SCOPUS 정보 검색 플랫폼

Journal of Computer-Aided Molecular Design

Volumn 23, Issue 11, 2009, Pages 773-784

Identification of family-specific residue packing motifs and their use for structure-based protein function prediction: I. Method development

(6) Bandyopadhyay, Deepak a Huan, Jun b Prins, Jan c Snoeyink, Jack c Wang, Wei c Tropsha, Alexander d

a GLAXOSMITHKLINE (United States)

b University of Kansas (United States)

c Brooks Computer Science Building (United States)

d UNIVERSITY OF NORTH CAROLINA (United States)

Author keywords

Family specific motifs; FFSM; Frequent subgraph mining; Protein function prediction; Protein graphs; Structural genomics

Indexed keywords

DATA MINING; FORECASTING; QUERY PROCESSING;

FAMILY-SPECIFIC MOTIF; FFSM; FREQUENT SUBGRAPH MINING; I METHODS; PACKING MOTIFS; PROTEIN FUNCTION PREDICTION; PROTEIN GRAPH; PROTEINS STRUCTURES; STRUCTURAL GENOMICS; STRUCTURE-BASED;

PROTEINS;

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; AUTOMATION; BIOLOGY; CHEMICAL STRUCTURE; ENZYME ACTIVE SITE; GEOMETRY; PREDICTION; PRIORITY JOURNAL; PROCESS DEVELOPMENT; PROCESS MODEL; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; STRUCTURAL GENOMICS;

EID: 72849113648 PISSN: 0920654X EISSN: 15734951 Source Type: Journal
DOI: 10.1007/s10822-009-9273-4 Document Type: Article

Times cited : (13)

References (100)

1
- 33751547539
- How many drug targets are there?
- DOI 10.1038/nrd2199, PII NRD2199
- J Overington B Al-Lazikani A Hopkins 2006 Nat Rev Drug Discov 5 993 10.1038/nrd2199 1:CAS:528:DC%2BD28Xht1Kju7jM (Pubitemid 44835126)
- (2006) Nature Reviews Drug Discovery , vol.5 , Issue.12 , pp. 993-996
- Overington, J.P.¹ Al-Lazikani, B.² Hopkins, A.L.³

2
- 0029785147
- 10.1126/science.273.5275.595 1:CAS:528:DyaK28Xks1ynt7w%3D
- L Holm C Sander 1996 Science 273 595 10.1126/science.273.5275.595 1:CAS:528:DyaK28Xks1ynt7w%3D
- (1996) Science , vol.273 , pp. 595
- Holm, L.¹ Sander, C.²

3
- 0024913945
- 1:CAS:528:DyaK3cXhtFaqsrg%3D
- LM Smith 1989 Genome 31 929 1:CAS:528:DyaK3cXhtFaqsrg%3D
- (1989) Genome , vol.31 , pp. 929
- Smith, L.M.¹

4
- 0033757822
- An overview of structural genomics
- DOI 10.1038/80697
- SK Burley 2000 Nat Struct Biol 7 Suppl 932 10.1038/80697 1:CAS:528:DC%2BD3cXnvVOgt7w%3D (Pubitemid 30823268)
- (2000) Nature Structural Biology , vol.7 , Issue.SUPPL. , pp. 932-934
- Burley, S.K.¹

5
- 0003584921
- Kluwer Academic Publishers, Dordrecht, The Netherlands (published online on NCBI bookshelf, 2003)
- Koonin EV, Galperin MY (2002) Sequence-evolution-function: computational approaches in comparative genomics. Kluwer Academic Publishers, Dordrecht, The Netherlands (published online on NCBI bookshelf, 2003)
- (2002) Sequence-evolution-function: Computational Approaches in Comparative Genomics
- Koonin, E.V.¹ Galperin, M.Y.²

6
- 0035838976
- Automated structure-based prediction of functional sites in proteins: Applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking
- DOI 10.1006/jmbi.2001.4870
- P Aloy E Querol FX Aviles, et al. 2001 J Mol Biol 311 395 10.1006/jmbi.2001.4870 1:CAS:528:DC%2BD3MXlsFCgsro%3D (Pubitemid 32744549)
- (2001) Journal of Molecular Biology , vol.311 , Issue.2 , pp. 395-408
- Aloy, P.¹ Querol, E.² Aviles, F.X.³ Sternberg, M.J.E.⁴

7
- 33744491290
- Structure-based function inference using protein family-specific fingerprints
- DOI 10.1110/ps.062189906
- D Bandyopadhyay J Huan J Liu, et al. 2006 Protein Sci 15 1537 10.1110/ps.062189906 1:CAS:528:DC%2BD28XlsVOjsr4%3D (Pubitemid 43800028)
- (2006) Protein Science , vol.15 , Issue.6 , pp. 1537-1543
- Bandyopadhyay, D.¹ Huan, J.² Liu, J.³ Prins, J.⁴ Snoeyink, J.⁵ Wang, W.⁶ Tropsha, A.⁷

8
- 23844484183
- Comparing graph representations of protein structure for mining family-specific residue-based packing motifs
- DOI 10.1089/cmb.2005.12.657
- J Huan D Bandyopadhyay W Wang, et al. 2005 J Comput Biol 12 657 10.1089/cmb.2005.12.657 1:CAS:528:DC%2BD2MXotFemsL0%3D (Pubitemid 41170474)
- (2005) Journal of Computational Biology , vol.12 , Issue.6 , pp. 657-671
- Huan, J.¹ Bandyopadhyay, D.² Wang, W.³ Snoeyink, J.⁴ Prins, J.⁵ Tropsha, A.⁶

9
- 72849145576
- Huan J, Wang W, Prins J (2003) ICDM '03: Proceedings of the Third IEEE International Conference on Data Mining
- (2003) ICDM '03: Proceedings of the Third IEEE International Conference on Data Mining
- Huan, J.¹ Wang, W.² Prins, J.³

