Advertisement

Structural Bioinformatics: Life Through The 3D Glasses

  • Ankita Punetha
  • Payel Sarkar
  • Siddharth Nimkar
  • Himanshu Sharma
  • Yoganand KNR
  • Siranjeevi Nagaraj
Chapter

Abstract

Structural bioinformatics is the branch of bioinformatics that uses advanced computational approaches to investigate macromolecules in atomistic details and their various interactions to address biological questions. The biological data exists in various forms, which increases the complexity − the linear data represented in one dimension (1D) includes sequence information, and the nonlinear data represented in three dimensions (3D) includes structural information. Structural information provides insight on how the biological function is linked with the structure and the effect of perturbations on its mechanism. Extensive computation or judicious approximations are vital to handle the huge system encompassing 3D structure of biomolecules, the nonlinear forces between atoms, and their interacting environment. The flexibility, dynamics, experimental noise, and veracity in structural data can further pose limitations in understanding the function of biomolecules. Thus, in order to have comprehensive understanding of biological systems, one requires sound understanding of fundamentals of macromolecular structure, its experimental determination, or prediction using computational approaches, data representation, visualization, and integration. The recent technological advances have generated enormous amount of omics data at various levels – genome, proteome, transcriptome, metabolome, and phenome – which has further raised the demand of reliable and efficient bioinformatics tools to access, analyze, and integrate the biological data.

This chapter is primarily framed to assist in understanding the expanse of structural bioinformatics and its inevitability for structural biologist.

Keywords

Macromolecules RNA DNA Proteins X-ray crystallography NMR Cryo-EM Cryo-ET Homology modeling Fold recognition Threading Ab initiomethods Simulations CADD QSAR Docking Virtual screening 

References

  1. Adrian M, Heddi B, Phan AT (2012) NMR spectroscopy of G-quadruplexes. Methods (San Diego, Calif) 57(1):11–24.  https://doi.org/10.1016/j.ymeth.2012.05.003 CrossRefGoogle Scholar
  2. Agarwal T, Jayaraj G, Pandey SP, Agarwala P, Maiti S (2012) RNA G-quadruplexes: G-quadruplexes with “U” turns. Curr Pharm Des 18(14):2102–2111PubMedCrossRefPubMedCentralGoogle Scholar
  3. Ahmed YL, Ficner R (2014) RNA synthesis and purification for structural studies. RNA Biol 11(5):427–432.  https://doi.org/10.4161/rna.28076 CrossRefPubMedPubMedCentralGoogle Scholar
  4. Allen WJ, Balius TE, Mukherjee S, Brozell SR, Moustakas DT, Lang PT, Case DA, Kuntz ID, Rizzo RC (2015) DOCK 6: Impact of new features and current docking performance. J Comput Chem 36(15):1132–1156.  https://doi.org/10.1002/jcc.23905 CrossRefPubMedPubMedCentralGoogle Scholar
  5. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25(17):3389–3402PubMedPubMedCentralCrossRefGoogle Scholar
  6. Amunts A, Brown A, Toots J, Scheres SH, Ramakrishnan V (2015) Ribosome. The structure of the human mitochondrial ribosome. Science 348(6230):95–98.  https://doi.org/10.1126/science.aaa1193 CrossRefPubMedPubMedCentralGoogle Scholar
  7. Amzel LM, Poljak RJ (1979) Three-dimensional structure of immunoglobulins. Annu Rev Biochem 48:961–997.  https://doi.org/10.1146/annurev.bi.48.070179.004525 CrossRefPubMedPubMedCentralGoogle Scholar
  8. Anfinsen CB (1973) Principles that govern the folding of protein chains. Science 181(4096):223–230PubMedPubMedCentralCrossRefGoogle Scholar
  9. Arcella A, Portella G, Ruiz ML, Eritja R, Vilaseca M, Gabelica V, Orozco M (2012) Structure of triplex DNA in the gas phase. J Am Chem Soc 134(15):6596–6606.  https://doi.org/10.1021/ja209786t CrossRefPubMedPubMedCentralGoogle Scholar
  10. Arieti F (2014) Structural studies of RNA-binding domainsGoogle Scholar
  11. Arnott S (1970) Crystallography of DNA: difference synthesis supports Watson-Crick base pairing. Science 167(3926):1694–1700PubMedCrossRefPubMedCentralGoogle Scholar
  12. Arnott S, Chandrasekaran R, Hukins DW, Smith PJ, Watts L (1974a) Structural details of double-helix observed for DNAs containing alternating purine and pyrimidine sequences. J Mol Biol 88(2):523–533PubMedCrossRefPubMedCentralGoogle Scholar
  13. Arnott S, Chandrasekaran R, Marttila CM (1974b) Structures for polyinosinic acid and polyguanylic acid. Biochem J 141(2):537–543PubMedPubMedCentralCrossRefGoogle Scholar
  14. Arnott S, Chandrasekaran R, Leslie AG (1976) Structure of the single-stranded polyribonucleotide polycytidylic acid. J Mol Biol 106(3):735–748PubMedCrossRefPubMedCentralGoogle Scholar
  15. Artusi S, Perrone R, Lago S, Raffa P, Di Iorio E, Palu G, Richter SN (2016) Visualization of DNA G-quadruplexes in herpes simplex virus 1-infected cells. Nucleic Acids Res 44(21):10343–10353.  https://doi.org/10.1093/nar/gkw968 CrossRefPubMedPubMedCentralGoogle Scholar
  16. Asano S, Engel BD, Baumeister W (2016) In situ cryo-electron tomography: a post-reductionist approach to structural biology. J Mol Biol 428(2 Pt A):332–343.  https://doi.org/10.1016/j.jmb.2015.09.030 CrossRefPubMedPubMedCentralGoogle Scholar
  17. Avdeef A (2001) Physicochemical profiling (solubility, permeability and charge state). Curr Top Med Chem 1(4):277–351PubMedCrossRefPubMedCentralGoogle Scholar
  18. Bae S, Kim D, Kim KK, Kim YG, Hohng S (2011) Intrinsic Z-DNA is stabilized by the conformational selection mechanism of Z-DNA-binding proteins. J Am Chem Soc 133(4):668–671.  https://doi.org/10.1021/ja107498y CrossRefPubMedPubMedCentralGoogle Scholar
  19. Bai X-C, McMullan G, Scheres SHW (2015) How cryo-EM is revolutionizing structural biology. Trends Biochem Sci 40(1):49–57.  https://doi.org/10.1016/j.tibs.2014.10.005 CrossRefPubMedPubMedCentralGoogle Scholar
  20. Baker D, Agard DA (1994) Influenza hemagglutinin: kinetic control of protein function. Structure 2(10):907–910PubMedCrossRefPubMedCentralGoogle Scholar
  21. Baker D, Sali A (2001) Protein structure prediction and structural genomics. Science 294(5540):93–96PubMedCrossRefPubMedCentralGoogle Scholar
  22. Basak SC (2012) Chemobioinformatics: the advancing frontier of computer-aided drug design in the post-genomic era. Curr Comput-Aided Drug Des 8(1):1–2PubMedCrossRefPubMedCentralGoogle Scholar
  23. Basu HS, Feuerstein BG, Zarling DA, Shafer RH, Marton LJ (1988) Recognition of Z-RNA and Z-DNA determinants by polyamines in solution: experimental and theoretical studies. J Biomol Struct Dyn 6(2):299–309.  https://doi.org/10.1080/07391102.1988.10507714 CrossRefPubMedPubMedCentralGoogle Scholar
  24. Bates PA, Kelley LA, MacCallum RM, Sternberg MJ (2001) Enhancement of protein modeling by human intervention in applying the automatic programs 3D-JIGSAW and 3D-PSSM. Proteins Suppl 5:39–46CrossRefGoogle Scholar
  25. Beddell CR, Goodford PJ, Norrington FE, Wilkinson S, Wootton R (1976) Compounds designed to fit a site of known structure in human haemoglobin. Br J Pharmacol 57(2):201–209PubMedPubMedCentralCrossRefGoogle Scholar
  26. Bender BJ, Cisneros A 3rd, Duran AM, Finn JA, Fu D, Lokits AD, Mueller BK, Sangha AK, Sauer MF, Sevy AM, Sliwoski G, Sheehan JH, DiMaio F, Meiler J, Moretti R (2016) Protocols for molecular modeling with Rosetta3 and RosettaScripts. Biochemistry 55(34):4748–4763.  https://doi.org/10.1021/acs.biochem.6b00444 CrossRefPubMedPubMedCentralGoogle Scholar
  27. Berjanskii M, Liang Y, Zhou J, Tang P, Stothard P, Zhou Y, Cruz J, MacDonell C, Lin G, Lu P, Wishart DS (2010) PROSESS: a protein structure evaluation suite and server. Nucleic Acids Res 38(suppl_2):W633–W640.  https://doi.org/10.1093/nar/gkq375 CrossRefPubMedPubMedCentralGoogle Scholar
  28. Berman HM, Bhat TN, Bourne PE, Feng Z, Gilliland G, Weissig H, Westbrook J (2000a) The protein data bank and the challenge of structural genomics. Nat Struct Biol 7(Suppl):957–959.  https://doi.org/10.1038/80734 CrossRefPubMedPubMedCentralGoogle Scholar
  29. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000b) The protein data bank. Nucleic Acids Res 28(1):235–242PubMedPubMedCentralCrossRefGoogle Scholar
  30. Bernstein FC, Koetzle TF, Williams GJ, Meyer EF Jr, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M (1977) The protein data bank: a computer-based archival file for macromolecular structures. J Mol Biol 112(3):535–542PubMedCrossRefPubMedCentralGoogle Scholar
  31. Bharat TA, Scheres SH (2016) Resolving macromolecular structures from electron cryo-tomography data using subtomogram averaging in RELION. Nat Protoc 11(11):2054–2065.  https://doi.org/10.1038/nprot.2016.124 CrossRefPubMedPubMedCentralGoogle Scholar
