title: Protein structural similarity search by Ramachandran codes.
abstract: BACKGROUND
  Protein structural data has increased exponentially, such that fast and accurate tools are necessary to access structure similarity search. To improve the search speed, several methods have been designed to reduce three-dimensional protein structures to one-dimensional text strings that are then analyzed by traditional sequence alignment methods; however, the accuracy is usually sacrificed and the speed is still unable to match sequence similarity search tools. Here, we aimed to improve the linear encoding methodology and develop efficient search tools that can rapidly retrieve structural homologs from large protein databases.
  
  
  RESULTS
  We propose a new linear encoding method, SARST (Structural similarity search Aided by Ramachandran Sequential Transformation). SARST transforms protein structures into text strings through a Ramachandran map organized by nearest-neighbor clustering and uses a regenerative approach to produce substitution matrices. Then, classical sequence similarity search methods can be applied to the structural similarity search. Its accuracy is similar to Combinatorial Extension (CE) and works over 243,000 times faster, searching 34,000 proteins in 0.34 sec with a 3.2-GHz CPU. SARST provides statistically meaningful expectation values to assess the retrieved information. It has been implemented into a web service and a stand-alone Java program that is able to run on many different platforms.
  
  
  CONCLUSIONS
  As a database search method, SARST can rapidly distinguish high from low similarities and efficiently retrieve homologous structures. It demonstrates that the easily accessible linear encoding methodology has the potential to serve as a foundation for efficient protein structural similarity search tools. These search tools are supposed applicable to automated and high-throughput functional annotations or predictions for the ever increasing number of published protein structures in this post-genomic era.
authors: Institute of Bioinformatics and Structural Biology, National Tsing Hua University, 101, Section 2 Kuang Fu Road, Hsinchu 30013, Taiwan. b861636@life.nthu.edu.tw
authors: Wei-Cheng
authors: WC
authors: Lo
authors: Po-Jung
authors: PJ
authors: Huang
authors: Chih-Hung
authors: CH
authors: Chang
authors: Ping-Chiang
authors: PC
authors: Lyu
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D003628:Database Management Systems; D030562:Databases, Protein; D016247:Information Storage and Retrieval / Q000379:methods*; D008969:Molecular Sequence Data; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid
chemical_list: D011506:Proteins
references: Nucleic Acids Res. 2000 Jan 1;28(1):254-6
references: 10592239
references: J Biosci. 2007 Jan;32(1):51-70
references: 17426380
references: Proteins. 2000 Jul 1;40(1):6-22
references: 10813826
references: J Mol Biol. 2000 Jun 2;299(2):499-520
references: 10860755
references: Proteins. 2000 Nov 15;41(3):271-87
references: 11025540
references: Protein Eng. 2000 Dec;13(12):829-37
references: 11239082
references: J Mol Biol. 2001 Jun 29;310(1):243-57
references: 11419950
references: Nucleic Acids Res. 2002 Jan 1;30(1):260-3
references: 11752310
references: Proteins. 2002 Mar 1;46(4):405-15
references: 11835515
references: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D189-92
references: 14681391
references: Bioinformatics. 2004 May 1;20(7):1045-52
references: 14962928
references: J Mol Biol. 2004 Jun 4;339(3):591-605
references: 15147844
references: Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W545-8
references: 15215446
references: Adv Protein Chem. 1968;23:283-438
references: 4882249
references: Biopolymers. 1985 Oct;24(10):1995-2023
references: 4074850
references: EMBO J. 1986 Apr;5(4):823-6
references: 3709526
references: Proc Natl Acad Sci U S A. 1988 May;85(10):3338-42
references: 3368445
references: J Mol Biol. 1990 Mar 5;212(1):151-66
references: 2319595
references: Proteins. 1990;7(3):249-56
references: 2362946
references: J Mol Biol. 1990 Oct 5;215(3):403-10
references: 2231712
references: Proteins. 1991;9(4):280-95
references: 1866432
references: Proc Natl Acad Sci U S A. 1992 Nov 15;89(22):10915-9
references: 1438297
references: Prog Biophys Mol Biol. 1993;60(3):201-39
references: 8372226
references: J Mol Biol. 1993 Sep 5;233(1):123-38
references: 8377180
references: J Mol Biol. 1994 Mar 11;236(5):1369-81
references: 8126726
references: Nucleic Acids Res. 1994 Sep;22(17):3600-9
references: 7937067
references: Nucleic Acids Res. 1994 Nov 11;22(22):4673-80
references: 7984417
references: Methods Enzymol. 1996;266:383-402
references: 8743695
references: Methods Enzymol. 1996;266:460-80
references: 8743700
references: J Biomol NMR. 1996 Dec;8(4):477-86
references: 9008363
references: Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
references: 9254694
references: Curr Opin Struct Biol. 1998 Jun;8(3):380-7
references: 9666335
references: Protein Eng. 1998 Sep;11(9):739-47
references: 9796821
references: J Mol Biol. 1998 Dec 11;284(4):1201-10
references: 9837738
references: In Silico Biol. 2004;4(3):381-6
references: 15724288
references: Proteins. 2005 Feb 15;58(3):618-27
references: 15609341
references: J Am Med Inform Assoc. 2005 May-Jun;12(3):296-8
references: 15684123
references: Proteins. 2005 Jun 1;59(4):810-27
references: 15822101
references: Proteins. 2005 Oct 1;61(1):137-51
references: 16049912
references: Nucleic Acids Res. 2006;34(13):3646-59
references: 16885238
references: Proteins. 2006 Oct 1;65(1):32-9
references: 16894618
references: Protein Eng. 1999 Dec;12(12):1063-73
references: 10611400