10
- 72849130934
- doi: 10.1007/s10822-009-9277-0
- Bandyopadhyay D, Huan J, Prins J et al (2009) J Comput Aided Mol Des. doi: 10.1007/s10822-009-9277-0
- (2009) J Comput Aided Mol Des.
- Bandyopadhyay, D.¹ Huan, J.² Prins, J.³ Al, E.⁴

11
- 53249156104
- 10.1093/bfgp/eln030 1:CAS:528:DC%2BD1cXhtlyjtLjP
- P Gherardini M Helmer-Citterich 2008 Brief Funct Genomic Proteomic 7 291 10.1093/bfgp/eln030 1:CAS:528:DC%2BD1cXhtlyjtLjP
- (2008) Brief Funct Genomic Proteomic , vol.7 , pp. 291
- Gherardini, P.¹ Helmer-Citterich, M.²

12
- 50949093079
- 10.1007/s00726-008-0077-y 1:CAS:528:DC%2BD1cXhtVGntr7L
- X Zhao L Chen K Aihara 2008 Amino Acids 35 517 10.1007/s00726-008-0077-y 1:CAS:528:DC%2BD1cXhtVGntr7L
- (2008) Amino Acids , vol.35 , pp. 517
- Zhao, X.¹ Chen, L.² Aihara, K.³

13
- 44949122425
- 10.1016/j.sbi.2008.05.007 1:CAS:528:DC%2BD1cXntlWntr8%3D
- O Redfern B Dessailly C Orengo 2008 Curr Opin Struct Biol 18 394 10.1016/j.sbi.2008.05.007 1:CAS:528:DC%2BD1cXntlWntr8%3D
- (2008) Curr Opin Struct Biol , vol.18 , pp. 394
- Redfern, O.¹ Dessailly, B.² Orengo, C.³

14
- 0032962457
- 10.1093/protein/12.2.85 1:CAS:528:DyaK1MXhvFehs70%3D
- B Rost 1999 Protein Eng 12 85 10.1093/protein/12.2.85 1:CAS:528:DyaK1MXhvFehs70%3D
- (1999) Protein Eng , vol.12 , pp. 85
- Rost, B.¹

15
- 0142106373
- How well is enzyme function conserved as a function of pairwise sequence identity?
- DOI 10.1016/j.jmb.2003.08.057
- W Tian J Skolnick 2003 J Mol Biol 333 863 10.1016/j.jmb.2003.08.057 1:CAS:528:DC%2BD3sXot1GktLs%3D (Pubitemid 37268023)
- (2003) Journal of Molecular Biology , vol.333 , Issue.4 , pp. 863-882
- Tian, W.¹ Skolnick, J.²

16
- 0032944238
- The PROSITE database, its status in 1999
- DOI 10.1093/nar/27.1.215
- SK Hofmann P Bucher L Falquet, et al. 1999 Nucleic Acids Res 27 1 215 10.1093/nar/27.1.215 1:CAS:528:DyaK1MXpsVKitg%3D%3D (Pubitemid 29209443)
- (1999) Nucleic Acids Research , vol.27 , Issue.1 , pp. 215-219
- Hofmann, K.¹ Bucher, P.² Falquet, L.³ Bairoch, A.⁴

17
- 0025341905
- 10.1016/0076-6879(90)83011-W 1:CAS:528:DyaK3cXkslChsr8%3D
- M Gribskov R Luthy D Eisenberg 1990 Meth Enzymol 183 146 10.1016/0076-6879(90)83011-W 1:CAS:528:DyaK3cXkslChsr8%3D
- (1990) Meth Enzymol , vol.183 , pp. 146
- Gribskov, M.¹ Luthy, R.² Eisenberg, D.³

18
- 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, et al. 1997 Nucleic Acids Res 25 3389 10.1093/nar/25.17.3389 1:CAS:528:DyaK2sXlvFyhu7w%3D (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

19
- 0028181441
- 10.1006/jmbi.1994.1104 1:CAS:528:DyaK2cXitFWjt7g%3D
- A Krogh M Brown IS Mian, et al. 1994 J Mol Biol 235 1501 10.1006/jmbi.1994.1104 1:CAS:528:DyaK2cXitFWjt7g%3D
- (1994) J Mol Biol , vol.235 , pp. 1501
- Krogh, A.¹ Brown, M.² Mian, I.S.³

20
- 0036796379
- 10.1093/nar/gkf544 1:CAS:528:DC%2BD38XnvVemur0%3D
- M Madera J Gough 2002 Nucleic Acids Res 30 4321 10.1093/nar/gkf544 1:CAS:528:DC%2BD38XnvVemur0%3D
- (2002) Nucleic Acids Res , vol.30 , pp. 4321
- Madera, M.¹ Gough, J.²

21
- 0029913807
- An evolutionary trace method defines binding surfaces common to protein families
- DOI 10.1006/jmbi.1996.0167
- O Lichtarge HR Bourne FE Cohen 1996 J Mol Biol 257 342 10.1006/jmbi.1996.0167 1:CAS:528:DyaK28XhvVOqsLw%3D (Pubitemid 26114038)
- (1996) Journal of Molecular Biology , vol.257 , Issue.2 , pp. 342-358
- Lichtarge, O.¹ Bourne, H.R.² Cohen, F.E.³

22
- 38849090164
- Prediction of enzyme function based on 3D templates of evolutionarily important amino acids
- DOI 10.1186/1471-2105-9-17
- D Kristensen R Ward A Lisewski, et al. 2008 BMC Bioinformatics 9 17 10.1186/1471-2105-9-17 (Pubitemid 351189036)
- (2008) BMC Bioinformatics , vol.9 , pp. 17
- Kristensen, D.M.¹ Matthew, R.M.² Lisewski, A.³ Erdin, S.⁴ Chen, B.Y.⁵ Fofanov, V.Y.⁶ Kimmel, M.⁷ Kavraki, L.E.⁸ Lichtarge, O.⁹

