Selective prediction of interaction sites in protein structures with THEMATICS

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Wei, Ying ^a   Ko, Jaeju ^a,b   Murga, Leonel F ^a,c   Ondrechen, Mary Jo ^a  

^a NORTHEASTERN UNIVERSITY   (United States)

^b INDIANA UNIVERSITY OF PENNSYLVANIA   (United States)

^c BRANDEIS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CATALYTIC RESIDUE; FALSE POSITIVE RATES; INTERACTION SITE; PROTEIN 3-D STRUCTURE; PROTEIN STRUCTURES; RATE OF INTERACTIONS; RECALL AND PRECISION; TITRATION CURVES;

ENZYMES; PROTEINS; STATISTICAL TESTS;

FORECASTING;

ACCURACY; ANALYTIC METHOD; ANALYTICAL ERROR; ARTICLE; CATALYSIS; CONTROLLED STUDY; ENZYME ACTIVE SITE; ENZYME LOCALIZATION; INTERMETHOD COMPARISON; INTERNET; MATHEMATICAL COMPUTING; PREDICTION; PROTEIN DETERMINATION; PROTEIN INTERACTION; PROTEIN STRUCTURE; REFERENCE VALUE; SCORING SYSTEM; STRUCTURE ANALYSIS; BINDING SITE; CHEMICAL MODEL; CHEMISTRY; COMPARATIVE STUDY; COMPUTER PROGRAM; FACTUAL DATABASE; GENETICS; PREDICTION AND FORECASTING; PROTEIN SECONDARY STRUCTURE; STATISTICS;

PROTEIN;

BINDING SITES; DATABASES, FACTUAL; MODELS, CHEMICAL; PREDICTIVE VALUE OF TESTS; PROTEIN STRUCTURE, SECONDARY; PROTEINS; SOFTWARE;

EID: 34250671141     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-119     Document Type: Article

References (80)