  32. Bharat Tanmay A, Russo Christopher J, Löwe J, Passmore Lori A, Scheres Sjors H (2015) Advances in single-particle electron cryomicroscopy structure determination applied to sub-tomogram averaging. Structure (London, England:1993) 23(9):1743–1753.  https://doi.org/10.1016/j.str.2015.06.026 CrossRefPubMedCentralGoogle Scholar
  33. Bhattacharya D, Cao R, Cheng J (2016) UniCon3D: de novo protein structure prediction using united-residue conformational search via stepwise, probabilistic sampling. Bioinformatics (Oxford, England) 32(18):2791–2799.  https://doi.org/10.1093/bioinformatics/btw316 CrossRefGoogle Scholar
  34. Biasini M, Bienert S, Waterhouse A, Arnold K, Studer G, Schmidt T, Kiefer F, Cassarino TG, 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 CrossRefPubMedPubMedCentralGoogle Scholar
  35. Bickerton GR, Paolini GV, Besnard J, Muresan S, Hopkins AL (2012) Quantifying the chemical beauty of drugs. Nat Chem 4(2):90–98.  https://doi.org/10.1038/nchem.1243 CrossRefPubMedPubMedCentralGoogle Scholar
  36. Binkowski TA, Freeman P, Liang J (2004) pvSOAR: detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins. Nucleic Acids Res 32(Web Server issue):W555–W558.  https://doi.org/10.1093/nar/gkh390 CrossRefPubMedPubMedCentralGoogle Scholar
  37. Blake JD, Cohen FE (2001) Pairwise sequence alignment below the twilight zone. J Mol Biol 307(2):721–735PubMedCrossRefPubMedCentralGoogle Scholar
  38. Blaszczyk M, Jamroz M, Kmiecik S, Kolinski A (2013) CABS-fold: Server for the de novo and consensus-based prediction of protein structure. Nucleic Acids Res 41(Web Server issue):W406–W411.  https://doi.org/10.1093/nar/gkt462 CrossRefPubMedPubMedCentralGoogle Scholar
  39. Bowie JU, Luthy R, Eisenberg D (1991) A method to identify protein sequences that fold into a known three-dimensional structure. Science 253(5016):164–170PubMedCrossRefPubMedCentralGoogle Scholar
  40. Bradley P, Malmstrom L, Qian B, Schonbrun J, Chivian D, Kim DE, Meiler J, Misura KM, Baker D (2005a) Free modeling with Rosetta in CASP6. Proteins 61(Suppl 7):128–134PubMedCrossRefPubMedCentralGoogle Scholar
  41. Bradley P, Misura KM, Baker D (2005b) Toward high-resolution de novo structure prediction for small proteins. Science 309(5742):1868–1871PubMedCrossRefPubMedCentralGoogle Scholar
  42. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M (1983) CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J Comput Chem 4(2):187–217CrossRefGoogle Scholar
  43. Burge S, Parkinson GN, Hazel P, Todd AK, Neidle S (2006) Quadruplex DNA: sequence, topology and structure. Nucleic Acids Res 34(19):5402–5415.  https://doi.org/10.1093/nar/gkl655 CrossRefPubMedPubMedCentralGoogle Scholar
  44. Campbell NH, Parkinson GN (2007) Crystallographic studies of quadruplex nucleic acids. Methods (San Diego, Calif) 43(4):252–263.  https://doi.org/10.1016/j.ymeth.2007.08.005 CrossRefGoogle Scholar
  45. Chen JL, Greider CW (2005) Functional analysis of the pseudoknot structure in human telomerase RNA. Proc Natl Acad Sci U S A 102(23):8080–8085; discussion 8077–8089.  https://doi.org/10.1073/pnas.0502259102 CrossRefPubMedPubMedCentralGoogle Scholar
  46. Chen X, Ramakrishnan B, Sundaralingam M (1995) Crystal structures of B-form DNA-RNA chimers complexed with distamycin. Nat Struct Biol 2(9):733–735PubMedCrossRefPubMedCentralGoogle Scholar
  47. Chen VB, Arendall WB, Headd JJ, Keedy DA, Immormino RM, Kapral GJ, Murray LW, Richardson JS, Richardson DC (2010) MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr D: Biol Crystallogr 66(Pt 1):12–21.  https://doi.org/10.1107/S0907444909042073 CrossRefGoogle Scholar
  48. Chen VB, Wedell JR, Wenger RK, Ulrich EL, Markley JL (2015) MolProbity for the masses-of data. J Biomol NMR 63(1):77–83.  https://doi.org/10.1007/s10858-015-9969-9 CrossRefPubMedPubMedCentralGoogle Scholar
  49. Cheng YK, Pettitt BM (1992) Stabilities of double- and triple-strand helical nucleic acids. Prog Biophys Mol Biol 58(3):225–257PubMedCrossRefPubMedCentralGoogle Scholar
  50. Cheng F, Li W, Liu G, Tang Y (2013) In silico ADMET prediction: recent advances, current challenges and future trends. Curr Top Med Chem 13(11):1273–1289PubMedCrossRefPubMedCentralGoogle Scholar
  51. Choi J, Majima T (2011) Conformational changes of non-B DNA. Chem Soc Rev 40(12):5893–5909.  https://doi.org/10.1039/c1cs15153c CrossRefPubMedPubMedCentralGoogle Scholar
  52. Choi H, Kim JY, Chang YT, Nam HG (2014) Forward chemical genetic screening. Methods Mol Biol 1062:393–404.  https://doi.org/10.1007/978-1-62703-580-4_21 CrossRefPubMedPubMedCentralGoogle Scholar
  53. Chothia C, Lesk AM (1986) The relation between the divergence of sequence and structure in proteins. EMBO J 5(4):823–826PubMedPubMedCentralCrossRefGoogle Scholar
  54. Chou SH, Chin KH, Wang AH (2003) Unusual DNA duplex and hairpin motifs. Nucleic Acids Res 31(10):2461–2474PubMedPubMedCentralCrossRefGoogle Scholar
  55. Coimbatore Narayanan B, Westbrook J, Ghosh S, Petrov AI, Sweeney B, Zirbel CL, Leontis NB, Berman HM (2014) The nucleic acid database: new features and capabilities. Nucleic Acids Res 42(Database issue):D114–D122.  https://doi.org/10.1093/nar/gkt980 CrossRefPubMedPubMedCentralGoogle Scholar
  56. Congreve M, Carr R, Murray C, Jhoti H (2003) A ‘rule of three’ for fragment-based lead discovery? Drug Discov Today 8(19):876–877PubMedCrossRefPubMedCentralGoogle Scholar
  57. Corbeil CR, Williams CI, Labute P (2012) Variability in docking success rates due to dataset preparation. J Comput-Aided Mol Des 26(6):775–786.  https://doi.org/10.1007/s10822-012-9570-1 CrossRefPubMedPubMedCentralGoogle Scholar
  58. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA (1995) A 2nd generation force-field for the simulation of proteins, nucleic-acids, and organic-molecules. J Am Chem Soc 117(19):5179–5197.  https://doi.org/10.1021/Ja00124a002 CrossRefGoogle Scholar
  59. Dahm R (2008) Discovering DNA: Friedrich Miescher and the early years of nucleic acid research. Hum Genet 122(6):565–581.  https://doi.org/10.1007/s00439-007-0433-0 CrossRefPubMedPubMedCentralGoogle Scholar
  60. Daina A, Michielin O, Zoete V (2017) SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep 7:42717.  https://doi.org/10.1038/srep42717 CrossRefPubMedPubMedCentralGoogle Scholar
  61. Davies SP, Reddy H, Caivano M, Cohen P (2000) Specificity and mechanism of action of some commonly used protein kinase inhibitors. Biochem J 351(Pt 1):95–105PubMedPubMedCentralCrossRefGoogle Scholar
  62. Dawson NL, Lewis TE, Das S, Lees JG, Lee D, Ashford P, Orengo CA, Sillitoe I (2017) CATH: an expanded resource to predict protein function through structure and sequence. Nucleic Acids Res 45(Database issue):D289–D295.  https://doi.org/10.1093/nar/gkw1098 CrossRefPubMedPubMedCentralGoogle Scholar
  63. de Beer TAP, Berka K, Thornton JM, Laskowski RA (2014) PDBsum additions. Nucleic Acids Res 42(D1):D292–D296.  https://doi.org/10.1093/nar/gkt940 CrossRefPubMedPubMedCentralGoogle Scholar
  64. de Ruyck J, Brysbaert G, Blossey R, Lensink MF (2016) Molecular docking as a popular tool in drug design, an in silico travel. Adv Appl Bioinform Chem 9:1–11.  https://doi.org/10.2147/aabc.s105289 CrossRefPubMedPubMedCentralGoogle Scholar
  65. Derringer G, Suich R (1980) Simultaneous-optimization of several response variables. J Qual Technol 12(4):214–219CrossRefGoogle Scholar
  66. Desai N, Brown A, Amunts A, Ramakrishnan V (2017) The structure of the yeast mitochondrial ribosome. Science 355(6324):528–531.  https://doi.org/10.1126/science.aal2415 CrossRefPubMedPubMedCentralGoogle Scholar
  67. Desborough MJR, Keeling DM (2017) The aspirin story – from willow to wonder drug. Br J Haematol 177(5):674–683.  https://doi.org/10.1111/bjh.14520 CrossRefPubMedPubMedCentralGoogle Scholar
  68. Devi G, Zhou Y, Zhong Z, Toh DF, Chen G (2015) RNA triplexes: from structural principles to biological and biotech applications. Wiley Interdiscip Rev RNA 6(1):111–128.  https://doi.org/10.1002/wrna.1261 CrossRefPubMedPubMedCentralGoogle Scholar
  69. Di L, Kerns EH, Carter GT (2009) Drug-like property concepts in pharmaceutical design. Current Pharm Des 15(19):2184–2194CrossRefGoogle Scholar
  70. Dickerhoff J, Haase L, Langel W, Weisz K (2017) Tracing effects of fluorine substitutions on G-Quadruplex conformational changes. ACS Chem Biol 12(5):1308–1315.  https://doi.org/10.1021/acschembio.6b01096 CrossRefPubMedPubMedCentralGoogle Scholar
  71. DiMasi JA, Hansen RW, Grabowski HG (2003) The price of innovation: new estimates of drug development costs. J Health Econ 22(2):151–185.  https://doi.org/10.1016/S0167-6296(02)00126-1 CrossRefPubMedPubMedCentralGoogle Scholar
  72. Doherty EA, Doudna JA (2000) Ribozyme structures and mechanisms. Annu Rev Biochem 69:597–615.  https://doi.org/10.1146/annurev.biochem.69.1.597 CrossRefPubMedPubMedCentralGoogle Scholar
  73. Dolinnaya NG, Ogloblina AM, Yakubovskaya MG (2016) Structure, properties, and biological relevance of the DNA and RNA G-Quadruplexes: overview 50 years after their discovery. Biochem Biokhimiia 81(13):1602–1649.  https://doi.org/10.1134/s0006297916130034 CrossRefGoogle Scholar