23
- 47849086673
- De-orphaning the structural proteome through reciprocal comparison of evolutionarily important structural features
- DOI 10.1371/journal.pone.0002136
- R Ward S Erdin T Tran, et al. 2008 PLoS ONE 3 e2136 10.1371/journal.pone. 0002136 (Pubitemid 352034201)
- (2008) PLoS ONE , vol.3 , Issue.5
- Ward, R.M.¹ Erdin, S.² Tran, T.A.³ Kristensen, D.M.⁴ Lisewski, A.M.⁵ Lichtarge, O.⁶

24
- 0034780910
- Horizontal gene transfer in prokaryotes: Quantification and classification
- DOI 10.1146/annurev.micro.55.1.709
- EV Koonin KS Makarova L Aravind 2001 Annu Rev Microbiol 55 709 10.1146/annurev.micro.55.1.709 1:CAS:528:DC%2BD3MXnslKjtbw%3D (Pubitemid 32978121)
- (2001) Annual Review of Microbiology , vol.55 , pp. 709-742
- Koonin, E.V.¹ Makarova, K.S.² Aravind, L.³

25
- 0030660581
- A genomic perspective on protein families
- DOI 10.1126/science.278.5338.631
- RL Tatusov EV Koonin DJ Lipman 1997 Science 278 631 10.1126/science.278. 5338.631 1:CAS:528:DyaK2sXmvVOrsL0%3D (Pubitemid 27464953)
- (1997) Science , vol.278 , Issue.5338 , pp. 631-637
- Tatusov, R.L.¹ Koonin, E.V.² Lipman, D.J.³

26
- 4644231028
- 10.1186/gb-2004-5-5-r35
- PM Bowers M Pellegrini MJ Thompson, et al. 2004 Genome Biol 5 R35 10.1186/gb-2004-5-5-r35
- (2004) Genome Biol , vol.5 , pp. 35
- Bowers, P.M.¹ Pellegrini, M.² Thompson, M.J.³

27
- 19544393944
- Protein function prediction using the Protein Link EXplorer (PLEX)
- DOI 10.1093/bioinformatics/bti313
- SV Date EM Marcotte 2005 Bioinformatics 21 2558 10.1093/bioinformatics/ bti313 1:CAS:528:DC%2BD2MXktl2ru78%3D (Pubitemid 40731628)
- (2005) Bioinformatics , vol.21 , Issue.10 , pp. 2558-2559
- Date, S.V.¹ Marcotte, E.M.²

28
- 43849095772
- Graphical models of residue coupling in protein families
- DOI 10.1109/TCBB.2007.70225, 4359882
- J Thomas N Ramakrishnan C Bailey-Kellogg 2008 IEEE/ACM Trans Comput Biol Bioinform 5 183 10.1109/TCBB.2007.70225 1:CAS:528:DC%2BD1cXns1artr8%3D (Pubitemid 351695259)
- (2008) IEEE/ACM Transactions on Computational Biology and Bioinformatics , vol.5 , Issue.2 , pp. 183-197
- Thomas, J.¹ Ramakrishnan, N.² Bailey-Kellogg, C.³

29
- 44949207428
- Sequence similarity network reveals common ancestry of multidomain proteins
- DOI 10.1371/journal.pcbi.1000063
- N Song J Joseph G Davis, et al. 2008 PLoS Comput Biol 4 e1000063 10.1371/journal.pcbi.1000063 (Pubitemid 351811549)
- (2008) PLoS Computational Biology , vol.4 , Issue.5
- Song, N.¹ Joseph, J.M.² Davis, G.B.³ Durand, D.⁴

30
- 65649091582
- C Lanczycki S Chakrabarti 2008 Bioinformation 2 279
- (2008) Bioinformation , vol.2 , pp. 279
- Lanczycki, C.¹ Chakrabarti, S.²

31
- 45749119940
- Prediction of enzyme function by combining sequence similarity and protein interactions
- DOI 10.1186/1471-2105-9-249
- J Espadaler N Eswar E Querol, et al. 2008 BMC Bioinformatics 9 249 10.1186/1471-2105-9-249 (Pubitemid 351866017)
- (2008) BMC Bioinformatics , vol.9 , pp. 249
- Espadaler, J.¹ Eswar, N.² Querol, E.³ Aviles, F.X.⁴ Sali, A.⁵ Marti-Renom, M.A.⁶ Oliva, B.⁷

32
- 0024349252
- Protein structure alignment
- DOI 10.1016/0022-2836(89)90084-3
- W Taylor C Orengo 1989 J Mol Biol 208 1 10.1016/0022-2836(89)90084-3 1:CAS:528:DyaL1MXkvFentr8%3D (Pubitemid 19191513)
- (1989) Journal of Molecular Biology , vol.208 , Issue.1 , pp. 1-22
- Taylor, W.R.¹ Orengo, C.A.²

33
- 0346494941
- 10.1093/nar/gkh039 1:CAS:528:DC%2BD3sXhtVSrurzE
- A Andreeva D Howorth SE Brenner, et al. 2004 Nucleic Acids Res 32 D226 10.1093/nar/gkh039 1:CAS:528:DC%2BD3sXhtVSrurzE
- (2004) Nucleic Acids Res , vol.32 , pp. 226
- Andreeva, A.¹ Howorth, D.² Brenner, S.E.³

34
- 0030777303
- 10.1016/S0969-2126(97)00260-8 1:CAS:528:DyaK2sXmt1Wgs74%3D
- C Orengo A Michie S Jones, et al. 1997 Structure 5 1093 10.1016/S0969-2126(97)00260-8 1:CAS:528:DyaK2sXmt1Wgs74%3D
- (1997) Structure , vol.5 , pp. 1093
- Orengo, C.¹ Michie, A.² Jones, S.³

