ProCKSI: A decision support system for Protein (Structure) Comparison, Knowledge, Similarity and Information

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Barthel, Daniel ^a   Hirst, Jonathan D ^a   Błazewicz, Jacek ^b,c   Burke, Edmund K ^a   Krasnogor, Natalio ^a  

^a UNIVERSITY OF NOTTINGHAM   (United Kingdom)

^b INSTITUTE OF BIOORGANIC CHEMISTRY   (Poland)

^c POZNAN UNIVERSITY OF TECHNOLOGY   (Poland)

Author keywords

[No Author keywords available]

Indexed keywords

CLASSIFICATION SCHEME; INTUITIVE INTERFACES; INTUITIVE USER INTERFACE; MAXIMUM CONTACT MAP OVERLAP; SEQUENCE COMPARISONS; SIMILARITY MEASURE; STRUCTURAL SIMILARITY; UNIVERSAL SIMILARITY METRIC;

ARTIFICIAL INTELLIGENCE; DECISION SUPPORT SYSTEMS; FIRE FIGHTING EQUIPMENT; USER INTERFACES;

PROTEINS;

PROTEIN; PROTEIN KINASE;

AMINO ACID SEQUENCE; ARTICLE; ARTIFICIAL INTELLIGENCE; COMPARATIVE STUDY; COMPUTER INTERFACE; CONSENSUAL VALIDITY; DECISION SUPPORT SYSTEM; NONHUMAN; PERFORMANCE MEASUREMENT SYSTEM; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN PROCESSING; PROTEIN STRUCTURE; QUALITY CONTROL; SEQUENCE ANALYSIS; STRUCTURAL HOMOLOGY; STRUCTURE ANALYSIS; VISUAL INFORMATION; ANIMAL; AUTOMATED PATTERN RECOGNITION; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; EXPERT SYSTEM; HUMAN; METHODOLOGY; PROTEIN MOTIF; REPRODUCIBILITY; ROC CURVE; SEQUENCE HOMOLOGY; ULTRASTRUCTURE;

SANDER;

AMINO ACID MOTIFS; ANIMALS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; EXPERT SYSTEMS; HUMANS; MODELS, MOLECULAR; PATTERN RECOGNITION, AUTOMATED; PROTEINS; REPRODUCIBILITY OF RESULTS; ROC CURVE; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID; STRUCTURAL HOMOLOGY, PROTEIN; USER-COMPUTER INTERFACE;

EID: 38949177447     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-416     Document Type: Article

References (103)