  74. Doman TN, McGovern SL, Witherbee BJ, Kasten TP, Kurumbail R, Stallings WC, Connolly DT, Shoichet BK (2002) Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B. J Med Chem 45(11):2213–2221PubMedCrossRefPubMedCentralGoogle Scholar
  75. Dorn M, E Silva MB, Buriol LS, Lamb LC (2014) Three-dimensional protein structure prediction: methods and computational strategies. Comput Biol Chem 53:251–276.  https://doi.org/10.1016/j.compbiolchem.2014.10.001 CrossRefGoogle Scholar
  76. Duan Y, Kollman PA (1998) Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. Science 282(5389):740–744.  https://doi.org/10.1126/science.282.5389.740 CrossRefPubMedPubMedCentralGoogle Scholar
  77. Dudek CA, Dannheim H, Schomburg D (2017) BrEPS 2.0: optimization of sequence pattern prediction for enzyme annotation. PloS One 12(7):e0182216.  https://doi.org/10.1371/journal.pone.0182216 CrossRefPubMedPubMedCentralGoogle Scholar
  78. Dundas J, Ouyang Z, Tseng J, Binkowski A, Turpaz Y, Liang J (2006) CASTp: computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Res 34(Web Server issue):W116–W118.  https://doi.org/10.1093/nar/gkl282 CrossRefPubMedPubMedCentralGoogle Scholar
  79. Edwards PJ (2009) Current parallel chemistry principles and practice: application to the discovery of biologically active molecules. Curr Opin Drug Discov Dev 12(6):899–914Google Scholar
  80. Eisenberg D (2003) The discovery of the α-helix and β-sheet, the principal structural features of proteins. Proc Natl Acad Sci U S A 100(20):11207–11210.  https://doi.org/10.1073/pnas.2034522100 CrossRefPubMedPubMedCentralGoogle Scholar
  81. Eisenberg D, Luthy R, Bowie JU (1997) VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol 277:396–404PubMedCrossRefPubMedCentralGoogle Scholar
  82. Eyers PA, Craxton M, Morrice N, Cohen P, Goedert M (1998) Conversion of SB 203580-insensitive MAP kinase family members to drug-sensitive forms by a single amino-acid substitution. Chem Biol 5(6):321–328PubMedCrossRefPubMedCentralGoogle Scholar
  83. Fay MM, Lyons SM, Ivanov P (2017) RNA G-quadruplexes in biology: principles and molecular mechanisms. J Mol Biol 429(14):2127–2147.  https://doi.org/10.1016/j.jmb.2017.05.017 CrossRefPubMedPubMedCentralGoogle Scholar
  84. Ferre-D’Amare AR, Doudna JA (1999) RNA folds: insights from recent crystal structures. Annu Rev Biophys Biomol Struct 28:57–73.  https://doi.org/10.1146/annurev.biophys.28.1.57 CrossRefPubMedPubMedCentralGoogle Scholar
  85. Floudas CA (2007) Computational methods in protein structure prediction. Biotechnol Bioeng 97(2):207–213.  https://doi.org/10.1002/bit.21411 CrossRefPubMedPubMedCentralGoogle Scholar
  86. Frank J (2017) Advances in the field of single-particle cryo-electron microscopy over the last decade. Nat Protoc 12(2):209–212.  https://doi.org/10.1038/nprot.2017.004 CrossRefPubMedPubMedCentralGoogle Scholar
  87. Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH, Shelley M, Perry JK, Shaw DE, Francis P, Shenkin PS (2004) Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 47(7):1739–1749.  https://doi.org/10.1021/jm0306430 CrossRefPubMedPubMedCentralGoogle Scholar
  88. Frye SV (1999) Structure-activity relationship homology (SARAH): a conceptual framework for drug discovery in the genomic era. Chem Biol 6(1):R3–R7.  https://doi.org/10.1016/S1074-5521(99)80013-1 CrossRefPubMedPubMedCentralGoogle Scholar
  89. Fukuhara M, Ma Y, Nagasawa K, Toyoshima F (2017) A G-quadruplex structure at the 5′ end of the H19 coding region regulates H19 transcription. Sci Rep 7:45815.  https://doi.org/10.1038/srep45815 https://www.nature.com/articles/srep45815#supplementary-information CrossRefPubMedCentralGoogle Scholar
  90. Furnham N, Holliday GL, de Beer TA, Jacobsen JO, Pearson WR, Thornton JM (2014) The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes. Nucleic Acids Res 42(Database issue):D485–D489.  https://doi.org/10.1093/nar/gkt1243 CrossRefPubMedPubMedCentralGoogle Scholar
  91. Gajarsky M, Zivkovic ML, Stadlbauer P, Pagano B, Fiala R, Amato J, Tomaska L, Sponer J, Plavec J, Trantirek L (2017) Structure of a stable G-hairpin. J Am Chem Soc 139(10):3591–3594.  https://doi.org/10.1021/jacs.6b10786 CrossRefPubMedPubMedCentralGoogle Scholar
  92. Galaz-Montoya JG, Ludtke SJ (2017) The advent of structural biology in situ by single particle cryo-electron tomography. Biophys Rep 3(1):17–35.  https://doi.org/10.1007/s41048-017-0040-0 CrossRefPubMedPubMedCentralGoogle Scholar
  93. Gebetsberger J, Micura R (2017) Unwinding the twister ribozyme: from structure to mechanism. Wiley Interdiscip Rev RNA 8(3).  https://doi.org/10.1002/wrna.1402 CrossRefGoogle Scholar
  94. Ghose AK, Viswanadhan VN, Wendoloski JJ (1999) A knowledge-based approach in designing combinatorial or medicinal chemistry libraries for drug discovery. 1. A qualitative and quantitative characterization of known drug databases. J Comb Chem 1(1):55–68PubMedCrossRefPubMedCentralGoogle Scholar
  95. Ghosh A, Bansal M (2003) A glossary of DNA structures from A to Z. Acta Crystallogr D Biol Crystallogr 59(Pt 4):620–626PubMedCrossRefPubMedCentralGoogle Scholar
  96. Ghosh S, Kaushik A, Khurana S, Varshney A, Singh AK, Dahiya P, Thakur JK, Sarin SK, Gupta D, Malhotra P, Mukherjee SK, Bhatnagar RK (2017) An RNAi-based high-throughput screening assay to identify small molecule inhibitors of hepatitis B virus replication. J Biol Chem 292(30):12577–12588.  https://doi.org/10.1074/jbc.M117.775155 CrossRefPubMedPubMedCentralGoogle Scholar
  97. Ghouzam Y, Postic G, Guerin P-E, de Brevern AG, Gelly J-C (2016) ORION: a web server for protein fold recognition and structure prediction using evolutionary hybrid profiles. Sci Rep 6:28268.  https://doi.org/10.1038/srep28268 CrossRefPubMedPubMedCentralGoogle Scholar
  98. Gniewek P, Kolinski A, Kloczkowski A, Gront D (2014) BioShell-Threading: versatile Monte Carlo package for protein 3D threading. BMC Bioinf 15:22.  https://doi.org/10.1186/1471-2105-15-22 CrossRefGoogle Scholar
  99. Greider CW, Blackburn EH (1985) Identification of a specific telomere terminal transferase activity in Tetrahymena extracts. Cell 43(2 Pt 1):405–413PubMedCrossRefPubMedCentralGoogle Scholar
  100. Griffith JD, Comeau L, Rosenfield S, Stansel RM, Bianchi A, Moss H, de Lange T (1999) Mammalian telomeres end in a large duplex loop. Cell 97(4):503–514PubMedCrossRefPubMedCentralGoogle Scholar
  101. Groll M, Kim KB, Kairies N, Huber R, Crews CM (2000) Crystal structure of epoxomicin: 20S proteasome reveals a molecular basis for selectivity of α‘,β‘-epoxyketone proteasome inhibitors. J Am Chem Soc 122(6):1237–1238.  https://doi.org/10.1021/ja993588m CrossRefGoogle Scholar
  102. Hagler AT, Lifson S (1974) Energy functions for peptides and proteins. II. The amide hydrogen bond and calculation of amide crystal properties. J Am Chem Soc 96(17):5327–5335PubMedCrossRefPubMedCentralGoogle Scholar
  103. Hagler AT, Huler E, Lifson S (1974) Energy functions for peptides and proteins. I. Derivation of a consistent force field including the hydrogen bond from amide crystals. J Am Chem Soc 96(17):5319–5327PubMedCrossRefPubMedCentralGoogle Scholar
  104. Hall SR (1991) The star file – a new format for electronic data transfer and archiving. J Chem Inf Comp Sci 31(2):326–333.  https://doi.org/10.1021/Ci00002a020 CrossRefGoogle Scholar
  105. Hall SR, Allen FH, Brown ID (1991) The crystallographic information file (Cif) – a new standard archive file for crystallography. Acta Crystallogr A 47:655–685.  https://doi.org/10.1107/S010876739101067x CrossRefGoogle Scholar
  106. Harrington EC (1965) The desirability function. Ind Qual Control 21:494–498Google Scholar
  107. Hashi K, Ohki S, Matsumoto S, Nishijima G, Goto A, Deguchi K, Yamada K, Noguchi T, Sakai S, Takahashi M, Yanagisawa Y, Iguchi S, Yamazaki T, Maeda H, Tanaka R, Nemoto T, Suematsu H, Miki T, Saito K, Shimizu T (2015) Achievement of 1020MHz NMR. J Magn Reson 256:30–33.  https://doi.org/10.1016/j.jmr.2015.04.009 CrossRefPubMedPubMedCentralGoogle Scholar
  108. Holley RW (1965) Structure of an alanine transfer ribonucleic acid. Jama 194(8):868–871PubMedCrossRefPubMedCentralGoogle Scholar
  109. Holley RW, Apgar J, Everett GA, Madison JT, Marquisee M, Merrill SH, Penswick JR, Zamir A (1965) Structure of a ribonucleic acid. Science 147(3664):1462–1465PubMedCrossRefPubMedCentralGoogle Scholar
  110. Holliday GL, Brown SD, Akiva E, Mischel D, Hicks MA, Morris JH, Huang CC, Meng EC, Pegg SC, Ferrin TE, Babbitt PC (2017) Biocuration in the structure-function linkage database: the anatomy of a superfamily. Database: J Biol Databases Curation 2017(1).  https://doi.org/10.1093/database/bax006
  111. Hollyfield JG, Besharse JC, Rayborn ME (1976) The effect of light on the quantity of phagosomes in the pigment epithelium. Exp Eye Res 23(6):623–635PubMedCrossRefPubMedCentralGoogle Scholar