35
- 0029936121
- Surprising similarities in structure comparison
- DOI 10.1016/S0959-440X(96)80058-3
- J Gibrat T Madej S Bryant 1996 Curr Opin Struct Biol 6 377 10.1016/S0959-440X(96)80058-3 1:CAS:528:DyaK28XjvFSgsLg%3D (Pubitemid 26197439)
- (1996) Current Opinion in Structural Biology , vol.6 , Issue.3 , pp. 377-385
- Gibrat, J.-F.¹ Madej, T.² Bryant, S.H.³

36
- 2342491596
- 10.1002/spe.588
- EB Krissinel K Henrick 2004 Softw Pract Exp 34 591 10.1002/spe.588
- (2004) Softw Pract Exp , vol.34 , pp. 591
- Krissinel, E.B.¹ Henrick, K.²

37
- 0030623880
- Gaasterland T, Karp PD, Karplus K, Ouzonis CA, Sander C, Valencia A (eds) ISMB'97 Halkidiki, Greece, June 1997
- Holm L, Sander C (1997) In: Gaasterland T, Karp PD, Karplus K, Ouzonis CA, Sander C, Valencia A (eds) ISMB'97. 5th International conference on intelligent systems for molecular biology, Halkidiki, Greece, June 1997, p 140
- (1997) 5th International Conference on Intelligent Systems for Molecular Biology , pp. 140
- Holm, L.¹ Sander, C.²

38
- 0033597176
- The relationship between protein structure and function: A comprehensive survey with application to the yeast genome
- DOI 10.1006/jmbi.1999.2661
- H Hegyi M Gerstein 1999 J Mol Biol 288 147 10.1006/jmbi.1999.2661 1:CAS:528:DyaK1MXislWrsr4%3D (Pubitemid 29201511)
- (1999) Journal of Molecular Biology , vol.288 , Issue.1 , pp. 147-164
- Hegyi, H.¹ Gerstein, M.²

39
- 2542445427
- ConSurf: Identification of functional regions in proteins by surface-mapping of phylogenetic information
- DOI 10.1093/bioinformatics/19.1.163
- F Glaser T Pupko I Paz, et al. 2003 Bioinformatics 19 163 10.1093/bioinformatics/19.1.163 1:CAS:528:DC%2BD3sXltF2rtQ%3D%3D (Pubitemid 36150199)
- (2003) Bioinformatics , vol.19 , Issue.1 , pp. 163-164
- Glaser, F.¹ Pupko, T.² Paz, I.³ Bell, R.E.⁴ Bechor-Shental, D.⁵ Martz, E.⁶ Ben-Tal, N.⁷

40
- 0043130640
- Altman RB, Dunker AK, Hunter L, Jung TA (eds) PSB'03 Hawaii, January 2003
- Liang M, Brutlag D, Altman R (2003) In: Altman RB, Dunker AK, Hunter L, Jung TA (eds) PSB'03. 8th Pacific symposium on biocomputing, Hawaii, January 2003, p 204
- (2003) 8th Pacific Symposium on Biocomputing , pp. 204
- Liang, M.¹ Brutlag, D.² Altman, R.³

41
- 0032568859
- Detection of protein three-dimensional side-chain patterns: New examples of convergent evolution
- DOI 10.1006/jmbi.1998.1844
- RB Russell 1998 J Mol Biol 279 1211 10.1006/jmbi.1998.1844 1:CAS:528:DyaK1cXktlaiur8%3D (Pubitemid 28302396)
- (1998) Journal of Molecular Biology , vol.279 , Issue.5 , pp. 1211-1227
- Russell, R.B.¹

42
- 0041620372
- Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures
- DOI 10.1093/nar/gkg506
- A Stark R Russell 2003 Nucleic Acids Res 31 3341 10.1093/nar/gkg506 1:CAS:528:DC%2BD3sXltVWjs7w%3D (Pubitemid 37442154)
- (2003) Nucleic Acids Research , vol.31 , Issue.13 , pp. 3341-3344
- Stark, A.¹ Russell, R.B.²

43
- 4143145197
- Finding functional sites in structural genomics proteins
- DOI 10.1016/j.str.2004.05.012, PII S096921260400214X
- A Stark A Shkumatov RB Russell 2004 Structure (Camb) 12 1405 10.1016/j.str.2004.05.012 1:CAS:528:DC%2BD2cXmsVKnt7k%3D (Pubitemid 39092085)
- (2004) Structure , vol.12 , Issue.8 , pp. 1405-1412
- Stark, A.¹ Shkumatov, A.² Russell, R.B.³

44
- 0037172967
- Bradley P, Kim PS, Berger B (2002) Proc Natl Acad Sci 99:8500
- (2002) Proc Natl Acad Sci , vol.99 , pp. 8500
- Bradley, P.¹ Kim, P.S.² Berger, B.³

45
- 27544512084
- The SuMo server: 3D search for protein functional sites
- DOI 10.1093/bioinformatics/bti645
- M Jambon O Andrieu C Combet, et al. 2005 Bioinformatics 21 3929 10.1093/bioinformatics/bti645 1:CAS:528:DC%2BD2MXhtFWltrzN (Pubitemid 41535510)
- (2005) Bioinformatics , vol.21 , Issue.20 , pp. 3929-3930
- Jambon, M.¹ Andrieu, O.² Combet, C.³ Deleage, G.⁴ Delfaud, F.⁵ Geourjon, C.⁶

46
- 0025719208
- 10.1073/pnas.88.23.10495 1:CAS:528:DyaK38XlsFSntQ%3D%3D
- R Nussinov HJ Wolfson 1991 PNAS 88 10495 10.1073/pnas.88.23.10495 1:CAS:528:DyaK38XlsFSntQ%3D%3D
- (1991) PNAS , vol.88 , pp. 10495
- Nussinov, R.¹ Wolfson, H.J.²

