013) Packaging signals in two single-stranded RNA viruses imply a conserved assembly mechanism and geometry of the packaged genome. J Mol Biol 425:3235–3249

    Article  CAS  PubMed  Google Scholar 

  • Eckhardt F, Lewin J, Cortese R, Rakyan VK et al (2006) DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet 38:1378–1385

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Eder J, Sedrani R, Wiesmann C (2014) The discovery of first-in-class drugs: origins and evolution. Nat Rev Drug Discov 13:577–587

    Article  CAS  PubMed  Google Scholar 

  • Ehnman M, Missiaglia E et al (2013) Distinct effects of ligand-induced PDGFR alpha and PDGFR beta signaling in the human rhabdomyosarcoma tumor cell and stroma cell compartments. Cancer Res 73:2139–2149

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ekins S, de Siqueira-Neto JL, McCall LI, Sarker M, Yadav M, Ponder EL, Kallel EA, Kellar D, Chen S, Arkin M, Bunin BA, McKerrow JH, Talcott C (2015) Machine learning models and pathway genome data base for Trypanosoma cruzi drug discovery. PLoS Negl Trop Dis 9:e0003878

    Article  PubMed  PubMed Central  Google Scholar 

  • Elroy-Stein O, Merrick W, Mathews MB, Sonenberg N, Hershey J (2007) Translation initiation via cellular internal ribosome entry sites. In: Translational control in biology and medicine. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, pp 155–172

    Google Scholar 

  • Fernandez-Pinar R, Lo Sciuto A, Rossi A, Ranucci S, Bragonzi A, Imperi F (2015) In vitro and in vivo screening for novel essential cell-envelope proteins in Pseudomonas aeruginosa. Sci Rep 5:7593

    Article  Google Scholar 

  • Forrester WC, Epner E, Driscoll MC, Enver T, Brice M, Papayannopoulou T, Groudine M (1990) A deletion of the human beta-globin locus activation region causes a major alteration in chromatin structure and replication across the entire beta-globin locus. Genes Dev 4:1637–1649

    Article  CAS  PubMed  Google Scholar 

  • Furukawa R, Hachiya T, Ohmomo H, Shiwa Y, Ono K, Suzuk S, Satoh M, Hitomi J, Sobue K, Shimizu A (2016) Intraindividual dynamics of transcriptome and genome-wide stability of DNA methylation. Sci Rep 6:26424

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gabrielsson J, Green AR (2009) Quantitative pharmacology or pharmacokinetic pharmacodynamic integration should be a vital component in integrative pharmacology. J Pharmacol Exp Ther 331:767–774

    Article  CAS  PubMed  Google Scholar 

  • Gal-Mor O, Finlay BB (2006) Pathogenicity islands: a molecular toolbox for bacterial virulence. Cell Microbiol 8:1707–1719

    Article  CAS  PubMed  Google Scholar 

  • Gapp K, Jawaid A, Sarkies P, Bohacek J, Pelczar P, Prados J, Farinelli L, Miska E, Mansuy IM (2014) Implication of sperm RNAs in transgenerational inheritance of the effects of early trauma in mice. Nat Neurosci 17:667–669

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Garraway LA, Lander ES (2013) Lessons from the cancer genome. Cell 153:17–37

    Article  CAS  PubMed  Google Scholar 

  • Gaulton A, Bellis LJ, Bento AP, Chambers J, Davies M, Hersey A, Light Y, McGlinchey S, Michalovich D, AlLazikani B, Overington JP (2012) ChEMBL: a large-scale bioactivity database for drug discovery. Nucleic Acids Res 40:D1100–D1107

    Article  CAS  PubMed  Google Scholar 

  • Gentleman R, Carey V, Huber W, Irizarry R, Dudoit S (2005) Bioinformatics and computational biology solutions using R and bioconductor. Springer, New York, p 473

    Book  Google Scholar 

  • Gfeller D, Grosdidier A, Wirth M DA, Michielin O, Zoete V (2014) SwissTargetPrediction: a web server for target prediction of bioactive small molecules. Nucleic Acids Res 42:W32–W38

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gibbs JB (2000) Mechanism-based target identification and drug discovery in cancer research. Science 287:1969–1973

    Article  CAS  PubMed  Google Scholar 

  • Gilbert WV, Zhou K, Butler TK, Doudna JA (2007) Cap-independent translation is required for starvation-induced differentiation in yeast. Science 317:1224–1227

    Article  CAS  PubMed  Google Scholar 

  • Goto M, Washio T, Tomita M (2000) Causal analysis of CpG suppression in the Mycoplasma genome. Microb Comp Genomics 5:51–58

    Article  CAS  PubMed  Google Scholar 

  • Grigg G, Clark S (1994) Sequencing 5-methylcytosine residues in genomic DNA. BioEssays 16:431–436