1. Ondrechen MJ Clifton JG Ringe D THEMATICS: A simple computational predictor of enzyme function from structure Proc Natl Acad Sci (USA) 2001 98 12473-12478 10.1073/pnas.211436698
2. Shehadi IA Yang H Ondrechen MJ Future directions in protein function prediction Mol Biol Reports 2002 29 329-335 10.1023/A:1021220208562
3. Ringe D Wei Y Boino KR Ondrechen MJ Protein Structure to Function: Insights from Computation Cellular Molecular Life Sciences 2004 61 387-392 10.1007/s00018-003-3291-5
4. Murga LF Wei Y Andre P Clifton JG Ringe D Ondrechen MJ Physicochemical methods for prediction of functional information for proteins Israel Journal of Chemistry 2004 44 299-308 10.1560/Q3YD-PEDL-JRU8-8FVM
5. Shehadi IA Abyzov A Uzun A Wei Y Murga LF Ilyin V Ondrechen MJ Active Site Prediction for Comparative Model Structures with THEMATICS Journal of Bioinformatics and Computational Biology 2005 3 127-143 10.1142/ S0219720005000916
6. Ko J Murga LF Andre P Yang H Ondrechen MJ Williams RJ Agunwamba A Budil DE Statistical Criteria for the Identification of Protein Active Sites Using Theoretical Microscopic Titration Curves Proteins: Structure Function Bioinformatics 2005 59 183-195 10.1002/prot.20418
7. Ko J Murga LF Wei Y Ondrechen MJ Prediction of active sites for protein structures from computed chemical properties Bioinformatics 2005 21 i i258-i265 10.1093/bioinformatics/bti1039 15961465
8. Kim SH Shining a light on structural genomics Nature Struct Biol 1998 5 643-645 10.1038/1334 9699614
9. Terwilliger TC Waldo G Peat TS Newman JM Chu K Berendzen J Class-directed structure determination: Foundation for a protein structure initiative Protein Sci 1998 7 1851-1856 9761466
10. Sali A 100,000 protein structures for the biologist Nature Struct Biol 1998 5 1929-1932
11. Montelione GT Anderson S Structural Genomics: Keystone for a human proteome Nature Struct Biol 1999 6 11-12 10.1038/4878 9886282
12. Burley SK Almo SC Bonanno JB Capel M Chance MR Gaasterland T Lin D Sali A Studier FW Swaminathan S Structural Genomics: Beyond the human genome project Nature Genet 1999 23 151-157 10.1038/13783 10508510
13. Eisenstein E Gilliland GL Herzberg O Moult J Orban J Poljak RJ Banerjei L Richardson D Howard AJ Biological function made crystal clear - Annotation of hypothetical proteins via structural genomics Curr Opin Biotechnol 2000 11 25-30 10.1016/S0958-1669(99)00063-4 10679350
14. Vitkup D Melamud E Moult J Sander C Completeness in structural genomics Nat Struct Biol 2001 8 6 559 566 10.1038/88640 11373627
15. Warwicker J Watson HC Calculation of the electric potential in the active site cleft due to alpha-helix dipoles J Mol Biol 1982 157 4 671-679 10.1016/0022-2836(82)90505-8 6288964
16. Bashford D Karplus M Multiple-site Titration Curves of Proteins: An Analysis of Exact and Approximate Methods for Their Calculation J Phys Chem 1991 95 9556-9561 10.1021/j100176a093
17. Gilson MK Multiple-site titration and molecular modeling: Two rapid methods for computing energies and forces for ionizable groups in proteins Proteins 1993 15 3 266-282 10.1002/prot.340150305 8456096
18. Yang AS Gunner MR Sampogna R Sharp K Honig B On the calculation of pKas in proteins Proteins 1993 15 3 252-265 10.1002/prot.340150304 7681210
19. Madura JD Briggs JM Wade RC Davis ME Luty BA Ilin A Antosiewicz J Gilson MK Bagheri B Scott LR McCammon JA Electrostatics and diffusion of molecules in solution - Simulations with the University of Houston Brownian Dynamics program Comp Phys Commun 1995 91 57-95 10.1016/ 0010-4655(95)00043-F
20. Karshikoff A A simple algorithm for the calculation of multiple site titration curves Protein Engineering 1995 8 243-248 10.1093/protein/ 8.3.243 7479686
21. Antosiewicz J Briggs JM Elcock AH Gilson MK McCammon JA Computing the Ionization States of Proteins with a Detailed Charge Model J Comp Chem 1996 17 1633-1644 10.1002/(SICI)1096-987X(19961115)17:14<1633::AID- JCC5>3.0.CO;2-M
22. Antosiewicz J McCammon JA Gilson MK The determinants of pKa's in proteins Biochemistry 1996 35 7819-7833 10.1021/bi9601565 8672483
23. Alexov EG Gunner MR Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties Biophys J 1997 72 2075-2093 1184402 9129810
24. Koehl P Electrostatics calculations: Latest methodological advances Current Opinion in Structural Biology 2006 16 2 142-151 10.1016/ j.sbi.2006.03.001 16540310
25. Bashford D Gerwert K Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin J Mol Biol 1992 224 2 473-486 10.1016/0022-2836(92)91009-E 1313886
26. Sampogna RV Honig B Environmental effects on the protonation states of active site residues in bacteriorhodopsin Biophys J 1994 66 5 1341-1352 1275855 8061190
27. Beroza P Fredkin DR Okamura MY Feher G Electrostatic calculations of amino acid titration and electron transfer, Q-AQB→QAQ-B, in the reaction center Biophys J 1995 68 6 2233-2250 1282134 7647231
