Assisted assignment of ligands corresponding to unknown electron density

Journal of Structural and Functional Genomics

Volumn 11, Issue 1, 2010, Pages 21-30

  Binkowski, T Andrew ^a   Cuff, Marianne ^a   Nocek, Boguslaw ^a   Chang, Changsoo ^a   Joachimiak, Andrzej ^a  

^a ARGONNE NATIONAL LABORATORY   (United States)

Author keywords

Electron density assignment; Function annotation; Ligand assignment; Ligand identification; Protein surfaces

Indexed keywords

DEOXYGUANOSINE TRIPHOSPHATE; GAMMA TUBULIN; GUANOSINE DIPHOSPHATE; GUANOSINE TRIPHOSPHATE; INULINASE; ISOMERASE; PYRROLINE 5 CARBOXYLATE REDUCTASE;

ACCESS TO INFORMATION; ARABIDOPSIS; ARCHAEOGLOBUS FULGIDUS; ARTICLE; ASPERGILLUS AWAMORI; AUTOMATION; BINDING SITE; COMPUTER PROGRAM; CONTROLLED STUDY; CRYSTALLOGRAPHY; ELECTRON; HELICOBACTER PYLORI; HIGH THROUGHPUT SCREENING; HUMAN; INTERNET; LIGAND BINDING; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; NEISSERIA MENINGITIDIS; NONHUMAN; PHYSICAL CHEMISTRY; PRINCIPAL COMPONENT ANALYSIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; QUALITY CONTROL; STRUCTURAL GENOMICS;

COMPUTATIONAL BIOLOGY; CRYSTALLOGRAPHY, X-RAY; ELECTRONS; LIGANDS;

EID: 77951296316     PISSN: 1345711X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10969-010-9078-7     Document Type: Article

References (25)

1. DJ Diller E Pohl MR Redinbo BT Hovey WG Hol 1999 Proteins 36 4 512 25 10.1002/(SICI)1097-0134(19990901)36:4<512::AID-PROT15>3.0.CO;2-V 1:CAS:528:DyaK1MXltlKjt7w%3D 10450093 (Pubitemid 29387750)
2. TJ Oldfield 2001 Acta Crystallographica Section D 57 5 696 705 1:STN:280:DC%2BD3M3nsF2luw%3D%3D
3. TC Terwilliger 2002 Acta Crystallographica Section D 58 11 1937 1940
4. PH Zwart GG Langer VS Lamzin 2004 Acta Crystallographica Section D 60 12 Part 1 2230 2239 1:STN:280:DC%2BD2cnjs1SgsQ%3D%3D
5. J Aishima DS Russel LJ Guibas PD Adams AT Brunger 2005 Acta Crystallogr D Biol Crystallogr 61 Pt 10 1354 1363 10.1107/S0907444905023152 16204887 (Pubitemid 43943134)
6. S Wlodek AG Skillman A Nicholls 2006 Acta Crystallogr D Biol Crystallogr 62 Pt 7 741 749 10.1107/S0907444906016076 1:STN:280:DC%2BD28znsVaksw%3D%3D 16790930 (Pubitemid 43965900)
7. TC Terwilliger PD Adams NW Moriarty JD Cohn 2007 Acta Crystallogr D Biol Crystallogr 63 Pt 1 101 107 17164532
8. RA Laskowski JD Watson JM Thornton 2005 J Mol Biol 351 3 614 626 10.1016/j.jmb.2005.05.067 1:CAS:528:DC%2BD2MXmvVCmtrk%3D 16019027 (Pubitemid 41021944)
9. TA Binkowski L Adamian J Liang 2003 J Mol Biol 332 2 505 526 10.1016/S0022-2836(03)00882-9 1:CAS:528:DC%2BD3sXms1Oqurc%3D 12948498 (Pubitemid 37013514)
10. TA Binkowski A Joachimiak J Liang 2005 Protein Sci 14 12 2972 2981 10.1110/ps.051759005 1:CAS:528:DC%2BD2MXhtlWlsLzP 16322579 (Pubitemid 41770138)
11. TA Binkowski A Joachimiak 2008 BMC Struct Biol 8 45 10.1186/1472-6807-8- 45 18954462
12. GR Stockwell JM Thornton 2006 J Mol Biol 356 4 928 944 10.1016/j.jmb.2005.12.012 1:CAS:528:DC%2BD28XotVOitA%3D%3D 16405908 (Pubitemid 43145947)
13. A Kahraman RJ Morris RA Laskowski JM Thornton 2007 J Mol Biol 368 1 283 301 10.1016/j.jmb.2007.01.086 1:CAS:528:DC%2BD2sXjsVeqt78%3D 17337005 (Pubitemid 46454307)
14. TA Binkowski S Naghibzadeh J Liang 2003 Nucleic Acids Res 31 13 3352 3355 10.1093/nar/gkg512 1:CAS:528:DC%2BD3sXltVWjs7Y%3D 12824325 (Pubitemid 37442157)
15. Wei L, He Y (2006) In: Zha H, Pan Z, Thwaites H, Addison AC, Forte M (eds) Interactive technologies and sociotechnical systems, 12th international conference, VSMM 2006, Xi'an, China, 18-20 October 2006, Proceedings, volume 4270 of Lecture Notes in Computer Science. Springer, pp 263-268
16. R Osada T Funkhouser B Chazelle D Dobkin 2002 ACM Trans Graph 21 4 807 832 10.1145/571647.571648
17. J Liang H Edelsbrunner C Woodward 1998 Protein Sci 7 9 1884 1897 10.1002/pro.5560070905 1:CAS:528:DyaK1cXmtFGjsLo%3D 9761470
18. J Liang H Edelsbrunner P Fu PV Sudhakar S Subramaniam 1998 Proteins 33 1 1 17 10.1002/(SICI)1097-0134(19981001)33:1<1::AID-PROT1>3.0.CO;2-O 1:CAS:528:DyaK1cXlvFCis7w%3D 9741840 (Pubitemid 28413009)
19. J Liang H Edelsbrunner P Fu PV Sudhakar S Subramaniam 1998 Proteins 33 1 18 29 10.1002/(SICI)1097-0134(19981001)33:1<18::AID-PROT2>3.0.CO;2-H 1:CAS:528:DyaK1cXlvFCis70%3D 9741841 (Pubitemid 28413010)
20. Willett P, Barnard J, Downs G (1998) J Chem Inf Comput Sci (38):983-996
21. TSr Rush JA Grant L Mosyak A Nicholls 2005 J Med Chem 48 5 1489 1495 10.1021/jm040163o 1:CAS:528:DC%2BD2MXht1Ols78%3D 15743191 (Pubitemid 40364556)
22. M Nayal B Honig 2006 Proteins 63 4 892 906 10.1002/prot.20897 1:CAS:528:DC%2BD28Xlt1Wjsbg%3D 16477622 (Pubitemid 43765141)
23. P Emsley K Cowtan 2004 Acta Crystallogr D Biol Crystallogr 60 Pt 12 Pt 1 2126 2132 10.1107/S0907444904019158 15572765 (Pubitemid 41742764)
24. T Sing O Sander N Beerenwinkel T Lengauer 2005 Bioinformatics 21 20 3940 3941 10.1093/bioinformatics/bti623 1:CAS:528:DC%2BD2MXhtFWltr7P 16096348 (Pubitemid 41535515)
25. CW Yde I Ermakova O-G Issinger K Niefind 2005 J Mol Biol 347 2 399 414 10.1016/j.jmb.2005.01.003 1:CAS:528:DC%2BD2MXhvVGitLc%3D 15740749 (Pubitemid 40312467)