    Article  CAS  PubMed  Google Scholar 

  • Grigg GW (1996) Sequencing 5-methylcytosine residues by the bisulfite method. DNA Seq 6:189–198

    Article  CAS  PubMed  Google Scholar 

  • Grosdidier A, Zoete V, Michielin O (2011) SwissDock, a protein-small molecule docking web service based on EADock DSS. Nucleic Acids Res 39:W270–W277

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gruber TD, Borrok MJ, Westler WM, Forest KT, Kiessling LL (2009) Ligand binding and substrate discrimination by UDP-galactopyranose mutase. J Mol Biol 391:327–340

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hacker J, Blum-Oehler G, Muhldorfer I, Tschape H (1997) Pathogenicity islands of virulent bacteria: structure, function and impact on microbial evolution. Mol Microbiol 23:1089–1097

    Article  CAS  PubMed  Google Scholar 

  • Hacker J, Kaper JB (2000) Pathogenicity islands and the evolution of microbes. Annu Rev Microbiol 54:641–679

    Article  CAS  PubMed  Google Scholar 

  • Haustead DJ, Stevenson A, Saxena V, Marriage F, Firth M, Silla R, Martin L, Adcroft KF, Rea S, Day PJ, Melton P, Wood FM, Fear MW (2016) Transcriptome analysis of human ageing in male skin shows mid-life period of variability and central role of NF-kappaB. Sci Rep 6:26846

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Heal JW, Jimenez-Roldan JE, Wells SA, Freedman RB, Romer RA (2012) Inhibition of HIV-1 protease: the rigidity perspective. Bioinformatics 28:350–357

    Article  CAS  PubMed  Google Scholar 

  • Heath JR, Ribas A, Mischel PS (2016) Single-cell analysis tools for drug discovery and development. Nat Rev Drug Discov 15:204–216

    Article  CAS  PubMed  Google Scholar 

  • Hecker N, Ahmed J, von Eichborn J, Dunkel M, Macha K, Eckert A, Gilson MK, Bourne PE, Preissner R (2012) SuperTarget goes quantitative: update on drug-target interactions. Nucleic Acids Res 40:D1113–D1117

    Article  CAS  PubMed  Google Scholar 

  • Higgs PG, Attwood TK (2013) Bioinformatics and molecular evolution. Wiley, Chichester

    Google Scholar 

  • Hofer A, Steverding D, Chabes A, Brun R, Thelander L (2001) Trypanosoma brucei CTP synthetase: a target for the treatment of African sleeping sickness. Proc Natl Acad Sci U S A 98:6412–6416

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Holford NH, Sheiner LB (1981a) Pharmacokinetic and pharmacodynamic modeling in-vivo. Crit Rev Bioeng 5:273–322

    CAS  PubMed  Google Scholar 

  • Holford NH, Sheiner LB (1981b) Understanding the dose-effect relationship: clinical application of pharmacokinetic-pharmacodynamic models. Clin Pharmacokinet 6:429–453

    Article  CAS  PubMed  Google Scholar 

  • Hou C, Zhao H, Tanimoto K, Dean A (2008) CTCF-dependent enhancer-blocking by alternative chromatin loop formation. Proc Natl Acad Sci U S A 105:20398–20403

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hua S, Sun Z (2001) Support vector machine approach for protein subcellular localization prediction. Bioinformatics 17:721–728

    Article  CAS  PubMed  Google Scholar 

  • Huang HY, Chien CH, Jen KH, Huang HD (2006) RegRNA: an integrated web server for identifying regulatory RNA motifs and elements. Nucleic Acids Res 34:W429–W434

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ingolia NT, Brar GA, Stern-Ginossar N, Harris MS, Talhouarne GJ, Jackson SE, Wills MR, Weissman JS (2014) Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes. Cell Rep 8:1365–1379

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ingolia NT, Ghaemmaghami S, Newman JRS, Weissman JS (2009) Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324:218–223

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ingolia NT, Lareau LF, Weissman JS (2011) Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell 147:789–802

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ingrosso D, Cimmino A, Perna AF, Masella L, De Santo NG, De Bonis ML, Vacca M, D’Esposito M, D'Urso M, Galletti P, Zappia V (2003) Folate treatment and unbalanced methylation and changes of allelic expression induced by hyperhomocysteinaemia in patients with uraemia. Lancet 361:1693–1699

    Article  CAS  PubMed  Google Scholar 

  • Ingrosso D, Perna AF (2009) Epigenetics in hyperhomocysteinemic states. A special focus on uremia. Biochim Biophys Acta 1790:892–899

    Article  CAS  PubMed  Google Scholar 

  • Insinga A, Minucci S, Pelicci PG (2005a) Mechanisms of selective anticancer action of histone deacetylase inhibitors. Cell Cycle 4:741–743

