Empowering pharmacoinformatics by linked life science data

Journal of Computer-Aided Molecular Design

Volumn 31, Issue 3, 2017, Pages 319-328

  Goldmann, Daria ^a   Zdrazil, Barbara ^a   Digles, Daniela ^a   Ecker, Gerhard F ^a  

^a UNIVERSITY OF VIENNA   (Austria)

Author keywords

Computer aided drug discovery; Data curation; Data extraction; Data integration; Pharmacophore modeling; QSAR; TRPV1

Indexed keywords

COMPUTATIONAL CHEMISTRY; MOLECULAR GRAPHICS;

COMPUTER-AIDED DRUG DISCOVERY; DATA CURATION; DATA EXTRACTION; DATA-SOURCE; LARGE DATA; LIFE-SCIENCES; PHARMACOPHORE MODELS; QSAR; SCIENCE-DATA; TRPV1;

DATA INTEGRATION;

ARTICLE; BIOMEDICINE; COMPUTER AIDED DESIGN; DATA EXTRACTION; DATA PROCESSING; DRUG MECHANISM; INFORMATION RETRIEVAL; MEDICAL INFORMATICS; PRIORITY JOURNAL; QUANTITATIVE STRUCTURE ACTIVITY RELATION; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; DRUG DESIGN; DRUG INDUSTRY; PROCEDURES; SOFTWARE; STRUCTURE ACTIVITY RELATION; WORKFLOW;

PROTEIN;

BIOLOGICAL SCIENCE DISCIPLINES; COMPUTATIONAL BIOLOGY; DRUG DESIGN; DRUG INDUSTRY; MOLECULAR STRUCTURE; PROTEINS; SOFTWARE; STRUCTURE-ACTIVITY RELATIONSHIP; WORKFLOW;

EID: 84994391768     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-016-9990-4     Document Type: Article

References (64)

