SCOPUS 정보 검색 플랫폼

Protein Journal

Volumn 30, Issue 4, 2011, Pages 229-239

Sequence conservation in the prediction of catalytic sites

(6) Dou, Yongchao a Geng, Xingbo a Gao, Hongyun a Yang, Jialiang b Zheng, Xiaoqi c Wang, Jun c

a DALIAN UNIVERSITY OF TECHNOLOGY (China)

b MAX PLANCK INSTITUTE (Germany)

c SHANGHAI NORMAL UNIVERSITY (China)

Author keywords

Catalytic site prediction; Neighboring sites; Sequence conservation; Support vector machine

Indexed keywords

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; BIOINFORMATICS; ENZYME ACTIVE SITE; MACHINE LEARNING; PREDICTION; PROTEIN STRUCTURE; SUPPORT VECTOR MACHINE;

EID: 79958057774 PISSN: 15723887 EISSN: 18758355 Source Type: Journal
DOI: 10.1007/s10930-011-9324-2 Document Type: Article

Times cited : (5)

References (41)

1
- 0030801002
- Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
- DOI 10.1093/nar/25.17.3389
- SF Altschul TL Madden AA Schaffer J Zhang Z Zhang W Miller DJ Lipman 1997 Nucleic Acids Res 25 17 3398 3402 10.1093/nar/25.17.3389 (Pubitemid 27359211)
- (1997) Nucleic Acids Research , vol.25 , Issue.17 , pp. 3389-3402
- Altschul, S.F.¹ Madden, T.L.² Schaffer, A.A.³ Zhang, J.⁴ Zhang, Z.⁵ Miller, W.⁶ Lipman, D.J.⁷

2
- 0346733329
- Are protein-protein interfaces more conserved in sequence than the rest of the protein surface?
- DOI 10.1110/ps.03323604
- D Caffery S Somaroo J Hughes J Mintserlis E Hunang 2004 Protein Sci 13 190 202 10.1110/ps.03323604 (Pubitemid 38021153)
- (2004) Protein Science , vol.13 , Issue.1 , pp. 190-202
- Caffrey, D.R.¹ Somaroo, S.² Hughes, J.D.³ Mintseris, J.⁴ Huang, E.S.⁵

3
- 34548133728
- Predicting functionally important residues from sequence conservation
- DOI 10.1093/bioinformatics/btm270
- J Capra S Singh 2007 Bioinformatics 23 1875 1882 10.1093/bioinformatics/ btm270 1:CAS:528:DC%2BD2sXpt1Crurk%3D (Pubitemid 47299827)
- (2007) Bioinformatics , vol.23 , Issue.15 , pp. 1875-1882
- Capra, J.A.¹ Singh, M.²

4
- 77951192988
- 10.1186/1471-2105-11-115
- E Cilia A Passerini 2010 BMC Bioinformat 11 115 10.1186/1471-2105-11-115
- (2010) BMC Bioinformat , vol.11 , pp. 115
- Cilia, E.¹ Passerini, A.²

5
- 0037470597
- Automatic methods for predicting functionally important residues
- DOI 10.1016/S0022-2836(02)01451-1
- A del sol mesa F Pazos A Valencia 2003 J Mol Biol 326 1289 1302 10.1016/S0022-2836(02)01451-1 1:CAS:528:DC%2BD3sXhtVCiu7o%3D (Pubitemid 36263398)
- (2003) Journal of Molecular Biology , vol.326 , Issue.4 , pp. 1289-1302
- Del Sol Mesa, A.¹ Pazos, F.² Valencia, A.³

6
- 20744444583
- Determining functional specificity from protein sequences
- DOI 10.1093/bioinformatics/bti396
- JS Donald EI Shakhnovich 2005 Bioinformatics 21 2629 2635 10.1093/bioinformatics/bti396 1:CAS:528:DC%2BD2MXks1eru7k%3D (Pubitemid 40852308)
- (2005) Bioinformatics , vol.21 , Issue.11 , pp. 2629-2635
- Donald, J.E.¹ Shakhnovich, E.I.²

7
- 70450260600
- 10.1016/j.jtbi.2009.09.030
- YC Dou XQ Zheng J Wang 2009 J Theor Biol 262 2 317 322 10.1016/j.jtbi.2009.09.030
- (2009) J Theor Biol , vol.262 , Issue.2 , pp. 317-322
- Dou, Y.C.¹ Zheng, X.Q.² Wang, J.³

8
- 59449097392
- 10.1007/s10930-008-9161-0 1:CAS:528:DC%2BD1MXivFClug%3D%3D
- YC Dou XQ Zheng J Wang 2009 Protein J 28 29 33 10.1007/s10930-008-9161-0 1:CAS:528:DC%2BD1MXivFClug%3D%3D
- (2009) Protein J , vol.28 , pp. 29-33
- Dou, Y.C.¹ Zheng, X.Q.² Wang, J.³