    Article  CAS  PubMed  Google Scholar 

  • Insinga A, Monestiroli S, Ronzoni S, Gelmetti V, Marchesi F, Viale A, Altucci L, Nervi C, Minucci S, Pelicci PG (2005b) Erratum: Inhibitors of histone deacetylases induce tumor-selective apoptosis through activation of the death receptor pathway. Nat Med 11:71–76

    Article  CAS  PubMed  Google Scholar 

  • Jackson RJ, Hellen CU, Pestova TV (2010) The mechanism of eukaryotic translation initiation and principles of its regulation. Nat Rev Mol Cell Biol 11:113–127

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jacob F, Monod J (1961) Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol 3:318–356

    Article  CAS  PubMed  Google Scholar 

  • Jan E, Sarnow P (2002) Factorless ribosome assembly on the internal ribosome entry site of cricket paralysis virus. J Mol Biol 324:889–902

    Article  CAS  PubMed  Google Scholar 

  • Jan E, Thompson SR, Wilson JE, Pestova TV, Hellen CU, Sarnow P (2001) Initiator Met-tRNA-independent translation mediated by an internal ribosome entry site element in cricket paralysis virus-like insect viruses. Cold Spring Harb Symp Quant Biol 66:285–292

    Article  CAS  PubMed  Google Scholar 

  • Jiang YH, Bressler J, Beaudet AL (2004) Epigenetics and human disease. Annu Rev Genomics Hum Genet 5:479–510

    Article  CAS  PubMed  Google Scholar 

  • Jin P, Alisch RS, Warren ST (2004) RNA and microRNAs in fragile X mental retardation. Nat Cell Biol 6:1048–1053

    Article  CAS  PubMed  Google Scholar 

  • Kanehisa M (2013) Molecular network analysis of diseases and drugs in KEGG. Methods Mol Biol 939:263–275

    Article  CAS  PubMed  Google Scholar 

  • Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M (2016) KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res 44:D457–D642

    Article  CAS  PubMed  Google Scholar 

  • Kincaid VA, London N, Wangkanont K, Wesener DA, Marcus SA, Heroux A, Nedyalkova L, Talaat AM, Forest KT, Shoichet BK, Kiessling LL (2015) Virtual screening for UDP-galactopyranose mutase ligands identifies a new class of antimycobacterial agents. ACS Chem Biol 10:2209–2218

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kinnings SL, Xie L, Fung KH, Jackson RM, Bourne PE (2010) The Mycobacterium tuberculosis drugome and its polypharmacological implications. PLoS Comput Biol 6:e1000976

    Article  PubMed  PubMed Central  Google Scholar 

  • Kioussis D, Vanin E, deLange T, Flavell RA, Grosveld FG (1983) Beta-globin gene inactivation by DNA translocation in gamma beta-thalassaemia. Nature 306:662–666

    Article  CAS  PubMed  Google Scholar 

  • Komar AA, Hatzoglou M (2005) Internal ribosome entry sites in cellular mRNAs: mystery of their existence. J Biol Chem 280:23425–23428

    Article  CAS  PubMed  Google Scholar 

  • Korenke GC, Fuchs S, Krasemann E, Doerr HG, Wilichowski E, Hunneman DH, Hanefeld F (1996) Cerebral adrenoleukodystrophy (ALD) in only one of monozygotic twins with an identical ALD genotype. Ann Neurol 40:254–257

    Article  CAS  PubMed  Google Scholar 

  • Kotokorpi P, Venteclef N, Ellis E, Gustafsson JA, Mode A (2010) The human ADFP gene is a direct liver-X-receptor (LXR) target gene and differentially regulated by synthetic LXR ligands. Mol Pharmacol 77:79–86

    Article  CAS  PubMed  Google Scholar 

  • Kozak M (1980) Evaluation of the “scanning model” for initiation of protein synthesis in eucaryotes. Cell 22:7–8

    Article  CAS  PubMed  Google Scholar 

  • Krasemann EW, Meier V, Korenke GC, Hunneman DH, Hanefeld F (1996) Identification of mutations in the ALD-gene of 20 families with adrenoleukodystrophy/adrenomyeloneuropathy. Hum Genet 97:194–197

    Article  CAS  PubMed  Google Scholar 

  • Kungulovski G, Jeltsch A (2016) Epigenome editing: state of the art, concepts, and perspectives. Trends Genet 32:101–113

    Article  CAS  PubMed  Google Scholar 

  • Kutlar A (2007) Sickle cell disease: a multigenic perspective of a single gene disorder. Hemoglobin 31:209–224

    Article  CAS  PubMed  Google Scholar 

  • Langmead B, Hansen KD, Leek JT (2010) Cloud-scale RNA sequencing differential expression analysis with Myrna. Genome Biol 11:R83