47
- 0141850386
- An algorithm for constraint-based structural template matching: Application to 3D templates with statistical analysis
- DOI 10.1093/bioinformatics/btg226
- J Barker J Thornton 2003 Bioinformatics 19 1644 10.1093/bioinformatics/ btg226 1:CAS:528:DC%2BD3sXnt1Gqu7o%3D (Pubitemid 37121152)
- (2003) Bioinformatics , vol.19 , Issue.13 , pp. 1644-1649
- Barker, J.A.¹ Thornton, J.M.²

48
- 2442614144
- Recognition of functional sites in protein structures
- DOI 10.1016/j.jmb.2004.04.012, PII S0022283604004139
- A Shulman-Peleg R Nussinov H Wolfson 2004 J Mol Biol 339 607 10.1016/j.jmb.2004.04.012 1:CAS:528:DC%2BD2cXktVeqtbo%3D (Pubitemid 38625909)
- (2004) Journal of Molecular Biology , vol.339 , Issue.3 , pp. 607-633
- Shulman-Peleg, A.¹ Nussinov, R.² Wolfson, H.J.³

49
- 3242883091
- PvSOAR: Detecting similar surface patterns of pocket and void surfaces of amino acid residues on proteins
- DOI 10.1093/nar/gkh390
- TA Binkowski P Freeman J Liang 2004 Nucleic Acid Res 32 W555 10.1093/nar/gkh390 1:CAS:528:DC%2BD2cXlvFKms7o%3D (Pubitemid 38997395)
- (2004) Nucleic Acids Research , vol.32 , Issue.WEB SERVER ISS.
- Binkowski, T.A.¹ Freeman, P.² Liang, J.³

50
- 0030447531
- 1:CAS:528:DyaK2sXis1ai
- RA Laskowski NM Luscombe MB Swindells, et al. 1996 Protein Sci 5 2438 1:CAS:528:DyaK2sXis1ai
- (1996) Protein Sci , vol.5 , pp. 2438
- Laskowski, R.A.¹ Luscombe, N.M.² Swindells, M.B.³

51
- 0346494936
- 10.1093/nar/gkh054 1:CAS:528:DC%2BD3sXhtVSrurrP
- F Ferre G Ausiello A Zanzoni, et al. 2004 Nucleic Acids Res 32 D240 10.1093/nar/gkh054 1:CAS:528:DC%2BD3sXhtVSrurrP
- (2004) Nucleic Acids Res , vol.32 , pp. 240
- Ferre, F.¹ Ausiello, G.² Zanzoni, A.³

52
- 3042726390
- A structural pattern-based method for protein fold recognition
- DOI 10.1002/prot.20073
- WR Taylor I Jonassen 2004 Proteins 56 222 10.1002/prot.20073 1:CAS:528:DC%2BD2cXlsFGmsrw%3D (Pubitemid 38850157)
- (2004) Proteins: Structure, Function and Genetics , vol.56 , Issue.2 , pp. 222-234
- Taylor, W.R.¹ Jonassen, I.²

53
- 0027967593
- A graph-theoretic approach to the identification of three-dimensional patterns of amino acid side-chains in protein structures
- DOI 10.1006/jmbi.1994.1657
- PJ Artymiuk AR Poirrette HM Grindley, et al. 1994 J Mol Biol 243 327 10.1006/jmbi.1994.1657 1:STN:280:DyaK2M%2FhvVaksA%3D%3D (Pubitemid 24331985)
- (1994) Journal of Molecular Biology , vol.243 , Issue.2 , pp. 327-344
- Artymiuk, P.J.¹ Poirrette, A.R.² Grindley, H.M.³ Rice, D.W.⁴ Willett, P.⁵

54
- 0031410097
- Clique-detection algorithms for matching three-dimensional molecular structures
- DOI 10.1016/S1093-3263(97)00089-2, PII S1093326397000892
- EJ Gardiner PJ Artymiuk P Willett 1997 J Mol Graph Model 15 245 10.1016/S1093-3263(97)00089-2 1:CAS:528:DyaK1cXhs1yhs74%3D (Pubitemid 28134940)
- (1997) Journal of Molecular Graphics and Modelling , vol.15 , Issue.4 , pp. 245-253
- Gardiner, E.J.¹ Artymiuk, P.J.² Willett, P.³

55
- 0032577270
- A graph-theoretic algorithm for comparative modeling of protein structure
- DOI 10.1006/jmbi.1998.1689
- R Samudrala J Moult 1998 J Mol Biol 279 1 287 10.1006/jmbi.1998.1689 1:CAS:528:DyaK1cXjvVyisro%3D (Pubitemid 28252146)
- (1998) Journal of Molecular Biology , vol.279 , Issue.1 , pp. 287-302
- Samudrala, R.¹ Moult, J.²

56
- 0036406643
- A new method to detect related function among proteins independent of sequence and fold homology
- DOI 10.1016/S0022-2836(02)00811-2
- S Schmitt D Kuhn G Klebe 2002 J Mol Biol 323 2 387 10.1016/S0022-2836(02) 00811-2 1:CAS:528:DC%2BD38XnslGqsrY%3D (Pubitemid 35283699)
- (2002) Journal of Molecular Biology , vol.323 , Issue.2 , pp. 387-406
- Schmitt, S.¹ Kuhn, D.² Klebe, G.³

57
- 0037424601
- 10.1016/S0022-2836(03)00045-7
- A Stark S Sunyaev RB Russell 1998 J Mol Biol 326 1307 10.1016/S0022-2836(03)00045-7
- (1998) J Mol Biol , vol.326 , pp. 1307
- Stark, A.¹ Sunyaev, S.² Russell, R.B.³