  112. Holm L, Laakso LM (2016) Dali server update. Nucleic Acids Res 44(W1):W351–W355.  https://doi.org/10.1093/nar/gkw357 CrossRefPubMedPubMedCentralGoogle Scholar
  113. Holm L, Sander C (1996) The FSSP database: fold classification based on structure-structure alignment of proteins. Nucleic Acids Res 24(1):206–209PubMedPubMedCentralCrossRefGoogle Scholar
  114. Honorio KM, Moda TL, Andricopulo AD (2013) Pharmacokinetic properties and in silico ADME modeling in drug discovery. Med Chem (Shariqah (United Arab Emirates)) 9(2):163–176CrossRefGoogle Scholar
  115. Hospital A, Goñi JR, Orozco M, Gelpí JL (2015) Molecular dynamics simulations: advances and applications. Adv Appl Bioinforma Chem 8:37–47.  https://doi.org/10.2147/AABC.S70333 CrossRefGoogle Scholar
  116. Hung L-H, Ngan S-C, Liu T, Samudrala R (2005) PROTINFO: new algorithms for enhanced protein structure predictions. Nucleic Acids Res 33(Web Server issue):W77–W80.  https://doi.org/10.1093/nar/gki403 CrossRefPubMedPubMedCentralGoogle Scholar
  117. Huppert JL (2010) Structure, location and interactions of G-quadruplexes. FEBS J 277(17):3452–3458.  https://doi.org/10.1111/j.1742-4658.2010.07758.x CrossRefPubMedPubMedCentralGoogle Scholar
  118. Hynninen AP, Crowley MF (2014) New faster CHARMM molecular dynamics engine. J Comput Chem 35(5):406–413.  https://doi.org/10.1002/jcc.23501 CrossRefPubMedPubMedCentralGoogle Scholar
  119. Ilari A, Savino C (2008) Protein structure determination by x-ray crystallography. Methods Mol Biol 452:63–87.  https://doi.org/10.1007/978-1-60327-159-2_3 CrossRefPubMedPubMedCentralGoogle Scholar
  120. Ilari A, Savino C (2017) A Practical Approach to Protein Crystallography. Methods in molecular biology 1525:47–78.  https://doi.org/10.1007/978-1-4939-6622-6_3 CrossRefPubMedPubMedCentralGoogle Scholar
  121. Jauch R, Yeo HC, Kolatkar PR, Clarke ND (2007) Assessment of CASP7 structure predictions for template free targets. Proteins 69(Suppl 8):57–67PubMedCrossRefPubMedCentralGoogle Scholar
  122. Jayaram B, Dhingra P, Mishra A, Kaushik R, Mukherjee G, Singh A, Shekhar S (2014) Bhageerath-H: a homology/ab initio hybrid server for predicting tertiary structures of monomeric soluble proteins. BMC Bioinf 15(Suppl 16):S7–S7.  https://doi.org/10.1186/1471-2105-15-S16-S7 CrossRefGoogle Scholar
  123. Jones DT, Swindells MB (2002) Getting the most from PSI-BLAST. Trends Biochem Sci 27(3):161–164PubMedCrossRefPubMedCentralGoogle Scholar
  124. Jones DT, Taylor WR, Thornton JM (1992) A new approach to protein fold recognition. Nature 358(6381):86–89.  https://doi.org/10.1038/358086a0 CrossRefPubMedPubMedCentralGoogle Scholar
  125. Jorgensen WL, Tiradorives J (1988) The Opls potential functions for proteins – energy minimizations for crystals of cyclic-peptides and crambin. J Am Chem Soc 110(6):1657–1666.  https://doi.org/10.1021/Ja00214a001 CrossRefPubMedPubMedCentralGoogle Scholar
  126. Jorgensen WL, Tirado-Rives J (1998) Development of the OPLS-AA force field for organic and biomolecular systems. Abstr Pap Am Chem S 216:U696–U696Google Scholar
  127. Jorgensen WL, Maxwell DS, Tirado Rives J (1996) Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 118(45):11225–11236.  https://doi.org/10.1021/Ja9621760 CrossRefGoogle Scholar
  128. Kallberg M, Margaryan G, Wang S, Ma J, Xu J (2014) RaptorX server: a resource for template-based protein structure modeling. Methods Mol Biol 1137:17–27.  https://doi.org/10.1007/978-1-4939-0366-5_2 CrossRefPubMedPubMedCentralGoogle Scholar
  129. Kaminski GA, Friesner RA, Tirado-Rives J, Jorgensen WL (2001) Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J Phys Chem B 105(28):6474–6487.  https://doi.org/10.1021/jp003919d CrossRefGoogle Scholar
  130. Kaus JW, Pierce LT, Walker RC, McCammon JA (2013) Improving the efficiency of free energy calculations in the amber molecular dynamics package. J Chem Theory Comput 9(9):4131–4139.  https://doi.org/10.1021/ct400340s CrossRefGoogle Scholar
  131. Kelley LA, MacCallum RM, Sternberg MJE (1999) Recognition of remote protein homologies using three-dimensional information to generate a position specific scoring matrix in the program 3D-PSSM. In: Paper presented at the proceedings of the third annual international conference on computational molecular biology, Lyon, FranceGoogle Scholar
  132. Kelley LA, Mezulis S, Yates CM, Wass MN, Sternberg MJ (2015) The Phyre2 web portal for protein modeling, prediction and analysis. Nat Protoc 10(6):845–858.  https://doi.org/10.1038/nprot.2015.053 CrossRefPubMedPubMedCentralGoogle Scholar
  133. Kendrew JC, Bodo G, Dintzis HM, Parrish RG, Wyckoff H, Phillips DC (1958) A three-dimensional model of the myoglobin molecule obtained by x-ray analysis. Nature 181(4610):662–666PubMedCrossRefPubMedCentralGoogle Scholar
  134. Kim SH, Suddath FL, Quigley GJ, McPherson A, Sussman JL, Wang AH, Seeman NC, Rich A (1974) Three-dimensional tertiary structure of yeast phenylalanine transfer RNA. Science 185(4149):435–440PubMedCrossRefPubMedCentralGoogle Scholar
  135. Kim DE, Chivian D, Baker D (2004) Protein structure prediction and analysis using the Robetta server. Nucleic Acids Res 32(Web Server issue):W526–W531.  https://doi.org/10.1093/nar/gkh468 CrossRefPubMedPubMedCentralGoogle Scholar
  136. Kirkpatrick S, Gelatt CD Jr, Vecchi MP (1983) Optimization by simulated annealing. Science 220(4598):671–680.  https://doi.org/10.1126/science.220.4598.671 CrossRefGoogle Scholar
  137. Klepeis JL, Floudas CA (2003) ASTRO-FOLD: a combinatorial and global optimization framework for Ab initio prediction of three-dimensional structures of proteins from the amino acid sequence. Biophys J 85(4):2119–2146.  https://doi.org/10.1016/S0006-3495(03)74640-2 CrossRefPubMedPubMedCentralGoogle Scholar
  138. Klepeis JL, Wei Y, Hecht MH, Floudas CA (2005) Ab initio prediction of the three-dimensional structure of a de novo designed protein: a double-blind case study. Proteins 58(3):560–570PubMedCrossRefPubMedCentralGoogle Scholar
  139. Kleywegt GJ, Harris MR, Zou JY, Taylor TC, Wahlby A, Jones TA (2004) The uppsala electron-density server. Acta Crystallogr D Biol Crystallogr 60(Pt 12 Pt 1):2240–2249.  https://doi.org/10.1107/s0907444904013253 CrossRefPubMedPubMedCentralGoogle Scholar
  140. Knudsen M, Wiuf C (2010) The CATH database. Hum Genomics 4(3):207–212.  https://doi.org/10.1186/1479-7364-4-3-207 CrossRefPubMedPubMedCentralGoogle Scholar
  141. Kocman V, Plavec J (2017) Tetrahelical structural family adopted by AGCGA-rich regulatory DNA regions. Nat Commun 8:15355.  https://doi.org/10.1038/ncomms15355 CrossRefPubMedPubMedCentralGoogle Scholar
  142. Kriegel F, Ermann N, Forbes R, Dulin D, Dekker NH, Lipfert J (2017a) Probing the salt dependence of the torsional stiffness of DNA by multiplexed magnetic torque tweezers. Nucleic Acids Res 45(10):5920–5929.  https://doi.org/10.1093/nar/gkx280 CrossRefPubMedPubMedCentralGoogle Scholar
  143. Kriegel F, Ermann N, Lipfert J (2017b) Probing the mechanical properties, conformational changes, and interactions of nucleic acids with magnetic tweezers. J Struct Biol 197(1):26–36.  https://doi.org/10.1016/j.jsb.2016.06.022 CrossRefPubMedPubMedCentralGoogle Scholar
  144. Kroese DP, Brereton T, Taimre T, Botev ZI (2014) Why the Monte Carlo method is so important today. Wiley Interdiscip Rev: Comput Stat 6(6):386–392.  https://doi.org/10.1002/wics.1314 CrossRefGoogle Scholar
  145. Kuntal BK, Aparoy P, Reddanna P (2010) EasyModeller: a graphical interface to MODELLER. BMC Res Notes 3:226.  https://doi.org/10.1186/1756-0500-3-226 CrossRefPubMedPubMedCentralGoogle Scholar
  146. Kuntz ID, Blaney JM, Oatley SJ, Langridge R, Ferrin TE (1982) A geometric approach to macromolecule-ligand interactions. J Mol Biol 161(2):269–288PubMedCrossRefPubMedCentralGoogle Scholar
  147. Kuryavyi V, Phan AT, Patel DJ (2010) Solution structures of all parallel-stranded monomeric and dimeric G-quadruplex scaffolds of the human c-kit2 promoter. Nucleic Acids Res 38(19):6757–6773.  https://doi.org/10.1093/nar/gkq558 CrossRefPubMedPubMedCentralGoogle Scholar
  148. Lagorce D, Sperandio O, Baell JB, Miteva MA, Villoutreix BO (2015) FAF-Drugs3: a web server for compound property calculation and chemical library design. Nucleic Acids Res 43(W1):W200–W207.  https://doi.org/10.1093/nar/gkv353 CrossRefPubMedPubMedCentralGoogle Scholar
  149. Lagorce D, Douguet D, Miteva MA, Villoutreix BO (2017) Computational analysis of calculated physicochemical and ADMET properties of protein-protein interaction inhibitors. Sci Rep 7:46277.  https://doi.org/10.1038/srep46277 CrossRefPubMedPubMedCentralGoogle Scholar
  150. Lambert C, Leonard N, De Bolle X, Depiereux E (2002) ESyPred3D: Prediction of proteins 3D structures. Bioinformatics (Oxford, England) 18(9):1250–1256CrossRefGoogle Scholar
