Searching the protein structure database for ligand-binding site similarities using CPASS v.2

BMC Research Notes

Volumn 4, Issue , 2011, Pages

  Powers, Robert ^a   Copeland, Jennifer C ^a   Stark, Jaime L ^a   Caprez, Adam ^b   Guru, Ashu ^b   Swanson, David ^b  

^a UNIVERSITY OF NEBRASKA LINCOLN   (United States)

^b UNIVERSITY OF NEBRASKA LINCOLN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EUKARYOTA; PROKARYOTA;

EID: 79251536512     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/1756-0500-4-17     Document Type: Article

References (52)

1. Powers R, Copeland JC, Germer K, Mercier KA, Ramanathan V, Revesz P: Comparison of Protein Active Site Structures for Functional Annotation of Proteins and Drug Design. Proteins: Struct., Funct., Bioinf 2006, 65(1):124-135.
2. Powers R, Copeland J, Mercier K: Application of FAST-NMR in Drug Discovery. Drug Discov Today 2008, 13(3-4):172-179.
3. Mercier KA, Baran M, Ramanathan V, Revesz P, Xiao R, Montelione GT, Powers R: FAST-NMR: Functional Annotation Screening Technology Using NMR Spectroscopy. J Amer Chem Soc 2006, 128(47):15292-15299. (Pubitemid 44853540)
4. Zvelebil MJ, Barton GJ, Taylor WR, Sternberg MJE: Prediction of protein secondary structure and active sites using the alignment of homologous sequences. J Mol Biol 1987, 195(4):957-961.
5. Livingstone CD, Barton GJ: Protein sequence alignments: a strategy for the hierarchical analysis of residue conservation. Comput Appl Biosci 1993, 9(6):745-756. (Pubitemid 24016574)
6. Park K, Kim D: Binding similarity network of ligand. Proteins: Struct., Funct., Bioinf 2008, 71(2):960-971.
7. Powers R: Functional Genomics and NMR Spectroscopy. Comb Chem High Throughput Screening 2007, 10(8):676-697.
8. Mercier Kelly A, Cort John R, Kennedy Michael A, Lockert Erin E, Ni S, Shortridge Matthew D, Powers R: Structure and function of Pseudomonas aeruginosa protein PA1324 (21-170). Protein Sci 2009, 18(3):606-618.
9. Stark JL, Mercier KA, Mueller GA, Acton TB, Xiao R, Montelione GT, Powers R: Solution structure and function of YndB, an AHSA1 protein from Bacillus subtilis. Proteins Struct Funct Bioinf 2010, 78(16):3328-3340.
10. Shortridge MD, Powers R: Structural and Functional Similarity between the Bacterial Type III Secretion System Needle Protein PrgI and the Eukaryotic Apoptosis Bcl-2 Proteins. PLoS ONE 2009, 4(10):1-10.
11. Kinoshita K, Murakami Y, Nakamura H: eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape. Nucleic Acids Res 2007, , 35 Web Server: W398-402.
12. Stark A, Sunyaev S, Russell RB: A Model for Statistical Significance of Local Similarities in Structure. J Mol Biol 2003, 326(5):1307-1316. (Pubitemid 36269075)
13. Stark A, Russell RB: Annotation in three dimensions. PINTS: Patterns in non-nonomologous tertiary structures. Nucleic Acids Res 2003, 31(13):3341-3344.
14. Laskowski RA, Watson JD, Thornton JM: ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res 2005, , 33 Web Server: W89-93.
15. Watson James D, Laskowski Roman A, Thornton Janet M: Predicting protein function from sequence and structural data. Curr Opin Struct Biol 2005, 15(3):275-284.
16. Pons JL, Labesse G: @TOME-2: a new pipeline for comparative modeling of protein-proteinigand complexes. Nucleic Acids Res 2009, , 37 Web Server: W485-W491.
17. Wass MN, Kelley LA, Sternberg MJE: 3DLigandSite: predicting ligand-ligandinding sites using similar structures. Nucleic Acids Res 2010, , 38 Web Server: W469-W473.
18. Lopez G, Valencia A, Tress ML: firestar-prediction of functionally important residues using structural templates and alignment reliability. Nucleic Acids Res 2007, (35 Web Server):W573-577.
19. Chang DT-H, Chen CY, Chung WC, Oyang YJ, Juan HF, Huang HC: ProteMiner-SSM: A web server for efficient analysis of similar protein tertiary substructures. Nucleic Acids Res 2004, , 32 Web Server: W76-W82. (Pubitemid 38997305)
20. Ausiello G, Via A, Helmer-Citterich M: Query3d: a new method for high-highhroughput analysis of functional residues in protein structures. BMC Bioinf 2005, 6(Suppl. 4), No pp. given.
21. Gold ND, Jackson RM: A Searchable Database for Comparing Protein- Ligand Binding Sites for the Analysis of Structure-Function Relationships. J Chem Inf Model 2006, 46(2):736-742.
22. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res 2000, 28(1):235-242. (Pubitemid 30047768)
23. Huang YJ, Tejero R, Powers R, Montelione GT: A topology- topologyonstrained distance network algorithm for protein structure determination from NOESY data. Proteins: Struct., Funct., Bioinf 2006, 62(3):587-603.