58
- 0037459071
- Functional sites in protein families uncovered via an objective and automated graph theoretic approach
- DOI 10.1016/S0022-2836(02)01384-0
- PP Wangikar AV Tendulkar S Ramya, et al. 2003 J Mol Biol 326 955 10.1016/S0022-2836(02)01384-0 1:CAS:528:DC%2BD3sXhtVCisbc%3D (Pubitemid 36279330)
- (2003) Journal of Molecular Biology , vol.326 , Issue.3 , pp. 955-978
- Wangikar, P.P.¹ Tendulkar, A.V.² Ramya, S.³ Mali, D.N.⁴ Sarawagi, S.⁵

59
- 0141482410
- 10.1093/protein/gzg080 1:CAS:528:DC%2BD3sXnt1KisL8%3D
- M Milik S Szalma K Olszewski 2003 Protein Eng 16 8 543 10.1093/protein/gzg080 1:CAS:528:DC%2BD3sXnt1KisL8%3D
- (2003) Protein Eng , vol.16 , Issue.8 , pp. 543
- Milik, M.¹ Szalma, S.² Olszewski, K.³

60
- 0035936692
- Automated discovery of structural signatures of protein fold and function
- DOI 10.1006/jmbi.2000.4414
- M Turcotte S Muggleton M Sternberg 2001 J Mol Biol 306 3 591 10.1006/jmbi.2000.4414 1:CAS:528:DC%2BD3MXhtFKrurk%3D (Pubitemid 33027725)
- (2001) Journal of Molecular Biology , vol.306 , Issue.3 , pp. 591-605
- Turcotte, M.¹ Muggleton, S.H.² Sternberg, M.J.E.³

61
- 0032483312
- 1 ribonucleases
- DOI 10.1006/jmbi.1998.1993
- JS Fetrow J Skolnick 1998 J Mol Biol 281 949 10.1006/jmbi.1998.1993 1:CAS:528:DyaK1cXmtVygs70%3D (Pubitemid 28408440)
- (1998) Journal of Molecular Biology , vol.281 , Issue.5 , pp. 949-968
- Fetrow, J.S.¹ Skolnick, J.²

62
- 46749103736
- 10.1142/9781860949852-0010 1:CAS:528:DC%2BD1cXms1eju70%3D
- L Murga Y Wei M Ondrechen 2007 Genome Inform 19 107 10.1142/ 9781860949852-0010 1:CAS:528:DC%2BD1cXms1eju70%3D
- (2007) Genome Inform , vol.19 , pp. 107
- Murga, L.¹ Wei, Y.² Ondrechen, M.³

63
- 34447645811
- A robust and efficient algorithm for the shape description of protein structures and its application in predicting ligand binding sites
- DOI 10.1186/1471-2105-8-S4-S9
- L Xie P Bourne 2007 BMC Bioinformatics 8 Suppl 4 S9 10.1186/1471-2105-8- S4-S9 (Pubitemid 351833828)
- (2007) BMC Bioinformatics , vol.8 , Issue.SUPPL. 4
- Xie, L.¹ Bourne, P.E.²

64
- 3543053391
- Efficient similarity search in protein structure databases by k-clique hashing
- DOI 10.1093/bioinformatics/bth113
- N Weskamp D Kuhn E Hullermeier, et al. 2004 Bioinformatics 20 1522 10.1093/bioinformatics/bth113 1:CAS:528:DC%2BD2cXltlOqtL0%3D (Pubitemid 39023156)
- (2004) Bioinformatics , vol.20 , Issue.10 , pp. 1522-1526
- Weskamp, N.¹ Kuhn, D.² Hullermeier, E.³ Klebe, G.⁴

65
- 22544441094
- ProFunc: A server for predicting protein function from 3D structure
- DOI 10.1093/nar/gki414
- RA Laskowski JD Watson JM Thornton 2005 Nucleic Acids Res 33 W89 10.1093/nar/gki414 1:CAS:528:DC%2BD2MXlslyqsrk%3D (Pubitemid 44529886)
- (2005) Nucleic Acids Research , vol.33 , Issue.WEB. SERV. ISS.
- Laskowski, R.A.¹ Watson, J.D.² Thornton, J.M.³

66
- 72849114387
- Chapter 2: Unit 2.7
- Mulder N, Apweiler R (2008) Curr Protoc Bioinformatics Chapter 2: Unit 2.7
- (2008) Curr Protoc Bioinformatics
- Mulder, N.¹ Apweiler, R.²

67
- 0036087169
- 10.1093/nar/30.1.268 1:CAS:528:DC%2BD38Xht12rsrw%3D
- J Gough C Chothia 2002 Nucleic Acids Res 30 268 10.1093/nar/30.1.268 1:CAS:528:DC%2BD38Xht12rsrw%3D
- (2002) Nucleic Acids Res , vol.30 , pp. 268
- Gough, J.¹ Chothia, C.²

68
- 0037436339
- Relibase: Design and development of a database for comprehensive analysis of protein-ligand interactions
- DOI 10.1016/S0022-2836(02)01408-0
- M Hendlich A Bergner J Gunther, et al. 2003 J Mol Biol 326 607 10.1016/S0022-2836(02)01408-0 1:CAS:528:DC%2BD3sXmt1WktA%3D%3D (Pubitemid 36279352)
- (2003) Journal of Molecular Biology , vol.326 , Issue.2 , pp. 607-620
- Hendlich, M.¹ Bergner, A.² Gunther, J.³ Klebe, G.⁴

69
- 0345864027
- 10.1093/nar/gkh028 1:CAS:528:DC%2BD3sXhtVSrur%2FL
- CT Porter GJ Bartlett JM Thornton 2004 Nucleic Acids Res 32 D129 10.1093/nar/gkh028 1:CAS:528:DC%2BD3sXhtVSrur%2FL
- (2004) Nucleic Acids Res , vol.32 , pp. 129
- Porter, C.T.¹ Bartlett, G.J.² Thornton, J.M.³