  151. Lamiable A, Thevenet P, Rey J, Vavrusa M, Derreumaux P, Tuffery P (2016) PEP-FOLD3: faster de novo structure prediction for linear peptides in solution and in complex. Nucleic Acids Res 44(W1):W449–W454.  https://doi.org/10.1093/nar/gkw329 CrossRefPubMedPubMedCentralGoogle Scholar
  152. Laskowski RA, MacArthur MW, Moss DS, Thornton JM (1993) PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26(2):283–291.  https://doi.org/10.1107/S0021889892009944 CrossRefGoogle Scholar
  153. Laskowski RA, Rullmannn JA, MacArthur MW, Kaptein R, Thornton JM (1996) AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J Biomol NMR 8(4):477–486PubMedPubMedCentralCrossRefGoogle Scholar
  154. Lee J (1993) New Monte Carlo algorithm: Entropic sampling. Physical Rev Lett 71(2):211–214.  https://doi.org/10.1103/PhysRevLett.71.211 CrossRefGoogle Scholar
  155. Lee J, Scheraga HA, Rackovsky S (1998) Conformational analysis of the 20-residue membrane-bound portion of melittin by conformational space annealing. Biopolymers 46(2):103–116. https://doi.org/10.1002/(SICI)1097-0282(199808)46:2<103::AID-BIP5>3.0.CO;2-Q CrossRefPubMedPubMedCentralGoogle Scholar
  156. Leeson P (2012) Drug discovery: chemical beauty contest. Nature 481(7382):455–456PubMedCrossRefPubMedCentralGoogle Scholar
  157. Levitt DG, Banaszak LJ (1992) POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids. J Mol Graph 10(4):229–234PubMedCrossRefPubMedCentralGoogle Scholar
  158. Li MH, Wang ZF, Kuo MH, Hsu ST, Chang TC (2014) Unfolding kinetics of human telomeric G-quadruplexes studied by NMR spectroscopy. J Phys Chem B 118(4):931–936.  https://doi.org/10.1021/jp410034d CrossRefPubMedPubMedCentralGoogle Scholar
  159. Li H, O’Donoghue AJ, van der Linden WA, Xie SC, Yoo E, Foe IT, Tilley L, Craik CS, da Fonseca PC, Bogyo M (2016) Structure- and function-based design of Plasmodium-selective proteasome inhibitors. Nature 530(7589):233–236.  https://doi.org/10.1038/nature16936 CrossRefPubMedPubMedCentralGoogle Scholar
  160. Liang J, Edelsbrunner H, Woodward C (1998) Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Sci: Publ Protein Soc 7(9):1884–1897.  https://doi.org/10.1002/pro.5560070905 CrossRefGoogle Scholar
  161. Lipinski CA (2004) Lead- and drug-like compounds: the rule-of-five revolution. Drug Discov Today: Technol 1(4):337–341.  https://doi.org/10.1016/j.ddtec.2004.11.007 CrossRefGoogle Scholar
  162. Lipinski CA, Lombardo F, Dominy BW, Feeney PJ (2001) Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev 46(1-3):3–26PubMedCrossRefPubMedCentralGoogle Scholar
  163. Liu Z, Gutierrez-Vargas C, Wei J, Grassucci RA, Sun M, Espina N, Madison-Antenucci S, Tong L, Frank J (2017) Determination of the ribosome structure to a resolution of 2.5 A by single-particle cryo-EM. Protein Sci: Publ Protein Soc 26(1):82–92.  https://doi.org/10.1002/pro.3068 CrossRefGoogle Scholar
  164. Liwo A, Khalili M, Scheraga HA (2005) Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains. Proc Natl Acad Sci U S A 102(7):2362–2367PubMedPubMedCentralCrossRefGoogle Scholar
  165. Lo Conte L, Ailey B, Hubbard TJP, Brenner SE, Murzin AG, Chothia C (2000) SCOP: a structural classification of proteins database. Nucleic Acids Res 28(1):257–259PubMedPubMedCentralCrossRefGoogle Scholar
  166. Lobley A, Sadowski MI, Jones DT (2009) pGenTHREADER and pDomTHREADER: new methods for improved protein fold recognition and superfamily discrimination. Bioinformatics (Oxford, England) 25(14):1761–1767.  https://doi.org/10.1093/bioinformatics/btp302 CrossRefGoogle Scholar
  167. Lohning AE, Levonis SM, Williams-Noonan B, Schweiker SS (2017) a practical guide to molecular docking and homology modelling for medicinal chemists. Curr Top Med Chem 17(18):2023–2040.  https://doi.org/10.2174/1568026617666170130110827 CrossRefPubMedPubMedCentralGoogle Scholar
  168. Lovering F, Bikker J, Humblet C (2009) Escape from flatland: increasing saturation as an approach to improving clinical success. J Med Chem 52(21):6752–6756.  https://doi.org/10.1021/jm901241e CrossRefPubMedPubMedCentralGoogle Scholar
  169. Lu H, Skolnick J (2001) A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins-Struct Funct Genet 44(3):223–232.  https://doi.org/10.1002/Prot.1087 CrossRefPubMedPubMedCentralGoogle Scholar
  170. MacKerell AD, Bashford D, Bellott M, Dunbrack RL, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau FTK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe M, Wiorkiewicz-Kuczera J, Yin D, Karplus M (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102(18):3586–3616PubMedCrossRefPubMedCentralGoogle Scholar
  171. Madera M, Vogel C, Kummerfeld SK, Chothia C, Gough J (2004) The SUPERFAMILY database in 2004: additions and improvements. Nucleic Acids Res 32(Database issue):D235–D239.  https://doi.org/10.1093/nar/gkh117 CrossRefPubMedPubMedCentralGoogle Scholar
  172. Matter H, Baringhaus KH, Naumann T, Klabunde T, Pirard B (2001) Computational approaches towards the rational design of drug-like compound libraries. Comb Chem High Throughput Screen 4(6):453–475PubMedCrossRefPubMedCentralGoogle Scholar
  173. McClary B, Zinshteyn B, Meyer M, Jouanneau M, Pellegrino S, Yusupova G, Schuller A, Reyes JCP, Lu J, Guo Z, Ayinde S, Luo C, Dang Y, Romo D, Yusupov M, Green R, Liu JO (2017) Inhibition of eukaryotic translation by the antitumor natural product Agelastatin A. Cell Chem Biol 24(5):605–613 e605.  https://doi.org/10.1016/j.chembiol.2017.04.006 CrossRefPubMedPubMedCentralGoogle Scholar
  174. Meanwell NA (2011) Improving drug candidates by design: a focus on physicochemical properties as a means of improving compound disposition and safety. Chem Res Toxicol 24(9):1420–1456.  https://doi.org/10.1021/tx200211v CrossRefPubMedPubMedCentralGoogle Scholar
  175. Meanwell NA (2016) Improving drug design: an update on recent applications of efficiency metrics, strategies for replacing problematic elements, and compounds in nontraditional drug space. Chem Res Toxicol 29(4):564–616.  https://doi.org/10.1021/acs.chemrestox.6b00043 CrossRefPubMedPubMedCentralGoogle Scholar
  176. Millevoi S, Moine H, Vagner S (2012) G-quadruplexes in RNA biology. Wiley Interdiscip Rev RNA 3(4):495–507.  https://doi.org/10.1002/wrna.1113 CrossRefPubMedPubMedCentralGoogle Scholar
  177. Miteva MA, Villoutreix BO (2017) Computational biology and chemistry in MTi: emphasis on the prediction of some ADMET properties. Mol Inf 36.  https://doi.org/10.1002/minf.201700008 CrossRefGoogle Scholar
  178. Mixon MB, Lee E, Coleman DE, Berghuis AM, Gilman AG, Sprang SR (1995) Tertiary and quaternary structural changes in Gi alpha 1 induced by GTP hydrolysis. Science 270(5238):954–960PubMedCrossRefPubMedCentralGoogle Scholar
  179. Montgomerie S, Cruz JA, Shrivastava S, Arndt D, Berjanskii M, Wishart DS (2008) PROTEUS2: a web server for comprehensive protein structure prediction and structure-based annotation. Nucleic Acids Res 36(Web Server issue):W202–W209.  https://doi.org/10.1093/nar/gkn255 CrossRefPubMedPubMedCentralGoogle Scholar
  180. Murat P, Balasubramanian S (2014) Existence and consequences of G-quadruplex structures in DNA. Curr Opin Genet Dev 25:22–29.  https://doi.org/10.1016/j.gde.2013.10.012 CrossRefPubMedPubMedCentralGoogle Scholar
  181. Myasnikov AG, Kundhavai Natchiar S, Nebout M, Hazemann I, Imbert V, Khatter H, Peyron JF, Klaholz BP (2016) Structure-function insights reveal the human ribosome as a cancer target for antibiotics. Nat Commun 7:12856.  https://doi.org/10.1038/ncomms12856 CrossRefPubMedPubMedCentralGoogle Scholar
  182. Nagano N, Nakayama N, Ikeda K, Fukuie M, Yokota K, Doi T, Kato T, Tomii K (2015) EzCatDB: the enzyme reaction database, 2015 update. Nucleic Acids Res 43(Database issue):D453–D458.  https://doi.org/10.1093/nar/gku946 CrossRefPubMedPubMedCentralGoogle Scholar
  183. Neria E, Fischer S, Karplus M (1996) Simulation of activation free energies in molecular systems. J Chem Phys 105(5):1902–1921.  https://doi.org/10.1063/1.472061 CrossRefGoogle Scholar
  184. Newman DJ, Cragg GM (2012) Natural products as sources of new drugs over the 30 years from 1981 to 2010. J Nat Prod 75(3):311–335.  https://doi.org/10.1021/np200906s CrossRefPubMedPubMedCentralGoogle Scholar
  185. Nguyen LA, Wang J, Steitz TA (2017) Crystal structure of Pistol, a class of self-cleaving ribozyme. Proc Natl Acad Sci U S A 114(5):1021–1026.  https://doi.org/10.1073/pnas.1611191114 CrossRefPubMedPubMedCentralGoogle Scholar
  186. Nicholls A, Sharp KA, Honig B (1991) Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11(4):281–296.  https://doi.org/10.1002/prot.340110407 CrossRefPubMedGoogle Scholar
  187. Nugent CI, Lundblad V (1998) The telomerase reverse transcriptase: components and regulation. Genes Dev 12(8):1073–1085PubMedCrossRefPubMedCentralGoogle Scholar
  188. Oefner C, D’Arcy A, Hennig M, Winkler FK, Dale GE (2000) Structure of human neutral endopeptidase (Neprilysin) complexed with phosphoramidon. J Mol Biol 296(2):341–349.  https://doi.org/10.1006/jmbi.1999.3492 CrossRefPubMedGoogle Scholar