    Article  PubMed  PubMed Central  Google Scholar 

  • Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25

    Article  PubMed  PubMed Central  Google Scholar 

  • Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326:289–293

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ling S, Hu Z, Yang Z, Yang F, Li Y, Lin P, Chen K, Dong L, Cao L, Tao Y, Hao L, Chen Q, Gong Q, Wu D, Li W, Zhao W, Tian X, Hao C, Hungate EA, Catenacci DV, Hudson RR, Li WH, Lu X, Wu CI (2015) Extremely high genetic diversity in a single tumor points to prevalence of non-Darwinian cell evolution. Proc Natl Acad Sci U S A 112:E6496–E6505

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu X, Jiang H, Gu Z, Roberts JW (2015) High-resolution view of bacteriophage lambda gene expression by ribosome profiling. Proc Natl Acad Sci U S A 110:11928–11933

    Article  Google Scholar 

  • Ma P, Xia X (2011) Factors affecting splicing strength of yeast genes. Comp Funct Genomics 2011:212146, 13 pages

    Article  PubMed  PubMed Central  Google Scholar 

  • MacKay VL, Li X, Flory MR, Turcott E, Law GL, Serikawa KA, Xu XL, Lee H, Goodlett DR, Aebersold R, Zhao LP, Morris DR (2004) Gene expression analyzed by high-resolution state array analysis and quantitative proteomics: response of yeast to mating pheromone. Mol Cell Proteomics 3:478–489

    Article  CAS  PubMed  Google Scholar 

  • Manocheewa S, Mittler JE, Samudrala R, Mullins JI (2015) Composite sequence-structure stability models as screening tools for identifying vulnerable targets for HIV drug and vaccine development. Viruses 7:5718–5735

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Miller LH, Su X (2011) Artemisinin: discovery from the Chinese herbal garden. Cell 146:855–858

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mlera L, Lam J, Offerdahl DK, Martens C, Sturdevant D, Turner CV, Porcella SF, Bloom ME (2016) Transcriptome analysis reveals a signature profile for tick-borne flavivirus persistence in HEK 293T cells. MBio 7

    Google Scholar 

  • Moffat JG, Rudolph J, Bailey D (2014) Phenotypic screening in cancer drug discovery - past, present and future. Nat Rev Drug Discov 13:588–602

    Article  CAS  PubMed  Google Scholar 

  • Morita M, Shimozawa N, Kashiwayama Y, Suzuki Y, Imanaka T (2011) ABC subfamily D proteins and very long chain fatty acid metabolism as novel targets in adrenoleukodystrophy. Curr Drug Targets 12:694–706

    Article  CAS  PubMed  Google Scholar 

  • Muller HJ, Altenburg E (1930) The frequency of translocations produced by X-rays in drosophila. Genetics 15:283–311

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Muller PY, Milton MN (2012) The determination and interpretation of the therapeutic index in drug development. Nat Rev Drug Discov 11:751–761

    Article  CAS  PubMed  Google Scholar 

  • Murphy J, Mahony J, Ainsworth S, Nauta A, van Sinderen D (2013) Bacteriophage orphan DNA methyltransferases: insights from their bacterial origin, function, and occurrence. Appl Environ Microbiol 79:7547–7555

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Naveed H, Hameed US, Harrus D, Bourguet W, Arold ST, Gao X (2015) An integrated structure- and system-based framework to identify new targets of metabolites and known drugs. Bioinformatics 31:3922–3929

    CAS  PubMed  PubMed Central  Google Scholar 

  • Noedl H, Se Y, Schaecher K, Smith BL, Socheat D, Fukuda MM (2008) Evidence of artemisinin-resistant malaria in western Cambodia. N Engl J Med 359:2619–2620

    Article  CAS  PubMed  Google Scholar 

  • Noedl H, Se Y, Sriwichai S, Schaecher K, Teja-Isavadharm P, Smith B, Rutvisuttinunt W, Bethell D, Surasri S, Fukuda MM, Socheat D, Chan Thap L (2010) Artemisinin resistance in Cambodia: a clinical trial designed to address an emerging problem in Southeast Asia. Clin Infect Dis 51:e82–e89

    Article  PubMed  Google Scholar 

  • Noedl H, Socheat D, Satimai W (2009) Artemisinin-resistant malaria in Asia. N Engl J Med 361:540–541

    Article  CAS  PubMed  Google Scholar 

  • O’Connell RJ, Kim JH, Excler JL (2014) The HIV-1 gp120 V1V2 loop: structure, function and importance for vaccine development. Expert Rev Vaccines 13:1489–1500