9
- 78449287914
- 10.1007/s00726-010-0587-2 1:CAS:528:DC%2BC3cXhtlaqtLbF
- YC Dou XQ Zheng JL Yang J Wang 2010 Amino Acids 39 1353 1361 10.1007/s00726-010-0587-2 1:CAS:528:DC%2BC3cXhtlaqtLbF
- (2010) Amino Acids , vol.39 , pp. 1353-1361
- Dou, Y.C.¹ Zheng, X.Q.² Yang, J.L.³ Wang, J.⁴

10
- 53749096681
- 10.1093/bioinformatics/btn454
- B Dukka R Dennis 2008 Bioinformatics 24 2308 2316 10.1093/bioinformatics/ btn454
- (2008) Bioinformatics , vol.24 , pp. 2308-2316
- Dukka, B.¹ Dennis, R.²

11
- 29144499905
- RE Fan PH Chen CJ Lin 2005 J Mach Learn Res 6 1889 1918
- (2005) J Mach Learn Res , vol.6 , pp. 1889-1918
- Fan, R.E.¹ Chen, P.H.² Lin, C.J.³

12
- 40049091146
- Prediction of protein functional residues from sequence by probability density estimation
- DOI 10.1093/bioinformatics/btm626
- JD Fischer CE Mayer J Soding 2008 Bioinformatics 24 613 620 10.1093/bioinformatics/btm626 1:CAS:528:DC%2BD1cXislKltb4%3D (Pubitemid 351321204)
- (2008) Bioinformatics , vol.24 , Issue.5 , pp. 613-620
- Fischer, J.D.¹ Mayer, C.E.² Soding, J.³

13
- 0042674397
- 10.1016/S0022-2836(03)00515-1
- A Gutteridge GJ Bartlett JM Thornton 2003 J Mol Biol 303 719 734 10.1016/S0022-2836(03)00515-1
- (2003) J Mol Biol , vol.303 , pp. 719-734
- Gutteridge, A.¹ Bartlett, G.J.² Thornton, J.M.³

14
- 1642325994
- 10.1016/j.jmb.2004.01.053
- CA Innis AP Anand R Sowdhamini 2003 J Mol Biol 337 1053 1068 10.1016/j.jmb.2004.01.053
- (2003) J Mol Biol , vol.337 , pp. 1053-1068
- Innis, C.A.¹ Anand, A.P.² Sowdhamini, R.³

15
- 77954662068
- 10.1186/1471-2105-11-383
- F Johansson H Toh 2010 BMC Bioinformat 11 383 10.1186/1471-2105-11-383
- (2010) BMC Bioinformat , vol.11 , pp. 383
- Johansson, F.¹ Toh, H.²

16
- 77955510363
- 10.1142/S021972001000494X 1:CAS:528:DC%2BC3cXhtlWmu77L
- F Johansson H Toh 2010 J Bioinform Comput Biol 8 5 809 823 10.1142/S021972001000494X 1:CAS:528:DC%2BC3cXhtlWmu77L
- (2010) J Bioinform Comput Biol , vol.8 , Issue.5 , pp. 809-823
- Johansson, F.¹ Toh, H.²

17
- 77956525295
- 10.1186/1471-2105-11-439
- GH Li JF Huang 2010 BMC Bioinformat 11 439 10.1186/1471-2105-11-439
- (2010) BMC Bioinformat , vol.11 , pp. 439
- Li, G.H.¹ Huang, J.F.²

18
- 79958057532
- Washington DC, USA
- Liu H, Setiono R (1995) IEEE computer society. Washington, DC, USA, pp 388-391
- (1995) IEEE Computer Society , pp. 388-391
- Liu, H.¹ Setiono, R.²

19
- 43149110628
- 10.1007/s00726-007-0017-2 1:CAS:528:DC%2BD1cXlsVOgs70%3D
- XS Liu WL Guo 2008 Amino Acids 34 643 652 10.1007/s00726-007-0017-2 1:CAS:528:DC%2BD1cXlsVOgs70%3D
- (2008) Amino Acids , vol.34 , pp. 643-652
- Liu, X.S.¹ Guo, W.L.²

20
- 77954185426
- 10.1093/bioinformatics/btq253 1:CAS:528:DC%2BC3cXnvVOiu78%3D
- ZP Liu LY Wu Y Wang XS Zhang LN Chen 2010 Bioinformatics 26 1616 1622 10.1093/bioinformatics/btq253 1:CAS:528:DC%2BC3cXnvVOiu78%3D
- (2010) Bioinformatics , vol.26 , pp. 1616-1622
- Liu, Z.P.¹ Wu, L.Y.² Wang, Y.³ Zhang, X.S.⁴ Chen, L.N.⁵