  189. Oldziej S, Czaplewski C, Liwo A, Chinchio M, Nanias M, Vila JA, Khalili M, Arnautova YA, Jagielska A, Makowski M, Schafroth HD, Kazmierkiewicz R, Ripoll DR, Pillardy J, Saunders JA, Kang YK, Gibson KD, Scheraga HA (2005) Physics-based protein-structure prediction using a hierarchical protocol based on the UNRES force field: assessment in two blind tests. Proc Natl Acad Sci U S A 102(21):7547–7552PubMedPubMedCentralCrossRefGoogle Scholar
  190. Oprea TI, Davis AM, Teague SJ, Leeson PD (2001) Is there a difference between leads and drugs? A historical perspective. J Chem Inf Comput Sci 41(5):1308–1315PubMedCrossRefGoogle Scholar
  191. Orlov I, Myasnikov AG, Andronov L, Natchiar SK, Khatter H, Beinsteiner B, Menetret JF, Hazemann I, Mohideen K, Tazibt K, Tabaroni R, Kratzat H, Djabeur N, Bruxelles T, Raivoniaina F, Pompeo LD, Torchy M, Billas I, Urzhumtsev A, Klaholz BP (2017) The integrative role of cryo electron microscopy in molecular and cellular structural biology. Biol Cell 109(2):81–93.  https://doi.org/10.1111/boc.201600042 CrossRefPubMedGoogle Scholar
  192. Osterberg F, Morris GM, Sanner MF, Olson AJ, Goodsell DS (2002) Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock. Proteins 46(1):34–40PubMedCrossRefGoogle Scholar
  193. Pagadala NS, Syed K, Tuszynski J (2017) Software for molecular docking: a review. Biophys Rev 9(2):91–102.  https://doi.org/10.1007/s12551-016-0247-1 CrossRefPubMedPubMedCentralGoogle Scholar
  194. Pandey RB, Jacobs DJ, Farmer BL (2017) Preferential binding effects on protein structure and dynamics revealed by coarse-grained Monte Carlo simulation. J Chem Phys 146(19):195101.  https://doi.org/10.1063/1.4983222 CrossRefPubMedPubMedCentralGoogle Scholar
  195. Paquet E, Viktor HL (2015) Molecular dynamics, Monte Carlo simulations, and langevin dynamics: a computational review. BioMed Res Int 2015:183918.  https://doi.org/10.1155/2015/183918 CrossRefPubMedPubMedCentralGoogle Scholar
  196. Parkinson GN, Lee MP, Neidle S (2002) Crystal structure of parallel quadruplexes from human telomeric DNA. Nature 417(6891):876–880.  https://doi.org/10.1038/nature755 CrossRefPubMedPubMedCentralGoogle Scholar
  197. Patel DJ, Phan AT, Kuryavyi V (2007) Human telomere, oncogenic promoter and 5’-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics. Nucleic Acids Res 35(22):7429–7455.  https://doi.org/10.1093/nar/gkm711 CrossRefPubMedPubMedCentralGoogle Scholar
  198. Patel TR, Chojnowski G, Astha, Koul A, McKenna SA, Bujnicki JM (2017) Structural studies of RNA-protein complexes: a hybrid approach involving hydrodynamics, scattering, and computational methods. Methods (San Diego, Calif) 118:146–162.  https://doi.org/10.1016/j.ymeth.2016.12.002 CrossRefGoogle Scholar
  199. Pauling L, Corey RB (1951) Configuration of polypeptide chains. Nature 168(4274):550–551PubMedCrossRefPubMedCentralGoogle Scholar
  200. Pauling L, Corey RB, Branson HR (1951) The structure of proteins; two hydrogen-bonded helical configurations of the polypeptide chain. Proc Natl Acad Sci U S A 37(4):205–211PubMedPubMedCentralCrossRefGoogle Scholar
  201. Perrone R, Lavezzo E, Palu G, Richter SN (2017) Conserved presence of G-quadruplex forming sequences in the Long Terminal Repeat Promoter of Lentiviruses. Sci Rep 7(1):2018.  https://doi.org/10.1038/s41598-017-02291-1 CrossRefPubMedPubMedCentralGoogle Scholar
  202. Piccirilli JA, Koldobskaya Y (2011) Crystal structure of an RNA polymerase ribozyme in complex with an antibody fragment. Philos Trans R Soc Lond Ser B Biol Sci 366(1580):2918–2928.  https://doi.org/10.1098/rstb.2011.0144 CrossRefGoogle Scholar
  203. Pillardy J, Czaplewski C, Liwo A, Lee J, Ripoll DR, Kazmierkiewicz R, Oldziej S, Wedemeyer WJ, Gibson KD, Arnautova YA, Saunders J, Ye YJ, Scheraga HA (2001) Recent improvements in prediction of protein structure by global optimization of a potential energy function. Proc Natl Acad Sci U S A 98(5):2329–2333.  https://doi.org/10.1073/pnas.041609598 CrossRefPubMedPubMedCentralGoogle Scholar
  204. Porrini M, Rosu F, Rabin C, Darre L, Gomez H, Orozco M, Gabelica V (2017) Compaction of duplex nucleic acids upon native electrospray mass spectrometry. ACS Cent Sci 3(5):454–461.  https://doi.org/10.1021/acscentsci.7b00084 CrossRefPubMedPubMedCentralGoogle Scholar
  205. Quester S, Schomburg D (2011) EnzymeDetector: an integrated enzyme function prediction tool and database. BMC Bioinf 12:376.  https://doi.org/10.1186/1471-2105-12-376 CrossRefGoogle Scholar
  206. Ramachandran GN (1963) Protein structure and crystallography. Science 141(3577):288–291.  https://doi.org/10.1126/science.141.3577.288 CrossRefPubMedPubMedCentralGoogle Scholar
  207. Ramachandran GN, Ramakrishnan C, Sasisekharan V (1963) Stereochemistry of polypeptide chain configurations. J Mol Biol 7:95–99PubMedCrossRefPubMedCentralGoogle Scholar
  208. Rarey M, Kramer B, Lengauer T, Klebe G (1996) A fast flexible docking method using an incremental construction algorithm. J Mol Biol 261(3):470–489.  https://doi.org/10.1006/jmbi.1996.0477 CrossRefPubMedPubMedCentralGoogle Scholar
  209. Razi A, Britton RA, Ortega J (2017) The impact of recent improvements in cryo-electron microscopy technology on the understanding of bacterial ribosome assembly. Nucleic Acids Res 45(3):1027–1040.  https://doi.org/10.1093/nar/gkw1231 CrossRefPubMedPubMedCentralGoogle Scholar
  210. Redfern OC, Harrison A, Dallman T, Pearl FMG, Orengo CA (2007) CATHEDRAL: a fast and effective algorithm to predict folds and domain boundaries from multidomain protein structures. PLOS Comput Biol 3(11):e232.  https://doi.org/10.1371/journal.pcbi.0030232 CrossRefPubMedPubMedCentralGoogle Scholar
  211. Redfern OC, Dessailly BH, Dallman TJ, Sillitoe I, Orengo CA (2009) FLORA: a novel method to predict protein function from structure in diverse superfamilies. PLoS Comput Biol 5(8):e1000485.  https://doi.org/10.1371/journal.pcbi.1000485 CrossRefPubMedPubMedCentralGoogle Scholar
  212. Rhodes D, Giraldo R (1995) Telomere structure and function. Curr Opin Struct Biol 5(3):311–322PubMedCrossRefPubMedCentralGoogle Scholar
  213. Rhodes D, Lipps HJ (2015) G-quadruplexes and their regulatory roles in biology. Nucleic Acids Res 43(18):8627–8637.  https://doi.org/10.1093/nar/gkv862 CrossRefPubMedPubMedCentralGoogle Scholar
  214. Rich A (1956) Recent studies on the structure of ribonucleic acid. Prog Neurobiol 1:114–121PubMedPubMedCentralGoogle Scholar
  215. Rich A (1960) A hybrid helix containing both deoxyribose and ribose polynucleotides and its relation to the transfer of information between the nucleic acids. Proc Natl Acad Sci U S A 46(8):1044–1053PubMedPubMedCentralCrossRefGoogle Scholar
  216. Rich A, Davies DR, Crick FH, Watson JD (1961) The molecular structure of polyadenylic acid. J Mol Biol 3:71–86PubMedCrossRefPubMedCentralGoogle Scholar
  217. Rietveld K, Van Poelgeest R, Pleij CW, Van Boom JH, Bosch L (1982) The tRNA-like structure at the 3’ terminus of turnip yellow mosaic virus RNA. Differences and similarities with canonical tRNA. Nucleic Acids Res 10(6):1929–1946PubMedPubMedCentralCrossRefGoogle Scholar
  218. Robertus JD, Ladner JE, Finch JT, Rhodes D, Brown RS, Clark BF, Klug A (1974) Structure of yeast phenylalanine tRNA at 3 A resolution. Nature 250(467):546–551PubMedCrossRefPubMedCentralGoogle Scholar
  219. Rodley GA, Scobie RS, Bates RH, Lewitt RM (1976) A possible conformation for double-stranded polynucleotides. Proc Natl Acad Sci U S A 73(9):2959–2963PubMedPubMedCentralCrossRefGoogle Scholar
  220. Roques BP (1985) Enkephalinase inhibitors and molecular study of the differences between active sites of enkephalinase and angiotensin-converting enzyme. J Pharmacol 16(Suppl 1):5–31PubMedPubMedCentralGoogle Scholar
  221. Rose PW, Prlić A, Altunkaya A, Bi C, Bradley AR, Christie CH, Costanzo LD, Duarte JM, Dutta S, Feng Z, Green RK, Goodsell DS, Hudson B, Kalro T, Lowe R, Peisach E, Randle C, Rose AS, Shao C, Tao Y-P, Valasatava Y, Voigt M, Westbrook JD, Woo J, Yang H, Young JY, Zardecki C, Berman HM, Burley SK (2017) The RCSB protein data bank: integrative view of protein, gene and 3D structural information. Nucleic Acids Res 45(D1):D271–D281.  https://doi.org/10.1093/nar/gkw1000 CrossRefPubMedPubMedCentralGoogle Scholar
  222. Rost B (1999) Twilight zone of protein sequence alignments. Protein Eng 12(2):85–94PubMedCrossRefPubMedCentralGoogle Scholar
  223. Ruiz-Blanco YB, Aguero-Chapin G (2017) Exploring general-purpose protein features for distinguishing enzymes and non-enzymes within the twilight zone. BMC Bioinf 18(1):349.  https://doi.org/10.1186/s12859-017-1758-x CrossRefGoogle Scholar
  224. Sammito M, Millan C, Rodriguez DD, de Ilarduya IM, Meindl K, De Marino I, Petrillo G, Buey RM, de Pereda JM, Zeth K, Sheldrick GM, Uson I (2013) Exploiting tertiary structure through local folds for crystallographic phasing. Nat Methods 10(11):1099–1101.  https://doi.org/10.1038/nmeth.2644 CrossRefPubMedPubMedCentralGoogle Scholar