1. Cramer RD, Patterson DE, Bunce JD (1988) J Am Chem Soc 110(18):5959–5967
2. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) Nucleic Acids Res 28(1):235–242
3. Markley JL, Ulrich EL, Berman HM, Henrick K, Nakamura H, Akutsu H (2008) J Biomol NMR 40(3):153–155
4. Lawson CL, Baker ML, Best C, Bi C, Dougherty M, Feng P, van Ginkel G, Devkota B, Lagerstedt I, Ludtke SJ, Newman RH, Oldfield TJ, Rees I, Sahni G, Sala R, Velankar S, Warren J, Westbrook JD, Henrick K, Kleywegt GJ, Berman HM, Chiu W (2011) Nucleic Acids Res 39(Database issue):D456–D464
5. Allen FH (2002) Acta Crystallogr B 58(Pt 3 Pt 1):380–388
6. Groom CR, Bruno IJ, Lightfoot MP, Ward SC (2016) Acta Crystallogr B Struct Sci Cryst Eng Mater 72(Pt 2):171–179
7. Berthold MR, Cebron N, Dill F, Gabriel TR, Kotter T, Meinl T, Ohl P, Sieb C, Thiel K, Wiswedel B (2008) Data analysis, machine learning and applications. In: Proceedings of the 31st Annual Conference of the Gesellschaft für Klassifikation eV (Studies in classification, data analysis, and knowledge organization). Springer, Berlin, p 319–326
8. Stevenson JM, Mulready PD (2003) J Am Chem Soc 125(5):1437–1438
9. Frank E, Hall M, Trigg L, Holmes G, Witten IH (2004) Bioinformatics 20(15):2479–2481
10. Pedregosa F, Varoquaux G, Gramfort A, Michel V, Thirion B, Grisel O, Blondel M, Prettenhofer P, Weiss R, Dubourg V, Vanderplas J, Passos A, Cournapeau D, Brucher M, Perrot M, Duchesnay E (2011) J Mach Learn Res 12:2825–2830
11. Zdrazil B, Hellsberg E, Viereck M, Ecker GF (2016) Med Chem Comm 7:1694–1715
12. Digles D, Zdrazil B, Neefs JM, Van Vlijmen H, Herhaus C, Caracoti A, Brea J, Roibas B, Loza MI, Queralt-Rosinach N, Furlong LI, Gaulton A, Bartek L, Senger S, Chichester C, Engkvist O, Evelo CT, Franklin NI, Marren D, Ecker GF, Jacoby E (2016) Medchemcomm 7(6):1237–1244
13. Chichester C, Digles D, Siebes R, Loizou A, Groth P, Harland L (2015) Drug Discov Today 20(4):399–405
14. Chiba P, Ecker GF, Schmid D, Drach J, Tell B, Goldenberg S, Gekeler V (1996) Mol Pharmacol 49(6):1122–1130
15. Ecker GF, Huber M, Schmid D, Chiba P (1999) Mol Pharmacol 56(4):791–796
16. Ecker GF, Chiba P (2004) Pure Appl Chem 76(5):997–1005
17. Kaiser D, Smiesko M, Kopp S, Chiba P, Ecker GF (2005) Med Chem 1(5):431–444
18. Langer T, Eder M, Hoffmann RD, Chiba P, Ecker GF (2004) Arch Pharm (Weinheim) 337(6):317–327
19. Kaiser D, Terfloth L, Kopp S, Schulz J, de Laet R, Chiba P, Ecker GF, Gasteiger J (2007) J Med Chem 50(7):1698–1702
20. Aller SG, Yu J, Ward A, Weng Y, Chittaboina S, Zhuo R, Harrell PM, Trinh YT, Zhang Q, Urbatsch IL, Chang G (2009) Science 323(5922):1718–1722
21. Li J, Jaimes KF, Aller SG (2014) Protein Sci 23(1):34–46
22. Klepsch F, Chiba P, Ecker GF (2011) Plos Comput Biol 7(5):e1002036
23. Sarker S, Weissensteiner R, Steiner I, Sitte HH, Ecker GF, Freissmuth M, Sucic S (2010) Mol Pharmacol 78(6):1026–1035
24. Richter L, de Graaf C, Sieghart W, Varagic Z, Mörzinger M, de Esch IJP, Ecker GF, Ernst M (2012) Nature Chem Biol 8:455–464
25. Jurik A, Zdrazil B, Holy M, Stockner T, Sitte HH, Ecker GF (2015) J Med Chem 58(5):2149–2158
26. Wolber G, Langer T (2005) J Chem Inf Model 45(1):160–169
27. Williams AJ, Harland L, Groth P, Pettifer S, Chichester C, Willighagen EL, Evelo CT, Blomberg N, Ecker GF, Goble C, Mons B (2012) Drug Discov Today 17(21–22):1188–1198
28. Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, Consortium O, Leontis OBI, Rocca-Serra P, Ruttenberg A, Sansone SA, Scheuermann RH, Shah N, Whetzel PL, Lewis S (2007) Nat Biotechnol 25(11):1251–1255
29. Elefsinioti A, Bellaire T, Wang A, Quast K, Seidel H, Braxenthaler M, Goeller G, Christianson A, Henderson D, Reischl J (2016) Nat Rev Drug Discov 15(6):369–370
30. Broccatelli F, Carosati E, Neri A, Frosini M, Goracci L, Oprea TI, Cruciani G (2011) J Med Chem 54(6):1740–1751
31. Chen L, Li YY, Zhao Q, Peng H, Hou TJ (2011) Mol Pharm 8(3):889–900
32. Klepsch F, Vasanthanathan P, Ecker GF (2014) J Chem Inf Model 54(1):218–229