24. Litzkow M, Livny M, Mutka M: Condor - A Hunter of Idle Workstations. Proceedings of the 8th International Conference of Distributed Computing Systems: June 13-17, 1988 San Jose, CA; 1988, 104-111.
25. Thain D, Tannenbaum T, Livny M: Distributed computing in practice: the Condor experience. Concurrency - Practice and Experience 2005, 17(323-356).
26. Sfiligoi I: glideinWMS-a generic pilot-pilotased workload management system. J. Phys.: Conf. Ser 2008, 119(6):062044.
27. Pordes R, et al: The open science grid. J. Phys.: Conf. Ser 2007, 78(1):012057.
28. Zhang W: Linux Virtual Server for Scalable Network Services. Proceedings of the Linux Symposium: July 19-22, 2000 Ottawa, Ca; 2000.
29. Henikoff S, Henikoff JG: Amino acid substitution matrices from protein blocks. Proc Natl Acad Sci USA 1992, 89(22):10915-10919.
30. Henikoff S, Henikoff JG: Performance evaluation of amino acid substitution matrixes. Proteins: Struct., Funct., Genet 1993, 17(1):49-61.
31. Hubbard SJ, Thornton JM: NACCESS. Department of Biochemistry and Molecular Biology, University College London; 1993 [http://www.bioinf. manchester.ac.uk/naccess/].
32. Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, Powell S, von MC, Doerks T, Jensen LJ, et al: eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-nonupervised orthologous groups, species and functional annotations. Nucleic Acids Res 2010, , 38 Database: D190-D195.
33. Triplet T, Shortridge MD, Griep MA, Stark JL, Powers R, Revesz P: PROFESS: a PROtein Function, Evolution, Structure and Sequence database. Database 2010, 2010:baq011.
34. Herraez A: Biomolecules in the computer. Jmol to the rescue. Biochem Mol Biol Educ 2006, 34(4):255-261.
35. Cammer SA: SChiSM: creating interactive Web page annotations of molecular structure models using Chime. Bioinformatics 2000, 16(7):658-659.
36. Schomburg I, Chang A, Ebeling C, Gremse M, Heldt C, Huhn G, Schomburg D: BRENDA, the enzyme database: updates and major new developments. Nucleic Acids Res 2004, , 32 Database: D431-D433. (Pubitemid 38081692)
37. Kolodny R, Koehl P, Levitt M: Comprehensive Evaluation of Protein Structure Alignment Methods: Scoring by Geometric Measures. J Mol Biol 2005, 346(4):1173-1188. (Pubitemid 40215537)
38. Friedberg I: Automated protein function prediction-predictionhe genomic challenge. Briefings Bioinf 2006, 7(3):225-242.
39. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, et al: The COG database: an updated version includes eukaryotes. BMC Bioinf 2003, 4:41.
40. Muller J, Szklarczyk D, Julien P, Letunic I, Roth A, Kuhn M, Powell S, von MC, Doerks T, Jensen LJ, et al: eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-nonupervised orthologous groups, species and functional annotations. Nucleic Acids Res , 38 Database Iss: D190-D195.
41. Schneider A, Dessimoz C, Gonnet GH: OMA Browser-exploring orthologous relations across 352 complete genomes. Bioinformatics 2007, 23(16):2180-2182. (Pubitemid 47394120)
42. Greene LH, Lewis TE, Addou S, Cuff A, Dallman T, Dibley M, Redfern O, Pearl F, Nambudiry R, Reid A, et al: The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution. Nucleic Acids Res 2007, , 35 Database: D291-297.
43. Lo Conte L, Ailey B, Hubbard TJ, Brenner SE, Murzin AG, Chothia C: SCOP: a structural classification of proteins database. Nucleic Acids Res 2000, 28(1):257-259.
44. Dessimoz C, Boeckmann B, Roth ACJ, Gonnet GH: Detecting non-nonrthology in the COGs database and other approaches grouping orthologs using genome-genomepecific best hits. Nucleic Acids Res 2006, 34(11):3309-3316.
45. Gerlt JA, Babbitt PC: Can sequence determine function? GenomeBiology 2000, 1(5), epub.
46. Rost B: Twilight zone of protein sequence alignments. Protein Eng 1999, 12(2):85-94.
47. Blake JD, Cohen FE: Pairwise Sequence Alignment Below the Twilight Zone. J Mol Biol 2001, 307(2):721-735. (Pubitemid 33027687)
48. Sangar V, Blankenberg DJ, Altman N, Lesk AM: Quantitative sequence-sequenceunction relationships in proteins based on gene ontology. BMC Bioinf 2007, 8, epub.
49. Hegyi H, Gerstein M: The Relationship between Protein Structure and Function: a Comprehensive Survey with Application to the Yeast Genome. J Mol Biol 1999, 288(1):147-164. (Pubitemid 29201511)
50. Todd AE: Deriving functions from structure: Approaches and limitations. The Proteomics Protocols Handbook Humana Press Inc; 2005, 801-829.
51. Petrey D, Fischer M, Honig B: Structural relationships among proteins with different global topologies and their implications for function annotation strategies. Proc Natl Acad Sci USA 2009, 106(41):17377-17382.
52. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE: UCSF Chimera-A visualization system for exploratory research and analysis. J Comput Chem 2004, 25(13):1605-1612.