28. Carlson HA Briggs JM McCammon JA Calculation of the pKa values for the ligands and side chains of Escherichia coli D-alanine:D-alanine ligase J Med Chem 1999 42 1 109-117 10.1021/jm980351c 9888837
29. Lichtarge O Bourne HR Cohen FE An evolutionary trace method defines binding surfaces common to protein families J Mol Biol 1996 257 2 342-358 10.1006/jmbi.1996.0167 8609628
30. Sjolander K Phylogenetic inference in protein superfamilies: Analysis of SH2 domains Proc Int Conf Intell Syst Mol Biol 1998 6 165-174 9783222
31. Marcotte EM Pellegrini M Thompson MJ Yeates TO Eisenberg D A combined algorithm for genome-wide prediction of protein function Nature 1999 402 6757 83-86 10.1038/47048 10573421
32. Marcotte EM Pellegrini M Ng HL Rice DW Yeates TO Eisenberg D Detecting protein function and protein-protein interactions from genome sequences Science 1999 285 5428 751-753 10.1126/science.285.5428.751 10427000
33. Marcotte EM Computational genetics: Finding protein function by nonhomology methods Curr Opin Struct Biol 2000 10 3 359-365 10.1016/ S0959-440X(00)00097-X 10851184
34. Carter CW Jr LeFebvre BC Cammer SA Tropsha A Edgell MH Four-body potentials reveal protein-specific correlations to stability changes caused by hydrophobic core mutations J Mol Biol 2001 311 4 625-638 10.1006/jmbi.2001.4906 11518520
35. Innis CA Anand AP Sowdhamini R Prediction of functional sites in proteins using conserved functional group analysis Journal of Molecular Biology 2004 337 1053-1068 10.1016/j.jmb.2004.01.053 15033369
36. Greaves R Warwicker J Active site identification through geometry-based and sequence-profile based calculations: Burial of catalytic clefts J Mol Biol 2005 349 547-557 10.1016/j.jmb.2005.04.018 15882869
37. Petrova N Wu C Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties BMC Bioinformatics 2006 7 1 312 1534064 16790052 10.1186/1471-2105-7-312
38. Babbitt PC Klein TE Superfamily Analysis: Understanding Protein Function from Structure and Sequence Encyclopedia of Computational Chemistry Chichester, West Sussex, U.K: Wiley Schleyer PvR 1998 2859-2870
39. Fetrow JS Skolnick J Method for prediction of protein function from sequence using the sequence-to-structure-to-function paradigm with application to glutaredoxins/thioredoxins and T1 ribonucleases J Mol Biol 1998 281 5 949-968 10.1006/jmbi.1998.1993 9719646
40. Fetrow JS Siew N Skolnick J Structure-based functional motif identifies a potential disulfide oxidoreductase active site in the serine/threonine protein phosphatase-1 subfamily Faseb J 1999 13 13 1866-1874 10506591
41. Fetrow JS Siew N Di Gennaro JA Martinez-Yamout M Dyson HJ Skolnick J Genomic-scale comparison of sequence- and structure-based methods of function prediction: Does structure provide additional insight? Protein Sci 2001 10 5 1005-1014 10.1110/ps.49201 11316881
42. 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 10.1006/jmbi.1999.2661 10329133
43. Skolnick J Fetrow JS From genes to protein structure and function: Novel applications of computational approaches in the genomic era Trends Biotechnol 2000 18 1 34-39 10.1016/S0167-7799(99)01398-0 10631780
44. Teichmann SA Murzin AG Chothia C Determination of protein function, evolution and interactions by structural genomics Curr Opin Struct Biol 2001 11 3 354-363 10.1016/S0959-440X(00)00215-3 11406387
45. Wallace AC Borkakoti N Thornton JM TESS: A geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases. Application to enzyme active sites Protein Sci 1997 6 11 2308-2323 9385633
46. Laskowski RA Luscombe NM Swindells MB Thornton JM Protein clefts in molecular recognition and function Protein Sci 1996 5 2438-2452 8976552
47. Bate P Warwicker J Enzyme/non-enzyme discrimination and prediction of enzyme active site location using charge-based methods J Mol Biol 2004 340 263-276 10.1016/j.jmb.2004.04.070 15201051
48. Elcock AH Prediction of functionally important residues based solely on the computed energetics of protein structure J Mol Biol 2001 312 885-896 10.1006/jmbi.2001.5009 11575940
49. Ma B Wolfson HJ Nussinov R Protein Functional Epitopes: Hot Spots, Dynamics and Combinatorial Libraries Curr Opin Struct Biol 2001 11 364-369 10.1016/S0959-440X(00)00216-5 11406388
50. Ming D Wall ME Interactions in Native Binding Sites Cause a Large Change in Protein Dynamics Journal of Molecular Biology 2006 358 1 213-223 10.1016/j.jmb.2006.01.097 16513135
51. Gutteridge A Bartlett G Thornton JM Using a neural network and spatial clustering to predict the location of active sites in enzymes Journal of Molecular Biology 2003 330 719-734 10.1016/S0022-2836(03)00515-1 12850142
52. Amitai G Shemesh A Sitbon E Shklar M Netanely D Venger I Pietrokovski S Newwork analysis of protein structures identifies functional residues J Mol Biol 2004 344 1135-1146 10.1016/j.jmb.2004.10.055 15544817