  225. Samudrala R, Moult J (1998) An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J Mol Biol 275(5):895–916.  https://doi.org/10.1006/jmbi.1997.1479 CrossRefPubMedPubMedCentralGoogle Scholar
  226. Samudrala R, Xia Y, Huang E, Levitt M (1999) Ab initio protein structure prediction using a combined hierarchical approach. Proteins Suppl 3:194–198CrossRefGoogle Scholar
  227. Sander C, Schneider R (1991) Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins 9(1):56–68PubMedCrossRefPubMedCentralGoogle Scholar
  228. Sathyamoorthy B, Shi H, Zhou H, Xue Y, Rangadurai A, Merriman DK, Al-Hashimi HM (2017) Insights into Watson-Crick/Hoogsteen breathing dynamics and damage repair from the solution structure and dynamic ensemble of DNA duplexes containing m1A. Nucleic Acids Res 45(9):5586–5601.  https://doi.org/10.1093/nar/gkx186 CrossRefPubMedPubMedCentralGoogle Scholar
  229. Scapin G (2006) Structural biology and drug discovery. Current Pharm Des 12(17):2087–2097CrossRefGoogle Scholar
  230. Schlick T, Pyle AM (2017) Opportunities and challenges in RNA structural modeling and design. Biophys J 113(2):225–234.  https://doi.org/10.1016/j.bpj.2016.12.037 CrossRefPubMedPubMedCentralGoogle Scholar
  231. Sedova A, Banavali NK (2015) RNA approaches the B-form in stacked single strand dinucleotide contexts. Biopolymers.  https://doi.org/10.1002/bip.22750 CrossRefGoogle Scholar
  232. Shekhawat PB, Pokharkar VB (2017) Understanding peroral absorption: regulatory aspects and contemporary approaches to tackling solubility and permeability hurdles. Acta Pharm Sin B 7(3):260–280.  https://doi.org/10.1016/j.apsb.2016.09.005 CrossRefGoogle Scholar
  233. Shen MY, Sali A (2006) Statistical potential for assessment and prediction of protein structures. Protein Sci: Publ Protein Soc 15(11):2507–2524.  https://doi.org/10.1110/ps.062416606 CrossRefGoogle Scholar
  234. Simons KT, Kooperberg C, Huang E, Baker D (1997) Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. J Mol Biol 268(1):209–225PubMedCrossRefPubMedCentralGoogle Scholar
  235. Skiniotis G, Southworth DR (2016) Single-particle cryo-electron microscopy of macromolecular complexes. Microscopy (Oxford, England) 65(1):9–22.  https://doi.org/10.1093/jmicro/dfv366 CrossRefGoogle Scholar
  236. Skolnick J (2006) In quest of an empirical potential for protein structure prediction. Curr Opin Struct Biol 16(2):166–171.  https://doi.org/10.1016/j.sbi.2006.02.004 CrossRefPubMedPubMedCentralGoogle Scholar
  237. Skolnick J, Jaroszewski L, Kolinski A, Godzik A (1997) Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct? Protein Sci: Publ Protein Soc 6(3):676–688.  https://doi.org/10.1002/pro.5560060317 CrossRefGoogle Scholar
  238. Sleator RD, Walsh P (2010) An overview of in silico protein function prediction. Arch Microbiol 192(3):151–155.  https://doi.org/10.1007/s00203-010-0549-9 CrossRefPubMedPubMedCentralGoogle Scholar
  239. Smith C (2003) Drug target validation: hitting the target. Nature 422(6929): 341, 343, 345 passim.  https://doi.org/10.1038/422341a PubMedPubMedCentralGoogle Scholar
  240. Sneader W (2000) The discovery of aspirin: a reappraisal. BMJ: Br Med J 321(7276):1591–1594CrossRefGoogle Scholar
  241. Söding J, Biegert A, Lupas AN (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 33(Web Server issue):W244–W248.  https://doi.org/10.1093/nar/gki408 CrossRefPubMedPubMedCentralGoogle Scholar
  242. Stahl K, Schneider M, Brock O (2017) EPSILON-CP: using deep learning to combine information from multiple sources for protein contact prediction. BMC Bioinf 18:303.  https://doi.org/10.1186/s12859-017-1713-x CrossRefGoogle Scholar
  243. Stank A, Kokh DB, Horn M, Sizikova E, Neil R, Panecka J, Richter S, Wade RC (2017) TRAPP webserver: predicting protein binding site flexibility and detecting transient binding pockets. Nucleic Acids Res.  https://doi.org/10.1093/nar/gkx277 PubMedPubMedCentralCrossRefGoogle Scholar
  244. Staple DW, Butcher SE (2005) Pseudoknots: RNA structures with diverse functions. PLoS Biol 3(6):e213.  https://doi.org/10.1371/journal.pbio.0030213 CrossRefPubMedPubMedCentralGoogle Scholar
  245. Subramaniam S, Earl LA, Falconieri V, Milne JLS, Egelman EH (2016) Resolution advances in cryo-EM enable application to drug discovery. Curr Opin Struct Biol 41:194–202.  https://doi.org/10.1016/j.sbi.2016.07.009 CrossRefPubMedPubMedCentralGoogle Scholar
  246. Sugiki T, Kobayashi N, Fujiwara T (2017) Modern technologies of solution nuclear magnetic resonance spectroscopy for three-dimensional structure determination of proteins open avenues for life scientists. Comput Struct Biotechnol J 15:328–339.  https://doi.org/10.1016/j.csbj.2017.04.001 CrossRefPubMedPubMedCentralGoogle Scholar
  247. Sun LZ, Zhang D, Chen SJ (2017) Theory and modeling of RNA structure and interactions with metal ions and small molecules. Annu Rev Biophys 46:227–246.  https://doi.org/10.1146/annurev-biophys-070816-033920 CrossRefPubMedPubMedCentralGoogle Scholar
  248. Takahama K, Takada A, Tada S, Shimizu M, Sayama K, Kurokawa R, Oyoshi T (2013) Regulation of telomere length by G-quadruplex telomere DNA- and TERRA-binding protein TLS/FUS. Chem Biol 20(3):341–350.  https://doi.org/10.1016/j.chembiol.2013.02.013 CrossRefPubMedPubMedCentralGoogle Scholar
  249. Tice CM (2001) Selecting the right compounds for screening: does Lipinski’s Rule of 5 for pharmaceuticals apply to agrochemicals? Pest Manag Sci 57(1):3–16. https://doi.org/10.1002/1526-4998(200101)57:1<3::aid-ps269>3.0.co;2-6 CrossRefPubMedPubMedCentralGoogle Scholar
  250. Tice CM (2002) Selecting the right compounds for screening: use of surface-area parameters. Pest Manag Sci 58(3):219–233.  https://doi.org/10.1002/ps.441 CrossRefPubMedPubMedCentralGoogle Scholar
  251. Tilton RF, Dewan JC, Petsko GA (1992) Effects of temperature on protein structure and dynamics: x-ray crystallographic studies of the protein ribonuclease-A at nine different temperatures from 98 to 320K. Biochemistry 31(9):2469–2481.  https://doi.org/10.1021/bi00124a006 CrossRefPubMedPubMedCentralGoogle Scholar
  252. Tinoco I Jr, Bustamante C (1999) How RNA folds. J Mol Biol 293(2):271–281.  https://doi.org/10.1006/jmbi.1999.3001 CrossRefPubMedPubMedCentralGoogle Scholar
  253. Tosatto SC, Toppo S (2006) Large-scale prediction of protein structure and function from sequence. Curr Pharm Des 12(17):2067–2086PubMedCrossRefPubMedCentralGoogle Scholar
  254. Tripathi A, Kellogg GE (2010) A novel and efficient tool for locating and characterizing protein cavities and binding sites. Proteins 78(4):825–842.  https://doi.org/10.1002/prot.22608 CrossRefPubMedPubMedCentralGoogle Scholar
  255. Vaguine AA, Richelle J, Wodak SJ (1999) SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. Acta Crystallogr D Biol Crystallogr 55(Pt 1):191–205.  https://doi.org/10.1107/s0907444998006684 CrossRefPubMedPubMedCentralGoogle Scholar
  256. Vallianatou T, Giaginis C, Tsantili-Kakoulidou A (2015) The impact of physicochemical and molecular properties in drug design: navigation in the “drug-like” chemical space. Adv Exp Med Biol 822:187–194.  https://doi.org/10.1007/978-3-319-08927-0_21 CrossRefPubMedPubMedCentralGoogle Scholar
  257. Veber DF, Johnson SR, Cheng HY, Smith BR, Ward KW, Kopple KD (2002) Molecular properties that influence the oral bioavailability of drug candidates. J Med Chem 45(12):2615–2623PubMedCrossRefPubMedCentralGoogle Scholar
  258. Venclovas C, Margelevicius M (2005) Comparative modeling in CASP6 using consensus approach to template selection, sequence-structure alignment, and structure assessment. Proteins 61(Suppl 7):99–105PubMedCrossRefPubMedCentralGoogle Scholar
  259. Venkatachalam CM, Jiang X, Oldfield T, Waldman M (2003) LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites. J Mol Graph Model 21(4):289–307PubMedCrossRefPubMedCentralGoogle Scholar
  260. Venko K, Roy Choudhury A, Novic M (2017) Computational approaches for revealing the structure of membrane transporters: case study on bilitranslocase. Comput Struct Biotechnol J 15:232–242.  https://doi.org/10.1016/j.csbj.2017.01.008 CrossRefPubMedPubMedCentralGoogle Scholar
  261. Villoutreix BO (2016) Combining bioinformatics, chemoinformatics and experimental approaches to design chemical probes: applications in the field of blood coagulation. Ann Pharm Fr 74(4):253–266.  https://doi.org/10.1016/j.pharma.2016.03.006 CrossRefPubMedPubMedCentralGoogle Scholar
  262. Wahl MC, Sundaralingam M (1997) Crystal structures of A-DNA duplexes. Biopolymers 44(1):45–63. https://doi.org/10.1002/(sici)1097-0282(1997)44:1<45::aid-bip4>3.0.co;2-#CrossRefPubMedPubMedCentralGoogle Scholar
  263. Wan W, Briggs JA (2016) Cryo-electron tomography and subtomogram averaging. Methods Enzymol 579:329–367.  https://doi.org/10.1016/bs.mie.2016.04.014 CrossRefPubMedPubMedCentralGoogle Scholar