    Article  PubMed  Google Scholar 

  • Ohta T, Gray TA, Rogan PK, Buiting K, Gabriel JM, Saitoh S, Muralidhar B, Bilienska B, Krajewska-Walasek M, Driscoll DJ, Horsthemke B, Butler MG, Nicholls RD (1999) Imprinting-mutation mechanisms in Prader-Willi syndrome. Am J Hum Genet 64:397–413

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ow GS, Ivshina AV, Fuentes G, Kuznetsov VA (2014) Identification of two poorly prognosed ovarian carcinoma subtypes associated with CHEK2 germ-line mutation and non-CHEK2 somatic mutation gene signatures. Cell Cycle 13:2262–2280

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ozsvari B, Lamb R, Lisanti MP (2016) Repurposing of FDA approved drugs against cancer—focus on metastasis. Aging (Albany NY) 8:567–568

    Article  PubMed  Google Scholar 

  • Pandey RR, Mondal T, Mohammad F, Enroth S, Redrup L, Komorowski J, Nagano T, Mancini-Dinardo D, Kanduri C (2008) Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol Cell 32:232–246

    Article  CAS  PubMed  Google Scholar 

  • Pauling L, Itano HA, Singer SJ, Wells IC (1949) Sickle cell anemia a molecular disease. Science 110:543–548

    Article  CAS  PubMed  Google Scholar 

  • Pedersen LL, Turco SJ (2003) Galactofuranose metabolism: a potential target for antimicrobial chemotherapy. Cell Mol Life Sci 60:259–266

    Article  CAS  PubMed  Google Scholar 

  • Pereira B, Chin SF, Rueda OM et al (2016) The somatic mutation profiles of 2,433 breast cancers refines their genomic and transcriptomic landscapes. Nat Commun 7:11479

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pestova TV, Lomakin IB, Hellen CU (2004) Position of the CrPV IRES on the 40S subunit and factor dependence of IRES/80S ribosome assembly. EMBO Rep 5:906–913

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pestova TV, Shatsky IN, Fletcher SP, Jackson RJ, Hellen CU (1998) A prokaryotic-like mode of cytoplasmic eukaryotic ribosome binding to the initiation codon during internal translation initiation of hepatitis C and classical swine fever virus RNAs. Genes Dev 12:67–83

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Petronis A (2004) The origin of schizophrenia: genetic thesis, epigenetic antithesis, and resolving synthesis. Biol Psychiatry 55:965–970

    Article  CAS  PubMed  Google Scholar 

  • Petronis A (2006) Epigenetics and twins: three variations on the theme. Trends Genet 22:347–350

    Article  CAS  PubMed  Google Scholar 

  • Petronis A, Gottesman II, Kan P, Kennedy JL, Basile VS, Paterson AD, Popendikyte V (2003) Monozygotic twins exhibit numerous epigenetic differences: clues to twin discordance? Schizophr Bull 29:169–178

    Article  PubMed  Google Scholar 

  • Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF Chimera—a visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612

    Article  CAS  PubMed  Google Scholar 

  • Pietras K, Sjoblom T, Rubin K, Heldin CH, Ostman A (2003) PDGF receptors as cancer drug targets. Cancer Cell 3:439–443

    Article  CAS  PubMed  Google Scholar 

  • Popa A, Lebrigand K, Barbry P, Waldmann R (2016) Pateamine A sensitive ribosome profiling reveals the scope of translation in mouse embryonic stem cells. BMC Genomics 17:52

    Article  PubMed  PubMed Central  Google Scholar 

  • Prabhakaran R, Chithambaram S, Xia X (2015) E. coli and Staphylococcus phages: effect of translation initiation efficiency on differential codon adaptation mediated by virulent and temperate lifestyles. J Gen Virol 96:1169. https://doi.org/10.1099/vir.0.000050

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Pundhir S, Vijayvargiya H, Kumar A (2008) PredictBias: a server for the identification of genomic and pathogenicity islands in prokaryotes. In Silico Biol 8:223–234

    CAS  PubMed  Google Scholar 

  • Rhee SY, Taylor J, Fessel WJ, Kaufman D, Towner W, Troia P, Ruane P, Hellinger J, Shirvani V, Zolopa A, Shafer RW (2010) HIV-1 protease mutations and protease inhibitor cross-resistance. Antimicrob Agents Chemother 54:4253–42561

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rinn JL, Kertesz M, Wang JK, Squazzo SL, Xu X, Brugmann SA, Goodnough LH, Helms JA, Farnham PJ, Segal E, Chang HY (2007) Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129:1311–1323

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Roberts A, Schaeffer L, Pachter L (2013) Updating RNA-Seq analyses after re-annotation. Bioinformatics 29:1631–1637

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Roberts A, Trapnell C, Donaghey J, Rinn JL, Pachter L (2011) Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol 12:R22

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, Griffith OL, He A, Marra M, Snyder M, Jones S (2007) Genome-wide profiles of STAT1 DNA association using chromatin immune-precipitation and massively parallel sequencing. Nat Methods 4:651–657