70
- 0037930733
- Using structural motif templates to identify proteins with DNA binding function
- DOI 10.1093/nar/gkg386
- S Jones JA Barker I Nobeli, et al. 2003 Nucleic Acids Res 31 2811 10.1093/nar/gkg386 1:CAS:528:DC%2BD3sXkt1Wqs7k%3D (Pubitemid 37442125)
- (2003) Nucleic Acids Research , vol.31 , Issue.11 , pp. 2811-2823
- Jones, S.¹ Barker, J.A.² Nobeli, I.³ Thornton, J.M.⁴

71
- 21644476077
- Recurring main-chain anion-binding motifs in short polypeptides: Nests
- DOI 10.1107/S0907444904021390
- EJ Milner-White JW Nissink FH Allen, et al. 2004 Acta Crystallogr D Biol Crystallogr 60 1935 10.1107/S0907444904021390 (Pubitemid 41087522)
- (2004) Acta Crystallographica Section D: Biological Crystallography , vol.60 , Issue.11 , pp. 1935-1942
- Milner-White, E.J.¹ Nissink, J.W.M.² Allen, F.H.³ Duddy, W.J.⁴

72
- 22544486576
- Protein function prediction using local 3D templates
- DOI 10.1016/j.jmb.2005.05.067, PII S0022283605006340
- R Laskowski J Watson J Thornton 2005 J Mol Biol 351 614 10.1016/j.jmb.2005.05.067 1:CAS:528:DC%2BD2MXmvVCmtrk%3D (Pubitemid 41021944)
- (2005) Journal of Molecular Biology , vol.351 , Issue.3 , pp. 614-626
- Laskowski, R.A.¹ Watson, J.D.² Thornton, J.M.³

73
- 33947278347
- Towards Fully Automated Structure-based Function Prediction in Structural Genomics: A Case Study
- DOI 10.1016/j.jmb.2007.01.063, PII S0022283607001167
- J Watson S Sanderson A Ezersky, et al. 2007 J Mol Biol 367 1511 10.1016/j.jmb.2007.01.063 1:CAS:528:DC%2BD2sXjtFKiur4%3D (Pubitemid 46420706)
- (2007) Journal of Molecular Biology , vol.367 , Issue.5 , pp. 1511-1522
- Watson, J.D.¹ Sanderson, S.² Ezersky, A.³ Savchenko, A.⁴ Edwards, A.⁵ Orengo, C.⁶ Joachimiak, A.⁷ Laskowski, R.A.⁸ Thornton, J.M.⁹

74
- 72849124746
- New Orleans, LA, USA
- Bandyopadhyay D, Snoeyink J (2004) ACM-SIAM Symposium On Discrete Algorithms. New Orleans, LA, USA
- (2004) ACM-SIAM Symposium on Discrete Algorithms
- Bandyopadhyay, D.¹ Snoeyink, J.²

75
- 0016870630
- JR Ullman 1976 J Assoc Comput Mach 23 31
- (1976) J Assoc Comput Mach , vol.23 , pp. 31
- Ullman, J.R.¹

76
- 0033963089
- 10.1093/nar/28.1.304 1:CAS:528:DC%2BD3cXhvVKjtbw%3D
- A Bairoch 2000 Nucleic Acids Res 28 304 10.1093/nar/28.1.304 1:CAS:528:DC%2BD3cXhvVKjtbw%3D
- (2000) Nucleic Acids Res , vol.28 , pp. 304
- Bairoch, A.¹

77
- 0346801873
- Consortium Gene Ontology. 10.1093/nar/gkh036
- Consortium Gene Ontology 2004 Nucleic Acids Res 32 D258 10.1093/nar/gkh036
- (2004) Nucleic Acids Res , vol.32 , pp. 258

78
- 0043180474
- Wang G, Dunbrack RL (2003) Bioinformatics 19:1589 http://www.fccc.edu/ research/labs/dunbrack/pisces/culledpdb.html
- (2003) Bioinformatics , vol.19 , pp. 1589
- Wang, G.¹ Dunbrack, R.L.²

79
- 72849137057
- Stanford, CA, USA
- Huan J, Bandyopadhyay D, Snoeyink J et al (2006) IEEE Computational Systems Bioinformatics Conference (CSB). Stanford, CA, USA
- (2006) IEEE Computational Systems Bioinformatics Conference (CSB)
- Huan, J.¹ Bandyopadhyay, D.² Snoeyink, J.³ Al, E.⁴

80
- 2442564572
- Gusfield D, Bourne P, Istrail S (eds) RECOMB'04 San Diego, April 2004
- Huan J, Wang W, Bandyopadhyay D et al (2004) In: Gusfield D, Bourne P, Istrail S (eds) RECOMB'04. 8th Annual international conference on research in computational molecular biology, San Diego, April 2004, p 308
- (2004) 8th Annual International Conference on Research in Computational Molecular Biology , pp. 308
- Huan, J.¹ Wang, W.² Bandyopadhyay, D.³ Al, E.⁴

81
- 12244294770
- Kohavi R, Gehrke J, DuMouchel W, Ghosh J (eds) ACM SIGKDD'04 Chicago, August 2004
- Huan J, Wang W, Prins J et al (2004) In: Kohavi R, Gehrke J, DuMouchel W, Ghosh J (eds) ACM SIGKDD'04. 10th International conference on knowledge discovery and data mining, Chicago, August 2004, p 581
- (2004) 10th International Conference on Knowledge Discovery and Data Mining , pp. 581
- Huan, J.¹ Wang, W.² Prins, J.³ Al, E.⁴

82
- 15944418238
- Altman RB, Dunker AK, Hunter L, Jung TA (eds) PSB'05 Hawaii, January 2005
- Pegg SC, Brown S, Ojha S et al (2005) In: Altman RB, Dunker AK, Hunter L, Jung TA (eds) PSB'05. 10th Pacific symposium on biocomputing, Hawaii, January 2005, p 358
- (2005) 10th Pacific Symposium on Biocomputing , pp. 358
- Pegg, S.C.¹ Brown, S.² Al Et, O.S.³