1. Koehl P Protein structure similarities Curr Opin Struct Biol 2001, 11:348-353. 10.1016/S0959-440X(00)00214-1 11406386
2. Kryshtafovych A Milostan M Szajkowski L Daniluk P Fidelis K CASP6 Data Processing and Automatic Evaluation at the Protein Structure Prediction Center Proteins Struct Funct Bioinf 2005, (Suppl 7):19-23. 10.1002/ prot.20718
3. Ferro D Hermans J A Different Best Rigid-body Molecular Fit Routine Acta Crystallogr 1977, A33:345-347.
4. Kabsch W A Discussion of the Solution for the Best Rotation to Relate Two Sets of Vectors Acta Crystallogr 1978, A34:827-828.
5. Vriend G Sander C Detection of common three-dimensional substructures in proteins Proteins 1991, 11:51-58. 10.1002/prot.340110107
6. Alexandrow N Takahashi K Go N Common spatial arrangements of backbone fragments in homologous and nonhomologous proteins J Mol Biol 1992, 225:5-9. 10.1016/0022-2836(92)91021-G 1583693
7. Fischer D Bachar O Nussinov R Wolfson H An efficient automated computer vision based technique for detection of three-dimensional structural motifs in proteins J Biomol Struct Dyn 1992, 9(4):769-789. 1616630
8. Holm L Sander C Protein Structure Comparison by Alignment of Distance Matrices J Mol Biol 1993, 233:123-138. 10.1006/jmbi.1993.1489 8377180
9. Artymiuk PJ Poirrett AR Rice DW Willet P The use of graph theoretical methods for the comparison of the structure of biological macromolecules Top Curr Chem 1995, 174:73-103.
10. Wu T SC S Hastie T DL B Regression analysis of multiple protein structures J Comput Biol 1998, 5:585-595. 9773352
11. Shindyalov I Bourne P Protein structure alignment by incremental combinatorial extension (CE) of the optimal path Protein Eng 1998, 11:739-747. 10.1093/protein/11.9.739 9796821
12. Zemla A LGA program: A method for dinding 3D similarities in protein structures Nucleic Acids Res 2003, 31:3370-3374. 168977 12824330 10.1093/ nar/gkg571
13. Taylor WR Protein structure comparison using iterated double dynamic programming Protein Sci 1999, 8:654-665. 10091668
14. Gerstein M Levitt M Comprehensive assessment of automatic structural alignment against a manual standard: The SCOP classification of proteins Protein Sci 1998, 7:445-456. 9521122
15. Yang A Honig B An integrated approach to the analysis and modeling of protein sequences an structures. I. Protein structural alignment and a quantitative mesasure for protein structural distance J Mol Biol 2000, 301:665-678. 10.1006/jmbi.2000.3973 10966776
16. Szustakowski J Weng Z Protein structure alignment using genetic algorithm Proteins 2000, 38:428-440. 10.1002/ (SICI)1097-0134(20000301)38:4<428::AID-PROT8>3.0.CO;2-N 10707029
17. Chew LP Kedem K Finding the consensus shape for a protein family Proceedings of the 18th Annual Symposium on Computational Geometry (SCG) New York: Springer 2002:64-73.
18. Leluk J Konieczny L Roterman I Search for structural similarity in proteins Bioinformatics 2003, 19:117-124. 10.1093/bioinformatics/ 19.1.117 12499301
19. Goldman D Papadimitriou C Istrail S Algorithmic Aspects of Protein Structure Similarity Proceedings of the 40th Annual Symposium on Foundations of Computer Science Washington: IEEE Computer Society 1999:512-521.
20. Lancia G Carr R Walenz B Istrail S 101 optimal pdb structure alignments: a branch-and-cut algorithm for the maximum contact map overlap problem Proceedings of the 5th Annual Interantional Conference on Computational Molecular Biology (RECOMB) New York: ACM Press 2001:192-202.
21. Caprara A Lancia G Structural alignment of large-size proteins via lagrangian relaxation Proceedings of the 6th Annual Conference on Research in Computational Molecular Biology (RECOMB) New York: ACM Press 2002:100-108.
22. Carr B Hart W Krasnogor N Burke EK Hirst JD Smith J Alignment of protein structures with a memetic evolutionary algorithm Proceedings of the Genetic and Evolutionary Computation Conference (GECCO) San Francisco: Morgan Kaufmann 2002:1027-1034.
23. Caprara A Carr R Istrail S Lancia G Walenz B 1001 Optimal PDB Strurcture Alignments: Integer Programming Methods for Finding the Maximum Contact Map Overlap J Comput Biol 2004, 11:27-52. 10.1089/106652704773416876 15072687
24. Krasnogor N Pelta DA Measuring the similarity of protein structures by means of the universal similarity metric Bioinformatics 2004, 20:1015-1021. 10.1093/bioinformatics/bth031 14751983