    Article  CAS  PubMed  Google Scholar 

  • Rodgers AB, Morgan CP, Leu NA, Bale TL (2015) Transgenerational epigenetic programming via sperm microRNA recapitulates effects of paternal stress. Proc Natl Acad Sci U S A 112:13699–13704

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rose PW, Prlic A, Bi C, Bluhm WF, Christie CH, Dutta S, Green RK, Goodsell DS, Westbrook JD, Woo J, Young J, Zardecki C, Berman HM, Bourne PE, Burley SK (2015) The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. Nucleic Acids Res 43:D345–D356

    Article  CAS  PubMed  Google Scholar 

  • Rouchka EC (1997) A brief overview of Gibbs sampling. IBC Statistics Study Group, Washington University, Institute for Biomedical Computing

    Google Scholar 

  • Saadatpour A, Lai S, Guo G, Yuan GC (2015) Single-cell analysis in cancer genomics. Trends Genet 31:576–586

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schrider DR, Hourmozdi JN, Hahn MW (2011) Pervasive multi-nucleotide mutational events in eukaryotes. Curr Biol 21:1051–1054

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schuler M, Connell SR, Lescoute A, Giesebrecht J, Dabrowski M, Schroeer B, Mielke T, Penczek PA, Westhof E, Spahn CM (2006) Structure of the ribosome-bound cricket paralysis virus IRES RNA. Nat Struct Mol Biol 13:1092–1096

    Article  PubMed  Google Scholar 

  • Sharma U, Conine CC, Shea JM, Boskovic A, Derr AG, Bing XY, Belleannee C, Kucukural A, Serra RW, Sun F, Song L, Carone BR, Ricci EP, Li XZ, Fauquier L, Moore MJ, Sullivan R, Mello CC, Garber M, Rando OJ (2016) Biogenesis and function of tRNA fragments during sperm maturation and fertilization in mammals. Science 351:391–396

    Article  CAS  PubMed  Google Scholar 

  • Shoemaker R, Deng J, Wang W, Zhang K (2010) Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome. Genome Res 20:883–889

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shoemaker RH (2006) The NCI60 human tumour cell line anticancer drug screen. Nat Rev Cancer 6:813–823

    Article  CAS  PubMed  Google Scholar 

  • Singh VK, Chang HH, Kuo CC, Shiao HY, Hsieh HP, Coumar MS (2016) Drug repurposing for chronic myeloid leukemia: in silico and in vitro investigation of DrugBank database for allosteric Bcr-Abl inhibitors. J Biomol Struct Dyn 35:1833

    Article  PubMed  Google Scholar 

  • Smircich P, Eastman G, Bispo S, Duhagon MA, Guerra-Slompo EP, Garat B, Goldenberg S, Munroe DJ, Dallagiovanna B, Holetz F, Sotelo-Silveira JR (2015) Ribosome profiling reveals translation control as a key mechanism generating differential gene expression in Trypanosoma cruzi. BMC Genomics 16:443

    Article  PubMed  PubMed Central  Google Scholar 

  • Smyth RP, Davenport MP, Mak J (2012) The origin of genetic diversity in HIV-1. Virus Res 169:415–429

    Article  CAS  PubMed  Google Scholar 

  • Smyth RP, Schlub TE, Grimm AJ, Waugh C, Ellenberg P, Chopra A, Mallal S, Cromer D, Mak J, Davenport MP (2014) Identifying recombination hot spots in the HIV-1 genome. J Virol 88:2891–2902

    Article  PubMed  PubMed Central  Google Scholar 

  • Snell TW, Johnston RK, Srinivasan B, Zhou H, Gao M, Skolnick J (2016) Repurposing FDA-approved drugs for anti-aging therapies. Biogerontology 17(5–6):907–920

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sonenberg N, Meerovitch K (1990) Translation of poliovirus mRNA. Enzyme 44:278–291

    Article  CAS  PubMed  Google Scholar 

  • Song F, Amos CI, Lee JE, Lian CG et al (2014) Identification of a melanoma susceptibility locus and somatic mutation in TET2. Carcinogenesis 35:2097–2101

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Steinberg MH, Rodgers GP (2001) Pathophysiology of sickle cell disease: role of cellular and genetic modifiers. Semin Hematol 38:299–306

    Article  CAS  PubMed  Google Scholar 

  • Swinney DC (2009) The role of binding kinetics in therapeutically useful drug action. Curr Opin Drug Discov Devel 12:31–39

    CAS  PubMed  Google Scholar 

  • Swinney DC (2013) Phenotypic vs. target-based drug discovery for first-in-class medicines. Clin Pharmacol Ther 93:299–301