  264. Wang G, Vasquez KM (2007) Z-DNA, an active element in the genome. Front Biosci 12:4424–4438PubMedCrossRefPubMedCentralGoogle Scholar
  265. Wang AH, Quigley GJ, Kolpak FJ, Crawford JL, van Boom JH, van der Marel G, Rich A (1979) Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature 282(5740):680–686PubMedCrossRefPubMedCentralGoogle Scholar
  266. Wang Z, Yin P, Lee JS, Parasuram R, Somarowthu S, Ondrechen MJ (2013) Protein function annotation with Structurally Aligned Local Sites of Activity (SALSAs). BMC Bioinf 14(Suppl 3):S13–S13.  https://doi.org/10.1186/1471-2105-14-S3-S13 CrossRefGoogle Scholar
  267. Wang C, Zhang H, Zheng W-M, Xu D, Zhu J, Wang B, Ning K, Sun S, Li SC, Bu D (2016) FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition. Bioinformatics (Oxford, England) 32(3):462–464.  https://doi.org/10.1093/bioinformatics/btv581 CrossRefGoogle Scholar
  268. Wang S, Sun S, Li Z, Zhang R, Xu J (2017) Accurate de novo prediction of protein contact map by ultra-deep learning model. PLoS Comput Biol 13(1):e1005324.  https://doi.org/10.1371/journal.pcbi.1005324 CrossRefPubMedPubMedCentralGoogle Scholar
  269. Watson JD, Crick FH (1953) Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 171(4356):737–738PubMedCrossRefPubMedCentralGoogle Scholar
  270. Webb B, Sali A (2016) Comparative protein structure modeling using MODELLER. Current protocols in bioinformatics/editorial board, Andreas D Baxevanis [et al] 54:5.6.1–5.6.37.  https://doi.org/10.1002/cpbi.3
  271. Weichenberger CX, Sippl MJ (2007) NQ-Flipper: recognition and correction of erroneous asparagine and glutamine side-chain rotamers in protein structures. Nucleic Acids Res 35(Web Server issue):W403–W406.  https://doi.org/10.1093/nar/gkm263 CrossRefPubMedPubMedCentralGoogle Scholar
  272. Weiner SJ, Kollman PA, Case DA, Singh UC, Ghio C, Alagona G, Profeta S, Weiner P (1984) A new force-field for molecular mechanical simulation of nucleic-acids and proteins. J Am Chem Soc 106(3):765–784.  https://doi.org/10.1021/Ja00315a051 CrossRefGoogle Scholar
  273. Weisser M, Schafer T, Leibundgut M, Bohringer D, Aylett CHS, Ban N (2017) Structural and functional insights into human re-initiation complexes. Mol Cell 67(3):447–456.e447.  https://doi.org/10.1016/j.molcel.2017.06.032 CrossRefPubMedPubMedCentralGoogle Scholar
  274. Weldon C, Eperon IC, Dominguez C (2016) Do we know whether potential G-quadruplexes actually form in long functional RNA molecules? Biochem Soc Trans 44(6):1761–1768.  https://doi.org/10.1042/bst20160109 CrossRefPubMedPubMedCentralGoogle Scholar
  275. Weldon C, Behm-Ansmant I, Hurley LH, Burley GA, Branlant C, Eperon IC, Dominguez C (2017) Identification of G-quadruplexes in long functional RNAs using 7-deazaguanine RNA. Nat Chem Biol 13(1):18–20.  https://doi.org/10.1038/nchembio.2228 CrossRefPubMedPubMedCentralGoogle Scholar
  276. Westbrook JD, Hall RS (1995) DDL. A dictionary description language for structure macromolecular, V. 2.1.1. Rutgers University NDB-110, New BrunswickGoogle Scholar
  277. Whisstock JC, Lesk AM (2003) Prediction of protein function from protein sequence and structure. Q Rev Biophys 36(3):307–340PubMedCrossRefPubMedCentralGoogle Scholar
  278. Wiederstein M, Sippl MJ (2007) ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 35(Web Server issue):W407–W410.  https://doi.org/10.1093/nar/gkm290 CrossRefPubMedPubMedCentralGoogle Scholar
  279. Wilkins MH, Stokes AR, Wilson HR (1953) Molecular structure of deoxypentose nucleic acids. Nature 171(4356):738–740PubMedCrossRefPubMedCentralGoogle Scholar
  280. Wing R, Drew H, Takano T, Broka C, Tanaka S, Itakura K, Dickerson RE (1980) Crystal structure analysis of a complete turn of B-DNA. Nature 287(5784):755–758PubMedCrossRefPubMedCentralGoogle Scholar
  281. Wright WE, Tesmer VM, Huffman KE, Levene SD, Shay JW (1997) Normal human chromosomes have long G-rich telomeric overhangs at one end. Genes Dev 11(21):2801–2809PubMedPubMedCentralCrossRefGoogle Scholar
  282. Wu S, Zhang Y (2008) MUSTER: Improving protein sequence profile–profile alignments by using multiple sources of structure information. Proteins 72(2):547–556.  https://doi.org/10.1002/prot.21945 CrossRefPubMedPubMedCentralGoogle Scholar
  283. Xu J, Stevenson J (2000) Drug-like index: a new approach to measure drug-like compounds and their diversity. J Chem Inf Comput Sci 40(5):1177–1187PubMedCrossRefPubMedCentralGoogle Scholar
  284. Xu D, Zhang Y (2012) Ab initio protein structure assembly using continuous structure fragments and optimized knowledge-based force field. Proteins 80(7):1715–1735.  https://doi.org/10.1002/prot.24065 CrossRefPubMedPubMedCentralGoogle Scholar
  285. Yang J, Zhang Y (2015) I-TASSER server: new development for protein structure and function predictions. Nucleic Acids Res 43(W1):W174–W181.  https://doi.org/10.1093/nar/gkv342 CrossRefPubMedPubMedCentralGoogle Scholar
  286. Yang H, Guranovic V, Dutta S, Feng Z, Berman HM, Westbrook JD (2004) Automated and accurate deposition of structures solved by X-ray diffraction to the Protein Data Bank. Acta Crystallogr D Biol Crystallogr 60(Pt 10):1833–1839.  https://doi.org/10.1107/s0907444904019419 CrossRefPubMedPubMedCentralGoogle Scholar
  287. Yang Y, Faraggi E, Zhao H, Zhou Y (2011) Improving protein fold recognition and template-based modeling by employing probabilistic-based matching between predicted one-dimensional structural properties of query and corresponding native properties of templates. Bioinformatics (Oxford, England) 27(15):2076–2082.  https://doi.org/10.1093/bioinformatics/btr350 CrossRefGoogle Scholar
  288. Yella VR, Bansal M (2017) DNA structural features of eukaryotic TATA-containing and TATA-less promoters. FEBS Open Bio 7(3):324–334.  https://doi.org/10.1002/2211-5463.12166 CrossRefPubMedPubMedCentralGoogle Scholar
  289. Zamenhof S, Brawerman G, Chargaff E (1952) On the desoxypentose nucleic acids from several microorganisms. Biochim Biophys Acta 9(4):402–405PubMedCrossRefPubMedCentralGoogle Scholar
  290. Zeng B, Wang H, Zou L, Zhang A, Yang X, Guan Z (2010) Evaluation and target validation of indole derivatives as inhibitors of the AcrAB-TolC efflux pump. Biosci Biotechnol Biochem 74(11):2237–2241.  https://doi.org/10.1271/bbb.100433 CrossRefPubMedPubMedCentralGoogle Scholar
  291. Zhang Y, Skolnick J (2004) Automated structure prediction of weakly homologous proteins on a genomic scale. Proc Natl Acad Sci U S A 101(20):7594–7599.  https://doi.org/10.1073/pnas.0305695101 CrossRefPubMedPubMedCentralGoogle Scholar
  292. Zhang Y, Skolnick J (2005) The protein structure prediction problem could be solved using the current PDB library. Proc Natl Acad Sci U S A 102(4):1029–1034.  https://doi.org/10.1073/pnas.0407152101 CrossRefPubMedPubMedCentralGoogle Scholar
  293. Zhang Y, Kolinski A, Skolnick J (2003) TOUCHSTONE II: a new approach to ab initio protein structure prediction. Biophys J 85(2):1145–1164.  https://doi.org/10.1016/S0006-3495(03)74551-2 CrossRefPubMedPubMedCentralGoogle Scholar
  294. Zhang Y, Hubner IA, Arakaki AK, Shakhnovich E, Skolnick J (2006) On the origin and highly likely completeness of single-domain protein structures. Proc Natl Acad Sci U S A 103(8):2605–2610.  https://doi.org/10.1073/pnas.0509379103 CrossRefPubMedPubMedCentralGoogle Scholar
  295. Zhao C, Pyle AM (2017) Structural insights into the mechanism of group II intron splicing. Trends Biochem Sci 42(6):470–482.  https://doi.org/10.1016/j.tibs.2017.03.007 CrossRefPubMedPubMedCentralGoogle Scholar
  296. Zheng H, Cooper DR, Porebski PJ, Shabalin IG, Handing KB, Minor W (2017) CheckMyMetal: a macromolecular metal-binding validation tool. Acta Crystallogr D Struct Biol 73(Pt 3):223–233.  https://doi.org/10.1107/S2059798317001061 CrossRefPubMedPubMedCentralGoogle Scholar
  297. Zhou H, Zhou Y (2002) Distance-scaled, finite ideal-gas reference state improves structure-derived potentials of mean force for structure selection and stability prediction. Protein Sci: Publ Protein Soc 11(11):2714–2726.  https://doi.org/10.1110/ps.0217002 CrossRefGoogle Scholar
  298. Zhou H, Hintze BJ, Kimsey IJ, Sathyamoorthy B, Yang S, Richardson JS, Al-Hashimi HM (2015) New insights into Hoogsteen base pairs in DNA duplexes from a structure-based survey. Nucleic Acids Res 43(7):3420–3433.  https://doi.org/10.1093/nar/gkv241 CrossRefPubMedPubMedCentralGoogle Scholar
  299. Zwanzig R, Szabo A, Bagchi B (1992) Levinthal’s paradox. Proc Natl Acad Sci U S A 89(1):20–22PubMedPubMedCentralCrossRefGoogle Scholar

Copyright information

© Springer Nature Singapore Pte Ltd. 2018

Authors and Affiliations

  • Ankita Punetha
    • 1
  • Payel Sarkar
    • 1
  • Siddharth Nimkar
    • 1
  • Himanshu Sharma
    • 1
  • Yoganand KNR
    • 1
  • Siranjeevi Nagaraj
    • 1
  1. 1.Department of Biosciences and BioengineeringIndian Institute of Technology GuwahatiGuwahatiIndia

Personalised recommendations