21
- 4143051195
- Comparison of site-specific rate-inference methods for protein sequences: Empirical Bayesian methods are superior
- DOI 10.1093/molbev/msh194
- I Mayrose D Graur N Ben-Tal T Pupko 2004 Mol Biol Evol 21 1781 1791 10.1093/molbev/msh194 1:CAS:528:DC%2BD2cXntVCitb0%3D (Pubitemid 39096894)
- (2004) Molecular Biology and Evolution , vol.21 , Issue.9 , pp. 1781-1791
- Mayrose, I.¹ Graur, D.² Ben-Tal, N.³ Pupko, T.⁴

22
- 1242339659
- A Family of Evolution-Entropy Hybrid Methods for Ranking Protein Residues by Importance
- DOI 10.1016/j.jmb.2003.12.078
- I Mihalek I Reos O Lichtarge 2004 J Mol Biol 336 1265 1282 10.1016/j.jmb.2003.12.078 1:CAS:528:DC%2BD2cXht1Kiu7Y%3D (Pubitemid 38229712)
- (2004) Journal of Molecular Biology , vol.336 , Issue.5 , pp. 1265-1282
- Mihalek, I.¹ Res, I.² Lichtarge, O.³

23
- 0345062357
- Universally conserved positions in protein folds: Reading evolutionary signals about stability, folding kinetics and function
- DOI 10.1006/jmbi.1999.2911
- L Mirny E Shakhnovich 1999 J Mol Biol 291 177 196 10.1006/jmbi.1999.2911 1:CAS:528:DyaK1MXkvFKjtLY%3D (Pubitemid 29391413)
- (1999) Journal of Molecular Biology , vol.291 , Issue.1 , pp. 177-196
- Mirny, L.A.¹ Shakhnovich, E.I.²

24
- 55949106361
- 10.1007/s10930-008-9150-3 1:CAS:528:DC%2BD1cXhtlSrsLrF
- P Palenchar M Mount D Cusato J Dougherty 2008 Protein J 27 401 407 10.1007/s10930-008-9150-3 1:CAS:528:DC%2BD1cXhtlSrsLrF
- (2008) Protein J , vol.27 , pp. 401-407
- Palenchar, P.¹ Mount, M.² Cusato, D.³ Dougherty, J.⁴

25
- 1842454912
- 10.1110/ps.03465504
- A Panchenko F Kondrashov S Bryant 2003 Protein Sci 13 884 892 10.1110/ps.03465504
- (2003) Protein Sci , vol.13 , pp. 884-892
- Panchenko, A.¹ Kondrashov, F.² Bryant, S.³

26
- 84868117026
- S Pande A Raheja DR Livesay 2007 IEEE Symp CIBCB 7 247 253
- (2007) IEEE Symp CIBCB , vol.7 , pp. 247-253
- Pande, S.¹ Raheja, A.² Livesay, D.R.³

27
- 0034843597
- 10.1093/bioinformatics/17.8.700 1:CAS:528:DC%2BD3MXntFKjsb8%3D
- J Pei N Grishin 2001 Bioinformatics 17 700 712 10.1093/bioinformatics/17. 8.700 1:CAS:528:DC%2BD3MXntFKjsb8%3D
- (2001) Bioinformatics , vol.17 , pp. 700-712
- Pei, J.¹ Grishin, N.²

28
- 33746950964
- Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties
- DOI 10.1186/1471-2105-7-312
- N Petrova C Wu 2006 BMC Bioinformat 7 312 10.1186/1471-2105-7-312 (Pubitemid 44202790)
- (2006) BMC Bioinformatics , vol.7 , pp. 312
- Petrova, N.V.¹ Wu, C.H.²

29
- 77949602893
- 10.1093/bioinformatics/btq008
- S Sankararaman F Sha JF Kirsch MI Jordan K Kimmen Sjolander 2010 Bioinformatics 5 617 624 10.1093/bioinformatics/btq008
- (2010) Bioinformatics , vol.5 , pp. 617-624
- Sankararaman, S.¹ Sha, F.² Kirsch, J.F.³ Jordan, M.I.⁴ Kimmen Sjolander, K.⁵

30
- 0026342532
- 10.1002/prot.340110408 1:CAS:528:DyaK38XhsVOntL0%3D
- P Shenkin BLM Erman 1991 Proteins 11 297 313 10.1002/prot.340110408 1:CAS:528:DyaK38XhsVOntL0%3D
- (1991) Proteins , vol.11 , pp. 297-313
- Shenkin, P.¹ Erman, B.L.M.²

