Bioinformatics resources and tools for phage display.
Databases and computational tools for mimotopes have been an important part of phage display study. Five special databases and eighteen algorithms, programs and web servers and their applications are reviewed in this paper. Although these bioinformatics resources have been widely used to exclude target-unrelated peptides, characterize small molecules-protein interactions and map protein-protein interactions, a lot of problems are still waiting to be solved. With the improvement of these tools, they are expected to serve the phage display community better.
Key Laboratory for Neuroinformation of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, Sichuan 610054, China. hj@uestc.edu.cn
Jian
J
Huang
Beibei
B
Ru
Ping
P
Dai
D000465:Algorithms; D001435:Bacteriophages / Q000235:genetics*; D019295:Computational Biology; D012984:Software
Nature. 1996 Mar 28;380(6572):364-6
8598934
Oncogene. 2010 Aug 12;29(32):4517-27
20514015
Chem Rev. 1997 Apr 1;97(2):391-410
11848876
Bioinformatics. 2006 May 1;22(9):1088-95
16434442
EMBO J. 1998 Jul 1;17(13):3521-33
9649423
Anal Biochem. 2008 Feb 1;373(1):88-98
17976366
Science. 1990 Jul 27;249(4967):386-90
1696028
Biochemistry. 2009 Dec 22;48(50):11982-93
19899804
J Mol Biol. 2003 Nov 14;334(1):87-101
14596802
Bioinformatics. 2007 Dec 1;23(23):3244-6
17977889
Molecules. 2010 Nov 15;15(11):8279-88
21079566
J Mol Biol. 2006 May 26;359(1):190-201
16630634
J Biol Chem. 2006 Mar 10;281(10):6813-25
16407202
Nature. 1990 Dec 6;348(6301):552-4
2247164
Protein Sci. 2003 Jul;12(7):1344-59
12824481
Proc Natl Acad Sci U S A. 2006 May 16;103(20):7619-24
16684878
J Innate Immun. 2009;1(6):556-69
20375611
J Drug Target. 2010 Feb;18(2):115-24
19751096
Parasitology. 2008 Oct;135(12):1437-45
18812010
J Comput Biol. 2003;10(3-4):555-67
12935344
FASEB J. 2006 Sep;20(11):1762-74
16940148
Biomaterials. 2009 Mar;30(7):1287-98
19095299
Clin Exp Allergy. 2010 Jan;40(1):174-81
20205701
Mol Immunol. 1986 Jul;23(7):709-15
2432410
Proteomics. 2006 Aug;6(15):4210-22
16819727
Biopolymers. 1995 Nov;36(5):675-80
7578958
Anal Biochem. 2010 Dec 15;407(2):237-40
20692225
Immunome Res. 2010 Nov 03;6 Suppl 2:S6
21067548
Atherosclerosis. 2007 Sep;194(1):79-87
17097662
Biochimie. 2007 Sep;89(9):1145-58
17397983
J Mol Biol. 2006 Mar 17;357(1):236-51
16414071
Mol Immunol. 2008 Nov;46(1):125-34
18760481
BMC Biotechnol. 2007 Oct 05;7:65
17919322
Mol Immunol. 2009 Jan;46(3):429-36
19038455
Bioorg Med Chem. 2008 Nov 15;16(22):9837-46
18930404
Science. 2002 Oct 18;298(5593):621-2
12386335
Proc Natl Acad Sci U S A. 2010 Mar 16;107(11):5112-7
20190181
FASEB J. 2000 Nov;14(14):2177-84
11053238
Science. 2002 Jan 11;295(5553):321-4
11743162
Proteomics. 2004 May;4(5):1439-60
15188413
Cells Tissues Organs. 2009;189(1-4):245-51
18701808
Nucleic Acids Res. 2007;35(1):69-78
17151070
Science. 1990 Jul 27;249(4967):404-6
2143033
Nucleic Acids Res. 2002 Jan 1;30(1):200-2
11752292
Vaccine. 2010 Jul 26;28(33):5398-406
20594626
Mol Imaging Biol. 2006 Jul-Aug;8(4):201-7
16791746
J Immunol. 2007 Aug 15;179(4):2520-31
17675514
Science. 1996 Jul 26;273(5274):458-64
8662529
J Mol Recognit. 2006 Jan-Feb;19(1):21-9
16193533
Science. 1985 Jun 14;228(4705):1315-7
4001944
RNA Biol. 2005 Jan;2(1):28-33
17132933
Immunobiology. 2010;215(1):26-37
19261354
Proc Natl Acad Sci U S A. 2010 Mar 16;107(11):5118-23
20190183
Biomacromolecules. 2009 Mar 9;10(3):555-64
19186939
J Comput Chem. 2005 Jul 15;26(9):879-87
15834923
J Biomed Biotechnol. 2010;2010:101932
20339521
Bioinform Biol Insights. 2009 Jul 01;3:71-81
20140073
BMC Bioinformatics. 2007 Aug 01;8:280
17678535
Science. 1997 Jun 13;276(5319):1696-9
9180079
BMC Bioinformatics. 2006 Oct 12;7:451
17038191
J Biol Chem. 2006 Nov 17;281(46):35413-24
16928679
Stem Cells. 2008 Oct;26(10):2735-45
18583538
Protein Sci. 2003 Nov;12(11):2453-75
14573859
Hybridoma (Larchmt). 2008 Aug;27(4):291-301
18707547
BMC Bioinformatics. 2008 Dec 16;9:538
19087303
Proteins. 2007 Jul 1;68(1):294-304
17427229
Anal Biochem. 2005 Jan 15;336(2):145-57
15620878
N Engl J Med. 2009 Nov 5;361(19):1848-55
19890127
Comb Chem High Throughput Screen. 2010 Jan;13(1):75-87
20214576
Nat Biotechnol. 1997 Jan;15(1):29-34
9035102
Curr Opin Biotechnol. 1995 Feb;6(1):73-80
7534506