25. Pelta DA Krasnogor N Bousono-Calzon C Verdagay JL Hirst JD Burke E A fuzzy sets based generalization of contact maps for the overlap of protein structures Fuzzy Sets and Systems 2005, 152:102-123.
26. Krissinel E Henrick K Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions Acta Crystallogr D Biol Crystallogr 2004, 60(Pt 12 Pt 1):2256-2268. 10.1107/ S0907444904026460 15572779
27. Krasnogor N Self-Generating Metaheuristics in Bioinformatics: The Protein Structure Comparison Case Genetic Programming and Evolvable Machines 2004, 5:181-201. 10.1023/B:GENP.0000023687.41210.d7
28. Zhu J Z W FAST: A novel protein structure alignment algorithm Proteins Struct Funct Bioinf 2005, 58:618-627. 10.1002/prot.20331
29. Strickland D Barnes E Sokil J Optimal Protein Structure Alignment Using Maximum Cliques Opterations Research 2005, 53:389-402. 10.1287/ opre.1040.0189
30. Shatsky M Nussinov R Wolfson H Flexible protein alignment and hinge detection Proteins Struct Funct Genet 2002, 48:242-256. 10.1002/ prot.10100 12112693
31. Ye Y Godzik A FATCAT: A web server for flexible structure comparison and structure similarity searching Nucleic Acids Res 2004, 32:W582-W585. 441568 15215455 10.1093/nar/gkh430
32. Vesterstrom J Taylor W Flexible Secondary Structure Based Protein Structure Comparison Applied to the Detection of Circular Permutation J Comput Biol 2006, 13:43-63. 10.1089/cmb.2006.13.43 16472021
33. The Bioinformatics Links Directory http://bioinformatics.ca/ links_directory/?subcategory_id=136
34. Galperin M The Molecular Biology Database Collection: 2004 Update Nucleic Acids Res 2004, 32:D3-D22. 308877 14681349 10.1093/nar/gkh143
35. Galperin MY The Molecular Biology Database Collection: 2005 Update Nucleic Acids Res 2005, 33:D5-D24. 540093 15608247 10.1093/nar/gki139
36. Galperin M The Molecular Biology Database Collection: 2006 update Nucleic Acids Res 2006, 34:D3-D5. 1347524 16381871 10.1093/nar/gkj162
37. Webserver Issue Nucleic Acids Res 2005, 33:W1-W786. 10.1093/nar/gki592
38. Webserver Issue Nucleic Acids Res 2006, 34:W1-W751. 10.1093/nar/gkl385
39. Database Issue Nucleic Acids Res 2004, 32:D1-D599. 10.1093/nar/gkh142
40. Database Issue Nucleic Acids Res 2005, 33:D1-D679. 10.1093/nar/gki133
41. Database Issue Nucleic Acids Res 2006, 34:D1-D784. 10.1093/nar/gkj150
42. Database Issue Nucleic Acids Res 2007, 35:D1-D910. 10.1093/nar/gkl1051
43. Camoglu O Can T Singh A Integrating multi-attribute similarity networks for robust representation of the protein space Bioinformatics 2006, 22:1585-1592. 10.1093/bioinformatics/btl130 16595556
44. Filkov V Skiena S Heterogeneous Data Integration with the Consensus Clustering Formalism Proceedings of the 1st International Workshop on Data Integration in the Life Science (DILS) LNCS Berlin: Springer 2004:110-123.
45. Li M Chen X Li X Vitányi PMB Ma B The Similarity Metric IEEE Trans Inf Theor 2004, 50:3250-3264. 10.1109/TIT.2004.838101
46. Fischer D Rychlewski L Dunbrack RL Jr Ortiz AR Elofson A Servers for protein structure prediction Curr Opin Struct Biol 2006, 16:178-182. 10.1016/j.sbi.2006.03.004 16546376
47. Lapointe FJ Kirsch J Hutcheon J Total Evidence, Consensus, and Bat Phylogeny: A Distance-Based Approach Mol Phylogenet Evol 1999, 11:55-66. 10.1006/mpev.1998.0561 10082610
48. Kocsor A Kertesz-Farkas A Kajan L Pongor S Application of compression-based distance measures to protein sequence classification: a methodological study Bioinformatics 2006, 22:407-412. 10.1093/ bioinformatics/bti806 16317070
49. Holm L Park J DaliLite workbench for protein structure comparison Bioinformatics 2000, 16:566-567. 10.1093/bioinformatics/16.6.566 10980157
50. Zhang Y Skolnick J TM-align: A protein structure alignment algorithm based on TM-score Nucleic Acids Res 2005, 33:2302-2309. 1084323 15849316 10.1093/nar/gki524
51. Bingham J Sudarsanam S Visualizing large hierarchical clusters in hyperbolic space Bioinformatics 2000, 16:660-661. 10.1093/bioinformatics/ 16.7.660 11038340
52. Berman H Westbrook J Feng Z Gilliland G Bhat T Weissig H Shindyalov I Bourne P The Protein Data Bank Nucleic Acids Res 2000, 28:235-242. 102472 10592235 10.1093/nar/28.1.235
53. Hubbard TJ Ailey B Brenner SE Murzin AG Chothia C SCOP: A Structural Classification of Proteins database Nucleic Acids Res 1999, 27:254-256. 148149 9847194 10.1093/nar/27.1.254