    Article  CAS  PubMed  Google Scholar 

  • Swinney DC, Anthony J (2011) How were new medicines discovered? Nat Rev Drug Discov 10:507–519

    Article  CAS  PubMed  Google Scholar 

  • Swinney ZT, Haubrich BA, Xia S, Ramesha C, Gomez SR, Guyett P, Mensa-Wilmot K, Swinney DC (2016) A four-point screening method for assessing molecular mechanism of action (MMOA) identifies tideglusib as a time-dependent inhibitor of Trypanosoma brucei GSK3beta. PLoS Negl Trop Dis 10:e0004506

    Article  PubMed  PubMed Central  Google Scholar 

  • Tanabe M, Kanehisa M (2012) Using the KEGG database resource. Curr Protoc Bioinformatics Chapter 1:1.12.1. Unit 1:12

    PubMed  Google Scholar 

  • Taramelli R, Kioussis D, Vanin E, Bartram K, Groffen J, Hurst J, Grosveld FG (1986) Gamma delta beta-thalassaemias 1 and 2 are the result of a 100 kbp deletion in the human beta-globin cluster. Nucleic Acids Res 14:7017–7029

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105–1111

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L (2012) Differential gene and transcript expression analysis of RNA-seqexperiments with TopHat and Cufflinks. Nat Protoc 7:562–578

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ulferts R, de Boer SM, van der Linden L, Bauer L, Lyoo HR, Mate MJ, Lichiere J, Canard B, Lelieveld D, Omta W, Egan D, Coutard B, van Kuppeveld FJ (2016) Screening of a library of FDA-approved drugs identifies several enterovirus replication inhibitors that target viral protein 2C. Antimicrob Agents Chemother 60:2627–2638

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Vlasschaert C, Xia X, Coulombe J, Gray DA (2015) Evolution of the highly networked deubiquitinating enzymes USP4, USP15, and USP11. BMC Evol Biol 15:230

    Article  PubMed  PubMed Central  Google Scholar 

  • Vlasschaert C, Xia X, Gray DA (2016) Selection preserves Ubiquitin Specific Protease 4 alternative exon skipping in therian mammals. Sci Rep 6:20039

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Voelter-Mahlknecht S (2016) Epigenetic associations in relation to cardiovascular prevention and therapeutics. Clin Epigenetics 8:4

    Article  PubMed  PubMed Central  Google Scholar 

  • Wade PA, Wolffe AP (2001) Recognizing methylated DNA. Nat Struct Biol 8:575–577

    Article  CAS  PubMed  Google Scholar 

  • Wang M, Weiss M, Simonovic M, Haertinger G, Schrimpf SP, Hengartner MO, von Mering C (2012) PaxDb, a database of protein abundance averages across all three domains of life. Mol Cell Proteomics 11:492–500

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Waterfield MD, Scrace GT, Whittle N, Stroobant P, Johnsson A, Wasteson A, Westermark B, Heldin CH, Huang JS, Deuel TF (1983) Platelet-derived growth factor is structurally related to the putative transforming protein p28sis of simian sarcoma virus. Nature 304:35–39

    Article  CAS  PubMed  Google Scholar 

  • Wesener DA, May JF, Huffman EM, Kiessling LL (2013) UDP-galactopyranose mutase in nematodes. Biochemistry 52:4391–4398

    Article  CAS  PubMed  Google Scholar 

  • Westbrook J, Feng Z, Jain S, Bhat TN, Thanki N, Ravichandran V, Gilliland GL, Bluhm W, Weissig H, Greer DS, Bourne PE, Berman HM (2002) The Protein Data Bank: unifying the archive. Nucleic Acids Res 30:245–248

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wirth M, Zoete V, Michielin O, Sauer WH (2013) SwissBioisostere: a database of molecular replacements for ligand design. Nucleic Acids Res 41:D1137–D1143

    Article  CAS  PubMed  Google Scholar 

  • Wishart DS (2016a) Emerging applications of metabolomics in drug discovery and precision medicine. Nat Rev Drug Discov 15(7):473–484

    Article  CAS  PubMed  Google Scholar 

  • Wishart DS (2016b) Introduction to cheminformatics. Curr Protoc Bioinformatics 53:1411–1421

    Article  Google Scholar 

  • Wlodawer A, Erickson JW (1993) Structure-based inhibitors of HIV-1 protease. Annu Rev Biochem 62:543–585

    Article  CAS  PubMed  Google Scholar 

  • Wlodawer A, Vondrasek J (1998) Inhibitors of HIV-1 protease: a major success of structure-assisted drug design. Annu Rev Biophys Biomol Struct 27:249–284

    Article  CAS  PubMed  Google Scholar 

  • Wu J, Tzanakakis ES (2013) Deconstructing stem cell population heterogeneity: single-cell analysis and modeling approaches. Biotechnol Adv 31:1047–1062

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xia J, Psychogios N, Young N, Wishart DS (2009) MetaboAnalyst: a web server for metabolomic data analysis and interpretation. Nucleic Acids Res 37:W652–W660

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xia X (2003) DNA methylation and mycoplasma genomes. J Mol Evol 57:S21–S28

    Article  CAS  PubMed  Google Scholar 

  • Xia X (2007) Bioinformatics and the cell: modern computational approaches in genomics, proteomics and transcriptomics. Springer, New York, p 349

    Book  Google Scholar 

  • Xia X (2012) Position Weight Matrix, Gibbs Sampler, and the associated significance tests in motif characterization and prediction. Scientifica 2012:917540, 15pp.

