Sequence based prediction of protein mutant stability and discrimination of thermophilic proteins

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 5265 LNBI, Issue , 2008, Pages 1-12

  Gromiha, M Michael ^a   Huang, Liang Tsung ^b   Lai, Lien Fu ^c  

^a NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^b MINGDAO UNIVERSITY   (Taiwan)

^c NATIONAL CHANGHUA UNIVERSITY OF EDUCATION   (Taiwan)

Author keywords

Discrimination; Machine learning techniques; Neural network; Prediction; Protein stability; Rule generator; Thermophilic proteins

Indexed keywords

AMINO ACIDS; BIOINFORMATICS; CLASSIFICATION (OF INFORMATION); DECISION TREES; FORECASTING; LEARNING SYSTEMS; NEURAL NETWORKS; PATTERN RECOGNITION; STABILITY; STATISTICAL TESTS;

DISCRIMINATION; MACHINE LEARNING TECHNIQUES; PROTEIN STABILITY; RULE GENERATOR; THERMOPHILIC PROTEINS;

PROTEINS;

EID: 57049177027     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-88436-1_1     Document Type: Conference Paper

References (43)

1. Gilis, D., Rooman, M.: Stability changes upon mutation of solvent-accessible residues in proteins evaluated by database-derived potentials. J. Mol. Biol. 257, 1112-1126 (1996)
2. Parthiban, V., Gromiha, M.M., Hoppe, C., Schomburg, D.: Structural analysis and prediction of protein mutant stability using distance and torsion potentials: role of secondary structure and solvent accessibility. Proteins 66, 41-52 (2007)
3. Gromiha, M.M., Oobatake, M., Kono, H., Uedaira, H., Sarai, A.: Role of structural and sequence information in the prediction of protein stability changes: comparison between buried and partially buried mutations. Protein Eng. 12, 549-555 (1999)
4. Guerois, R., Nielsen, J.E., Serrano, L.: Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations, J. Mol. Biol. 320, 369-387 (2002)
5. Khatun, J., Khare, S.D., Dokholyan, N.V.: Can contact potentials reliably predict stability of proteins? J. Mol. Biol. 336, 1223-1238 (2004)
6. Capriotti, E., Fariselli, P., Casadio, R.: A neural-network-based method for predicting protein stability changes upon single point mutations. Bioinformatics 20(1), i63-68 (2004)
7. Capriotti, E., Fariselli, P., Casadio, R.: I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Res. 33, w306-310 (2005)
8. Cheng, J., Randall, A., Baldi, P.: Prediction of protein stability changes for single-site mutations using support vector machines. Proteins 62, 1125-1132 (2006)
9. Saraboji, K., Gromiha, M.M., Ponnuswamy, M.N.: Average assignment method for predicting the stability of protein mutants. Biopolymers 82, 80-92 (2006)
10. Huang, L.T., Saraboji, K., Ho, S.Y., Hwang, S.F., Ponnuswamy, M.N., Gromiha, M.M.: Prediction of protein mutant stability using classification and regression tool. Biophys. Chem. 125, 462-470 (2007)
11. Yin, S., Ding, F., Dokholyan, N.V.: Modeling backbone flexibility improves protein stability estimation. Structure 15, 1567-1576 (2007)
12. Gromiha, M.M.: Prediction of protein stability upon point mutations. Biochem. Soc. Trans. 35, 1569-1573 (2007)
13. Kumar, S., Tsai, C.J., Nussinov, R.: Factors enhancing protein thermostability. Protein Eng. 13, 179-191 (2000)
14. Gromiha, M.M., Oobatake, M., Sarai, A.: Important amino acid properties for enhanced thermostability from mesophilic to thermophilic proteins. Biophys. Chem. 82, 51-67 (1999)
15. Kannan, N., Vishveshwara, S.: Aromatic clusters: a determinant of thermal stability of thermophilic proteins. Protein Eng. 13, 753-761 (2000)
16. Gromiha, M.M.: Important inter-residue contacts for enhancing the thermal stability of thermophilic proteins. Biophys. Chem. 91, 71-77 (2001)
17. Gromiha, M.M., Selvaraj, S.: Inter-residue interactions in protein folding and stability. Prog. Biophys. Mol. Biol. 86, 235-277 (2004)
18. Kumar, S., Tsai, C.J., Nussinov, R.: Thermodynamic differences among homologous thermophilic and mesophilic proteins. Biochemistry 40, 14152-14165 (2001)