54. Andreeva A Howorth D Brenner SE Hubbard TJP Chothia C Murzin AG SCOP database in 2004: Refinements integrate structure and sequence family data Nucleic Acids Res 2004, 32:D226-D229. 308773 14681400 10.1093/nar/ gkh039
55. Orengo CA Michie AD Jones S Jones DT Swindells MB Thornton JM CATH - A Hierarchic Classification of Protein Domain Structures Structure 1997, 5:1093-1108. 10.1016/S0969-2126(97)00260-8 9309224
56. Pearl F Todd A Sillitoe I Dibley M Redfern O Lewis T Bennett C Marsden R Grant A Lee D Akpor A Maibaum M Harrison A Dallman T Reeves G Diboun I Addou S Lise S Johnston C Sillero A Thornton J Orengo C The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis Nucleic Acids Res 2005, 33:D247-D251. 539978 15608188 10.1093/nar/gki024
57. Hoffmann R Valencia A A Gene Network for Navigating the Literature Nat Genet 2004, 36:664-664. 10.1038/ng0704-664 15226743
58. Hoffmann R Valencia A Implementing the iHOP concept for navigation of biomedical literature Bioinformatics 2005, 21(Suppl 2):iI252-ii258. 10.1093/bioinformatics/bti1142 16204114
59. Cilibrasi R Vitanyi MB Clustering by Compression IEEE Trans Inf Theor 2005, 51:1523-1545. 10.1109/TIT.2005.844059
60. Vendruscolo M Najmanovich R Domany E Protein Folding in Contact Map Space Phys Rev Lett 1999, 82:656-659. 10.1103/PhysRevLett.82.656
61. Gelly JC de Brevern AG Hazout S Protein Peeling: An approach for splitting a 3D protein structure into compact fragments Bioinformatics 2006, 22:129-133. 10.1093/bioinformatics/bti773 16301202
62. Margara L Vassura M Di Lena P Medri F Fariselli P Casadio R Reconstruction of 3D Structures From Protein Contact Maps Proceedings of the 3rd International Symposium on Bioinformatics Research and Applications (ISBRA), LNBI 4463 Berlin: Springer 2007:578-589.
63. Berrera M Molinari H Fogolari F Amino acid empirical contact energy definitions for fold recognition in the space of contact maps BMC Bioinformatics 2003, 4:8. 153506 12689348 10.1186/1471-2105-4-8
64. Punta M Rost B PROFcon: Novel prediction of long-range contacts Bioinformatics 2005, 21:2960-2968. 10.1093/bioinformatics/bti454 15890748
65. Graña O Eyrich VA Pazos F Rost B Valencia A EVAcon: A protein contact prediction evaluation service Nucleic Acids Res 2005, 33:W347-W351. 1160172 15980486 10.1093/nar/gki411
66. Graña O Baker D MacCallum RM Meiler J Punta M B R Tress ML Valencia A CASP6 assessment of contact prediction Proteins Struct Funct Bioinf 2005, 61:214-224. 10.1002/prot.20739
67. Chung JL Beaver JE Scheeff ED Bourne PE Con-Struct Map: A Comparative Contact Map Analysis Tool Bioinformatics 2007, 23:2491-2492. 10.1093/ bioinformatics/btm356 17709340
68. Kraulis PJ MOLSCRIPT: A Program to Produce Both Detailed and Schematic Plots of Protein Structures J Appl Cryst 1991, 24:946-950. 10.1107/ S0021889891004399
69. Sokal RR Michener CD A statistical method for evaluating systematic relationships Univ Kansas Sci Bull 1958, 38:1409-1438.
70. Ward J Jr Hierarchical Grouping to Optimize an Objective Function J Amer Statist Assoc 1963, 58:236-244. 10.2307/2282967
71. Clustering Calculator http://www2.biology.ualberta.ca/jbrzusto/ cluster.php
72. Felsenstein J PHYLIP - Phylogeny Inference Package (Version 3.2) Cladistics 1989, 5:164-166.
73. Hanks S Hunter T The eurkaryotic protein kinase superfamily: Kinase (catalytic) domain structure and classification The FASEB Journal 1995, 9:576-596. 7768349
74. Fischer D Rychlewski L Dunbrack RL Jr Ortiz AR Elofson A CAFASP3: The third critical assessment of fully automated structure prediction methods Proteins 2003, 53(Suppl 6):503-516. 10.1002/prot.10538 14579340
75. Tress M Ezkurdia I Graña O López G Valencia A Assessmentof Predictions Submitted for the CASP6 Comparative Modeling Category Proteins Struct Funct Bioinf 2005, (Suppl 7):27-45. 10.1002/prot.20720
76. Valencia A Lee B Dunbrack RL Jr Domain definition and target classification for CASP6 Proteins 2005, 61(Suppl 7):8-18. 16187342
77. Petretti C Prigent C The Protein Kinase Resource: Everything you always wanted to know about protein kinases but were afraid to ask Biol Cell 2005, 97:113-118. 10.1042/BC20040077 15656777
78. Smith C The protein kinase resource and other bioinformation resources Prog Biophys Mol Biol 1999, 71:525-533. 10.1016/S0079-6107(98)00046-7 10354712