    Article  PubMed  PubMed Central  Google Scholar 

  • Xia X (2013) DAMBE5: a comprehensive software package for data analysis in molecular biology and evolution. Mol Biol Evol 30:1720–1728

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xia X (2016a) ARSDA: a Quick Start. XiaLab. http://dambe.bio.uottawa.ca/ARSDA/ARSDA.aspx.Ottawa2016. Accessed 3 Mar 2017

  • Xia X (2016b) PhyPA: phylogenetic method with pairwise sequence alignment outperforms likelihood methods in phylogenetics involving highly diverged sequences. Mol Phylogenet Evol 102:331–343

    Article  CAS  PubMed  Google Scholar 

  • Xia X, MacKay V, Yao X, Wu J, Miura F, Ito T, Morris DR (2011) Translation initiation: a regulatory role for poly(A) tracts in front of the AUG codon in Saccharomyces cerevisiae. Genetics 189:469–478

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xia X, Xie Z (2001) AMADA: analysis of microarray data. Bioinfomatics 17:569–570

    Article  CAS  Google Scholar 

  • Xie X, Rigor P, Baldi P (2009) MotifMap: a human genome-wide map of candidate regulatory motif sites. Bioinformatics 25:167–174

    Article  CAS  PubMed  Google Scholar 

  • Yoon JH, De S, Srikantan S et al (2014) PAR-CLIP analysis uncovers AUF1 impact on target RNA fate and genome integrity. Nat Commun 5:5248

    Article  CAS  PubMed  Google Scholar 

  • Yoon SH, Park YK, Kim JF (2015) PAIDB v2.0: exploration and analysis of pathogenicity and resistance islands. Nucleic Acids Res 43:D624–D630

    Article  CAS  PubMed  Google Scholar 

  • Young TP, Parkin NT, Stawiski E, Pilot-Matias T, Trinh R, Kempf DJ, Norton M (2010) Prevalence, mutation patterns, and effects on protease inhibitor susceptibility of the L76V mutation in HIV-1 protease. Antimicrob Agents Chemother 54:4903–4906

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yu Y, Sweeney TR, Kafasla P, Jackson RJ, Pestova TV, Hellen CU (2011) The mechanism of translation initiation on Aichivirus RNA mediated by a novel type of picornavirus IRES. EMBO J J30:4423–4436

    Article  Google Scholar 

  • Zhang W, Tan AY, Blumenfeld J, Liu G, Michaeel A, Zhang T, Robinson BD, Salvatore SP, Kapur S, Donahue S, Bobb WO, Rennert H (2016) Papillary renal cell carcinoma with a somatic mutation in MET in a patient with autosomal dominant polycystic kidney disease. Cancer Genet 209:11–20

    Article  CAS  PubMed  Google Scholar 

  • Zhang Y, Arakaki AK, Skolnick J (2005) TASSER: an automated method for the prediction of protein tertiary structures in CASP6. Proteins 61(Suppl 7):91–98

    Article  CAS  PubMed  Google Scholar 

  • Zien A, Ratsch G, Mika S, Scholkopf B, Lengauer T, Muller KR (2000) Engineering support vector machine kernels that recognize translation initiation sites. Bioinformatics 16:799–807

    Article  CAS  PubMed  Google Scholar 

  • Zoete V, Daina A, Bovigny C, Michielin O (2016) SwissSimilarity: a web tool for low to ultra high throughput ligand-based virtual screening. J Chem Inf Model 56:1399–1404

    Article  CAS  PubMed  Google Scholar 

  • Zoghbi HY, Beaudet AL (2016) Epigenetics and human disease. Cold Spring Harb Perspect Biol 8:a019497

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2023 The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Patel, P.H., Jha, A., Chakraborthy, G.S. (2023). Role of Bioinformatics in Drug Design and Discovery. In: Rudrapal, M., Khan, J. (eds) CADD and Informatics in Drug Discovery. Interdisciplinary Biotechnological Advances. Springer, Singapore. https://doi.org/10.1007/978-981-99-1316-9_1

Download citation

Publish with us

Policies and ethics