53. Bartlett GJ Porter CT Borkakoti N Thornton JM Analysis of Catalytic Residues in Enzyme Active Sites J Mol Biol 2002 324 105-121 10.1016/ S0022-2836(02)01036-7 12421562
54. Mattos C Ringe D Locating and characterizing binding sites on proteins Nat Biotechnol 1996 14 5 595-599 10.1038/nbt0596-595 9630949
55. Silberstein M Dennis S Brown L Kortvelyesi T Clodfelter K Vajda S Identification of substrate binding sites in enzymes by computational solvent mapping J Mol Biol 2003 332 1095-1113 10.1016/j.jmb.2003.08.019 14499612
56. Clodfelter KH Waxman DJ Vajda S Computational Solvent Mapping Reveals the Importance of Local Conformational Changes for Broad Substrate Specificity in Mammalian Cytochromes P450 Biochemistry 2006 45 31 9393-9407 10.1021/bi060343v 16878974
57. Laurie ATR Jackson RM Q-SiteFinder: An energy-based method for the prediction of protein-ligand binding sites Bioinformatics 2005 21 1908-1916 10.1093/bioinformatics/bti315 15701681
58. Ben-Shimon A Eisenstein M Looking at Enzymes from the Inside out: The Proximity of Catalytic Residues to the Molecular Centroid can be used for Detection of Active Sites and Enzyme-Ligand Interfaces Journal of Molecular Biology 2005 351 2 309-326 10.1016/j.jmb.2005.06.047 16019028
59. Catalytic Site Atlas http://www.ebi.ac.uk/thornton-srv/databases/CSA/
60. Porter CT Bartlett GJ Thornton JM The Catalytic Site Atlas: A resource of catalytic sites and residues identified in enzymes using structural data Nucl Acids Res %R 101093/nar/gkh028 2004 32 suppl 1 D129-133 10.1093/nar/gkh028
61. Sobolev V Sorokine A Prilusky J Abola EE Edelman M Automated analysis of interatomic contacts in proteins Bioinformatics 1999 15 327-332 10.1093/ bioinformatics/15.4.327 10320401
62. Saadat D Harrison D The crystal structure of methylglyoxal synthase from Escherichia coli Structure 1999 7 3 309-317 10.1016/ S0969-2126(99)80041-0 10368300
63. Saadat D Harrison DHT Mirroring Perfection: The Structure of Methylglyoxal Synthase Complexed with the Competitive Inhibitor 2-Phosphoglycolate Biochemistry 2000 39 11 2950-2960 10.1021/bi992666f 10715115
64. Marks GT Harris TK Massiah MA Mildvan AS Harrison DHT Mechanistic Implications of Methylglyoxal Synthase Complexed with Phosphoglycolohydroxamic Acid As Observed by X-ray Crystallography and NMR Spectroscopy Biochemistry 2001 40 23 6805-6818 10.1021/bi0028237 11389594
65. Marks GT Susler M Harrison DHT Mutagenic Studies on Histidine 98 of Methylglyoxal Synthase: Effects on Mechanism and Conformational Change Biochemistry 2004 43 13 3802-3813 10.1021/bi035838o 15049687
66. Computed Atlas of Surface Topography of Proteins http://sts.bioengr.uic.edu/castp/
67. Binkowski TA Naghibzadeh S Liang J CASTp: Computed atlas of surface topography of proteins Nucleic Acids Res 2003 31 3352-3355 168919 12824325 10.1093/nar/gkg512
68. Berry M Phillips G Crystal structures of Bacillus stearothermophilus adenylate kinase with bound Ap5A, Mg2+ Ap5A, and Mn2+ Ap5A reveal an intermediate lid position and six coordinate octahedral geometry for bound Mg2+ and Mn2+ Proteins: Structure, Function, and Genetics 1998 32 3 276-288 10.1002/(SICI)1097-0134(19980815)32:3<276::AID- PROT3>3.0.CO;2-G
69. Lima CD Klein MG Hendrickson WA Structure-based analysis of catalysis and substrate definition in the HIT protein family Science 1997 278 286-290 10.1126/science.278.5336.286 9323207
70. Brenner C Garrison P Gilmour J Peisach D Ringe D Petsko G Lowenstein J Crystal structures of HINT demonstrate that histidine triad proteins are GalT-related nucleotide-binding proteins Nat Struct Biol 1997 4 3 231-238 10.1038/nsb0397-231 9164465
71. Panchenko AR Kondrashov F Bryant S Prediction of functional sites by analysis of sequence and structure conservation Protein Sci %R 101110/ ps03465504 2004 13 4 884-892 10.1110/ps.03465504
72. Protein Data Bank http://www.pdb.org/pdb/Welcome.do
73. Swiss PDB Viewer http://www.expasy.org/spdbv/
74. Guex N Peitsch M SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling Electrophoresis 1997 18 15 2714-2723 10.1002/elps.1150181505 9504803
75. Ren P Ponder JW Polarizable atomic multipole water model for molecular mechanics simulation Journal of Physical Chemistry B 2003 107 5933-5947 10.1021/jp027815+
76. Jorgensen WL Chandrasekhar J Madura JD Impey RW Klein ML Comparison of simple potential functions for simulating liquid water Journal of Chemical Physics 1983 79 926-935 10.1063/1.445869
77. Jorgensen WL Tirado-Rives J The OPLS Potential Functions for Proteins. Energy Minimization for Crystals of Cyclic Peptides and Crambin J Am Chem Soc 1988 110 1657-1666 10.1021/ja00214a001
78. Zwillinger D (ed) CRC Standard Mathematical Tables and Formulae CRC press 30 1996
79. Q-SiteFinder http://www.bioinformatics.leeds.ac.uk/qsitefinder/
80. Structural Analysis of Residue Interaction Graphs (SARIG) http://bioinfo2.weizmann.ac.il/~pietro/SARIG/V3/index.html