79. Cheek S Zhang H Grishin N Sequence and structure classification of Kinases J Mol Biol 2002, 320:855-881. 10.1016/S0022-2836(02)00538-7 12095261
80. Manning G Whyte D Martinez R Hutner T Sudarsanam S The Protein Kinase Complement of the Human Genome Science 2002, 298:1912-1934. 10.1126/ science.1075762 12471243
81. Cheek S Ginalski K Zhang H Grishin N A comprehensive update of the sequence an structure classification of kinases BMC Struct Biol 2005, 5:6. 1079889 15771780 10.1186/1472-6807-5-6
82. Fernandez-Fuentes N Hermoso A Espandaler J Querol E Aviles F Oliva B Classification of Common Functional Loops of Kinase Super-Families Proteins 2004, 56:539-555. 10.1002/prot.20136 15229886
83. Mirror of the Protein Kinase Resourse (PKR) http://www.nih.go.jp/mirror/ Kinases
84. Smith C Shindyalov I S V Gribskov M Taylor S Ten Eyok L P B The Protein Kinase Resource Trends Biochem Sci 1997, 11:444-446. 10.1016/ S0968-0004(97)01131-6
85. SCOP: Structural Classification of Proteins http://scop.mrc-lmb.cam.ac.uk/scop [Release 1.69]
86. Fawcett T Introduction to ROC analysis Pattern Recog Lett 2006, 27:861-874. 10.1016/j.patrec.2005.10.010
87. Rost B Sander C Prediction of protein secondary structure at better than 70% accuracy J Mol Biol 1993, 232:584-599. 10.1006/jmbi.1993.1413 8345525
88. Hou J Jun SR Zhang C Kim SH Global mapping of the protein structure space and application in structure-based inference of protein function Proc Natl Acad Sci USA 2005, 102:3651-3656. 548596 15705717 10.1073/ pnas.0409772102
89. Egan J Signal detection theory and ROC analysis Series in Cognition and Perception New York: Academic Press 1995.
90. Spackman K Signal detection theory: Valuable tools for evaluating inductive learning Proceedings of the 6th International Workshop on Machine Learning San Francisco: Morgan Kaufman 1989, 283:160-163.
91. Receiver Operating Characteristic (ROC) Literature Research 2007 http://splweb.bwh.harvard.edu:8000/pages/ppl/zou/roc.html Active link not available; last accessed 26th Oct
92. Leplae R Hubbard T MaxBench: Evaluation of sequence and structure comparison methods Bioinformatics 2002, 18:494-495. 10.1093/ bioinformatics/18.3.494 11934754
93. Kolodny R Koehl P Levitt M Comprehensive Evaluation of Protein Structure Alignment Methods: Scoreing by Beometric Measures J Mol Biol 2005, 346:1173-1188. 10.1016/j.jmb.2004.12.032 15701525
94. Portugaly E Harel A Linial N Linial M EVEREST: Automatic identification and classification of protein domains in all protein sequences BMC Bioinformatics 2006, 7:277. 1533870 16749920 10.1186/1471-2105-7-277
95. Portugaly E Linial N Linial M EVEREST: A collection of evolutionary conserved protein domains Nucleic Acids Res 2007, 35:D241-D246. 1669739 17099230 10.1093/nar/gkl850
96. Ferragina P Giancarlo R Greco V Manzini G Valiente G Compression-based classification of biological sequences and structures via the Universal Similarity Metric: Experimental assessment BMC Bioinformatics 2007, 8:252. 1939857 17629909 10.1186/1471-2105-8-252
97. Stout M Bacardit J Hirst J Smith R Krasnogor N Prediction of Topological Contacts in Proteins Using Learning Classifier Systems Soft Comput J
98. Varshavsky R Linial M Horn D COMPACT - A Comparative Package for Clustering Assessment Proceedings of the ISPA Workshops, LNCS:3759 Berlin: Springer 2005:159-167.
99. Handl J Knowles J Kell D Computational cluster validation in post-genomic data analysis Bioinformatics 2005, 21:3201-3212. 10.1093/ bioinformatics/bti517 15914541
100. Munzner T Guimbretière F Tasiran S Zhang L Zhou Y TreeJuxtaposer: Scalable Tree Comparison using Focus+Context with Guaranteed Visibility ACM Transaction on Graphics 2003, 22:453-462. 10.1145/882262.882291
101. Lapointe FJ Cucumel G The Average Consensus Procedure: Combination of Weighted Trees Containing Identical or Overlapping Sets of Taxa Syst Biol 1997, 46:306-312. 10.2307/2413625
102. Lapointe JF Wilkinson M Bryant D Matrix Representations with Parsimony or with Distances: Two Sides of the Same Coin? Syst Biol 2003, 52:865-868. 10.1080/10635150390252297 14668125
103. Levasseur C Lapointe FJ Total Evidence, Average Consensus and Matrix Representation with Parsimony: What a Difference Distances Make Evol Bioinf Online 2006, 2:249-253.