33. Zdrazil B, Pinto M, Vasanthanathan P, Williams AJ, Balderud LZ, Engkvist O, Chichester C, Hersey A, Overington JP, Ecker GF (2012) Mol Inform 31(8):599–609
34. Zdrazil B, Chichester C, Zander Balderud L, Engkvist O, Gaulton A, Overington JP (2014) Drug Discov Today Technol 12:e47–e54
35. Groth P, Andrew G, Velterop J (2010) Inf Serv Use 30:51–56
36. Mons B, van Haagen H, Chichester C, Hoen PB, den Dunnen JT, van Ommen G, van Mulligen E, Singh B, Hooft R, Roos M, Hammond J, Kiesel B, Giardine B, Velterop J, Groth P, Schultes E (2011) Nat Genet 43(4):281–283
37. Montanari F, Ecker GF (2014) Mol Inform 33:322–331
38. Kalliokoski T, Kramer C, Vulpetti A, Gedeck P (2013) PLoS ONE 8(4):e61007
39. Karapetyan K, Batchelor C, Sharpe D, Tkachenko V, Williams AJ (2015) J Cheminform 7:30
40. Azzaoui K, Jacoby E, Senger S, Rodriguez EC, Loza M, Zdrazil B, Pinto M, Williams AJ, de la Torre V, Mestres J, Pastor M, Taboureau O, Rarey M, Chichester C, Pettifer S, Blomberg N, Harland L, Williams-Jones B, Ecker GF (2013) Drug Discov Today 18(17–18):843–852
41. Ratnam J, Zdrazil B, Digles D, Cuadrado-Rodriguez E, Neefs JM, Tipney H, Siebes R, Waagmeester A, Bradley G, Chau CH, Richter L, Brea J, Evelo CT, Jacoby E, Senger S, Loza MI, Ecker GF, Chichester C (2014) PLoS ONE 9(12):e115460
42. Montanari F, Zdrazil B, Digles D, Ecker GF (2016) J Cheminform 8:7
43. Steenland HW, Ko SW, Wu LJ, Zhuo M (2006) Mol Pain 2:34
44. Szolcsanyi J (2014) Prog Drug Res 68:1–37
45. Winter Z, Buhala A, Otvos F, Josvay K, Vizler C, Dombi G, Szakonyi G, Olah Z (2013) Mol Pain 9:30
46. Fernandez-Ballester G, Ferrer-Montiel A (2008) J Membr Biol 223(3):161–172
47. Lee JH, Lee Y, Ryu H, Kang DW, Lee J, Lazar J, Pearce LV, Pavlyukovets VA, Blumberg PM, Choi S (2011) J Comput Aided Mol Des 25(4):317–327
48. Westaway SM (2007) J Med Chem 50(11):2589–2596
49. Kym PR, Kort ME, Hutchins CW (2009) Biochem Pharmacol 78(3):211–216
50. Gaulton A, Bellis LJ, Bento AP, Chambers J, Davies M, Hersey A, Light Y, McGlinchey S, Michalovich D, Al-Lazikani B, Overington JP (2012) Nucleic Acids Res 40(Database issue):D1100–D1107
51. Tsareva DA, Ecker GF (2013) Mol Inform 32(5–6):555–562
52. Goldmann D, Montanari F, Richter L, Zdrazil B, Ecker GF (2014) Future Med Chem 6(5):503–514
53. Kotsampasakou E, Brenner S, Jager W, Ecker GF (2015) Mol Pharm 12(12):4395–4404
54. Kotsampasakou E, Escher SE, Ecker GF (2016) Eur J Pharm Sci (submitted)
55. Pastor M, Cruciani G, McLay I, Pickett S, Clementi S (2000) J Med Chem 43(17):3233–3243
56. Goldmann D, Pakfeifer P, Hering S, Ecker GF (2015) Future Med Chem 7(3):243–256
57. Montanari F, Pinto M, Khunweeraphong N, Wlcek K, Sohail MI, Noeske T, Boyer S, Chiba P, Stieger B, Kuchler K, Ecker GF (2016) Mol Pharm 13(1):163–171
58. Liao M, Cao E, Julius D, Cheng Y (2013) Nature 504(7478):107–112
59. Yang F, Xiao X, Cheng W, Yang W, Yu P, Song Z, Yarov-Yarovoy V, Zheng J (2015) Nat Chem Biol 11(7):518–524
60. Gao Y, Cao E, Julius D, Cheng Y (2016) Nature 534(7607):347–351
61. Wilkinson MD, Dumontier M, Aalbersberg IJ, Appleton G, Axton M, Baak A, Blomberg N, Boiten JW, da Silva Santos LB, Bourne PE, Bouwman J, Brookes AJ, Clark T, Crosas M, Dillo I, Dumon O, Edmunds S, Evelo CT, Finkers R, Gonzalez-Beltran A, Gray AJ, Groth P, Goble C, Grethe JS, Heringa J, t Hoen PA, Hooft R, Kuhn T, Kok R, Kok J, Lusher SJ, Martone ME, Mons A, Packer AL, Persson B, Rocca-Serra P, Roos M, van Schaik R, Sansone SA, Schultes E, Sengstag T, Slater T, Strawn G, Swertz MA, Thompson M, van der Lei J, van Mulligen E, Velterop J, Waagmeester A, Wittenburg P, Wolstencroft K, Zhao J, Mons B (2016) Sci Data 3:160018
62. Lee JA, Shinn P, Jaken S, Oliver S, Willard FS, Heidler S, Peery RB, Oler J, Chu S, Southall N, Dexheimer TS, Smallwood J, Huang R, Guha R, Jadhav A, Cox K, Austin CP, Simeonov A, Sittampalam GS, Husain S, Franklin N, Wild DJ, Yang JJ, Sutherland JJ, Thomas CJ (2015) PLoS ONE 10(7):e0130796
63. Gurinova J, Digles D, Ecker GF (2016) Open PHACTS Conference: Linking Life Science Data: Design to Implementation, and Beyond. Vienna
64. Klepsch F, Ecker GF (2010) Mol Inform 29:276–286