19. Gromiha, M.M., Thomas, S., Santhosh, C.: Role of cation-pi interactions to the stability of thermophilic proteins. Prep. Biochem. Biotechnol. 32, 355-362 (2002)
20. Chakravarty, S., Varadarajan, R.: Elucidation of factors responsible for enhanced thermal stability of proteins: a structural genomics based study. Biochemistry 41, 8152-8161 (2002)
21. Ibrahim, B.S., Pattabhi, V.: Role of weak interactions in thermal stability of proteins. Biochem. Biophys. Res. Commun. 325, 1082-1089 (2004)
22. Xiao, L., Honig, B.: Electrostatic contributions to the stability of hyperthermophilic proteins. J. Mol. Biol. 289, 1435-1444 (1999)
23. Dominy, B.N., Minoux, H., Brooks, C.L.: 3rd: An electrostatic basis for the stability of thermophilic proteins. Proteins 57, 128-141 (2004)
24. Liang, H.K., Huang, C.M., Ko, M.T., Hwang, J.K.: Amino acid coupling patterns in thermophilic proteins. Proteins 59, 58-63 (2005)
25. Saraboji, K., Gromiha, M.M., Ponnuswamy, M.N.: Importance of main-chain hydrophobic free energy to the stability of thermophilic proteins. Int. J. Biol. Macromol. 35, 211-220 (2005)
26. Sadeghi, M., Naderi-Manesh, H., Zarrabi, M., Ranjbar, B.: Effective factors in thermostability of thermophilic proteins. Biophys. Chem. 119, 256-270 (2006)
27. Das, R., Gerstein, M.: The stability of thermophilic proteins: a study based on comprehensive genome comparison. Funct. Integr. Genomics 1, 76-88 (2000)
28. Fukuchi, S., Nishikawa, K.: Protein surface amino acid compositions distinctively differ between thermophilic and mesophilic bacteria. J. Mol. Biol. 309, 835-843 (2001)
29. Ding, Y., Cai, Y., Zhang, G., Xu, W.: The influence of dipeptide composition on protein thermostability. FEBS Lett 569, 284-288 (2004)
30. Berezovsky, I.N., Zeldovich, K.B., Shakhnovich, E.I.: Positive and negative design in stability and thermal adaptation of natural proteins. PLoS Comput. Biol. 3, 52 (2007)
31. Gromiha, M.M., An, J., Kono, H., Oobatake, M., Uedaira, H., Sarai, A.: ProTherm: Thermodynamic Database for Proteins and Mutants. Nucleic Acids Res. 27, 286-288 (1999)
32. Bava, K.A., Gromiha, M.M., Uedaira, H., Kitajima, K., Sarai, A.: ProTherm, version 4.0: thermodynamic database for proteins and mutants. Nucleic Acids Res. 32, D120-D121 (2004)
33. Zhang, G., Fang, B.: Application of amino acid distribution along the sequence for discriminating mesophilic and thermophilic proteins. Process biochemistry 41, 1792-1798 (2006)
34. Li, W., Jaroszewski, L., Godzik, A.: Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics 17, 282-283 (2001)
35. Holm, L., Sander, C.: Removing near-neighbour redundancy from large protein sequence collections. Bioinformatics 14, 423-429 (1998)
36. Quinlan, J.R.: C4.5: programs for machine learning. Morgan Kaufmann Publishers, San Mateo (1993)
37. Freund, Y., Schapire, R.E.: A decision-theoretic generalization of on-line learning and an application to boosting. Journal of Computer and System Sciences 55, 119-139 (1997)
38. Breiman, L.: Classification and regression trees. Wadsworth International Group, Belmont (1984)
39. Witten, I.H., Frank, E.: Data Mining: Practical machine learning tools and techniques. Morgan Kaufmann, San Francisco (2005)
40. Gromiha, M.M., Suwa, M.: Discrimination of outer membrane proteins using machine learning algorithms. Proteins 63, 1031-1037 (2006)
41. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., Bourne, P.E.: The Protein Data Bank. Nucleic Acids Res. 28, 235-242 (2000)
42. Huang, L.T., Gromiha, M.M., Ho, S.Y.: iPTREE-STAB: interpretable decision tree based method for predicting protein stability changes upon mutations. Bioinformatics 23, 1292-1293 (2007)
43. Gromiha, M.M., Suresh, M.X.: Discrimination of mesophilic and thermophilic proteins using machine learning algorithms. Proteins 70, 1274-1279 (2008)