31
- 79958060973
- Smith LI (2002) http://www.cs.otago.ac.nz/cosc453/student-tutorials/ principal-components.pdf
- (2002)
- Smith, L.I.¹

32
- 35948961101
- Predicting and annotating catalytic residues: An information theoretic approach
- DOI 10.1089/cmb.2007.0042
- B Sterner R Singh B Berger 2007 J Comput Biol 14 1058 1073 10.1089/cmb.2007.0042 1:CAS:528:DC%2BD2sXht1CmsLjE (Pubitemid 350073526)
- (2007) Journal of Computational Biology , vol.14 , Issue.8 , pp. 1058-1073
- Sterner, B.¹ Singh, R.² Berger, B.³

33
- 48849085285
- 10.1093/protein/gzn003 1:CAS:528:DC%2BD1cXmsVyjtb0%3D
- Y Tang Z Sheng Y Chen Z Zhang 2008 Protein Eng Des Sel 21 295 302 10.1093/protein/gzn003 1:CAS:528:DC%2BD1cXmsVyjtb0%3D
- (2008) Protein Eng des Sel , vol.21 , pp. 295-302
- Tang, Y.¹ Sheng, Z.² Chen, Y.³ Zhang, Z.⁴

34
- 0022591495
- 10.1016/S0022-5193(86)80075-3 1:CAS:528:DyaL28XitVensbc%3D
- W Taylor 1986 J Theor Biol 119 205 218 10.1016/S0022-5193(86)80075-3 1:CAS:528:DyaL28XitVensbc%3D
- (1986) J Theor Biol , vol.119 , pp. 205-218
- Taylor, W.¹

35
- 0036681416
- Scoring residue conservation
- DOI 10.1002/prot.10146
- W Valdar 2002 Proteins 48 227 241 10.1002/prot.10146 1:CAS:528: DC%2BD38Xlt1Wqu7k%3D (Pubitemid 34743413)
- (2002) Proteins: Structure, Function and Genetics , vol.48 , Issue.2 , pp. 227-241
- Valdar, W.S.J.¹

36
- 33748505263
- Incorporating background frequency improves entropy-based residue conservation measures
- DOI 10.1186/1471-2105-7-385
- K Wang R Samudrala 2006 BMC Bioinformat 7 385 10.1186/1471-2105-7-385 (Pubitemid 44355306)
- (2006) BMC Bioinformatics , vol.7 , pp. 385
- Wang, K.¹ Samudrala, R.²

37
- 79958069735
- R Williamson 1995 J Theor Biol 24 908 915
- (1995) J Theor Biol , vol.24 , pp. 908-915
- Williamson, R.¹

38
- 41349115302
- Tracing evolutionary pressure
- DOI 10.1093/bioinformatics/btn057
- K Ye G Vriend AP IJzerman 2008 Bioinformatics 24 908 915 10.1093/bioinformatics/btn057 1:CAS:528:DC%2BD1cXktVWlu7Y%3D (Pubitemid 351448024)
- (2008) Bioinformatics , vol.24 , Issue.7 , pp. 908-915
- Ye, K.¹ Vriend, G.² Ijzerman, A.P.³

39
- 33846554792
- Evaluation of features for catalytic residue prediction in novel folds
- DOI 10.1110/ps.062523907
- E Youn 2007 Protein Sci 16 216 226 10.1110/ps.062523907 1:CAS:528:DC%2BD2sXksVKnurY%3D (Pubitemid 46155771)
- (2007) Protein Science , vol.16 , Issue.2 , pp. 216-226
- Youn, E.¹ Peters, B.² Radivojac, P.³ Mooney, S.D.⁴

40
- 49749105937
- 10.1007/s00726-007-0586-0
- SW Zhang YL Zhang Q Pan YM Cheng KC Chou 2008 Amino Acids 35 495 501 10.1007/s00726-007-0586-0
- (2008) Amino Acids , vol.35 , pp. 495-501
- Zhang, S.W.¹ Zhang, Y.L.² Pan, Q.³ Cheng, Y.M.⁴ Chou, K.C.⁵

41
- 53749083563
- 10.1093/bioinformatics/btn433 1:CAS:528:DC%2BD1cXht1elsLfF
- T Zhang H Zhang K Chen SY Shen JS Ruan L Kurgan 2008 Bioinformatics 24 2329 2338 10.1093/bioinformatics/btn433 1:CAS:528:DC%2BD1cXht1elsLfF
- (2008) Bioinformatics , vol.24 , pp. 2329-2338
- Zhang, T.¹ Zhang, H.² Chen, K.³ Shen, S.Y.⁴ Ruan, J.S.⁵ Kurgan, L.⁶

* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.