83
- 0037397439
- Definitions of enzyme function for the structural genomics era
- DOI 10.1016/S1367-5931(03)00028-0
- PC Babbitt 2003 Curr Opin Chem Biol 7 230 10.1016/S1367-5931(03)00028-0 1:CAS:528:DC%2BD3sXjtVKgsLg%3D (Pubitemid 36514955)
- (2003) Current Opinion in Chemical Biology , vol.7 , Issue.2 , pp. 230-237
- Babbitt, P.C.¹

84
- 0034677669
- Assessing annotation transfer for genomics: Quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores
- DOI 10.1006/jmbi.2000.3550
- CA Wilson J Kreychman M Gerstein 2000 J Mol Biol 297 233 10.1006/jmbi.2000.3550 1:CAS:528:DC%2BD3cXhsFSqu74%3D (Pubitemid 30695553)
- (2000) Journal of Molecular Biology , vol.297 , Issue.1 , pp. 233-249
- Wilson, C.A.¹ Kreychman, J.² Gerstein, M.³

85
- 0030979555
- Circular permutations of natural protein sequences: Structural evidence
- DOI 10.1016/S0959-440X(97)80061-9
- Y Lindqvist G Schneider 1997 Curr Opin Struct Biol 7 422 10.1016/S0959-440X(97)80061-9 1:CAS:528:DyaK2sXjvFWjsrs%3D (Pubitemid 27281414)
- (1997) Current Opinion in Structural Biology , vol.7 , Issue.3 , pp. 422-427
- Lindqvist, Y.¹ Schneider, G.²

86
- 0035783063
- 10.1006/jsbi.2001.4335 1:CAS:528:DC%2BD3MXms1altrs%3D
- NV Grishin 2001 J Struct Biol 134 167 10.1006/jsbi.2001.4335 1:CAS:528:DC%2BD3MXms1altrs%3D
- (2001) J Struct Biol , vol.134 , pp. 167
- Grishin, N.V.¹

87
- 0036848698
- The crystal structure of MT0146/CbiT suggests that the putative precorrin-8w decarboxylase is a methyltransferase
- DOI 10.1016/S0969-2126(02)00876-6, PII S0969212602008766
- J Keller P Smith J Benach, et al. 2002 Structure 10 1475 10.1016/S0969-2126(02)00876-6 1:CAS:528:DC%2BD38XoslGnt74%3D (Pubitemid 35351488)
- (2002) Structure , vol.10 , Issue.11 , pp. 1475-1487
- Keller, J.P.¹ Smith, P.M.² Benach, J.³ Christendat, D.⁴ De Titta, G.T.⁵ Hunt, J.F.⁶

88
- 0035059281
- Genomic-scale comparison of sequence- and structure-based methods of function prediction: Does structure provide additional insight?
- DOI 10.1110/ps.49201
- JS Fetrow N Siew JA Di Gennaro, et al. 2001 Protein Sci 10 1005 10.1110/ps.49201 1:CAS:528:DC%2BD3MXksFCjsbg%3D (Pubitemid 32367492)
- (2001) Protein Science , vol.10 , Issue.5 , pp. 1005-1014
- Fetrow, J.S.¹ Siew, N.² Di Gennaro, J.A.³ Martinez-Yamout, M.⁴ Dyson, H.J.⁵ Skolnick, J.⁶

89
- 0036792550
- 10.1016/S1471-4892(02)00202-3 1:CAS:528:DC%2BD38Xnt1Cku7k%3D
- D Michalovich J Overington R Fagan 2002 Curr Opin Pharmacol 2 574 10.1016/S1471-4892(02)00202-3 1:CAS:528:DC%2BD38Xnt1Cku7k%3D
- (2002) Curr Opin Pharmacol , vol.2 , pp. 574
- Michalovich, D.¹ Overington, J.² Fagan, R.³

90
- 0034767547
- 10.1101/gr. 183801 1:CAS:528:DC%2BD3MXnvFCmtr0%3D
- H Hegyi M Gerstein 2001 Genome Res 11 1632 10.1101/gr. 183801 1:CAS:528:DC%2BD3MXnvFCmtr0%3D
- (2001) Genome Res , vol.11 , pp. 1632
- Hegyi, H.¹ Gerstein, M.²

91
- 0036384350
- 10.1016/S0022-2836(02)00649-6 1:CAS:528:DC%2BD38Xms1Wmurg%3D
- N Nagano C Orengo J Thornton 2002 J Mol Biol 321 741 10.1016/S0022- 2836(02)00649-6 1:CAS:528:DC%2BD38Xms1Wmurg%3D
- (2002) J Mol Biol , vol.321 , pp. 741
- Nagano, N.¹ Orengo, C.² Thornton, J.³

92
- 0842271085
- New Science Press Ltd Waltham
- Petsko G, Ringe D (2004) Protein structure and function. New Science Press Ltd, Waltham, MA, USA
- (2004) Protein Structure and Function
- Petsko, G.¹ Ringe, D.²

93
- 0035874115
- Automated multiple structure alignment and detection of a common substructural motif
- DOI 10.1002/prot.1034
- N Leibowitz Z Fligelman R Nussinov, et al. 2001 Proteins 43 235 10.1002/prot.1034 1:CAS:528:DC%2BD3MXjtFOlsrc%3D (Pubitemid 32367798)
- (2001) Proteins: Structure, Function and Genetics , vol.43 , Issue.3 , pp. 235-245
- Leibowitz, N.¹ Fligelman, Z.Y.² Nussinov, R.³ Wolfson, H.J.⁴

94
- 33746373135
- Automated functional classification of experimental and predicted protein structures
- DOI 10.1186/1471-2105-7-278
- K Wang R Samudrala 2006 BMC Bioinformatics 7 278 10.1186/1471-2105-7-278 (Pubitemid 44110470)
- (2006) BMC Bioinformatics , vol.7 , pp. 278
- Wang, K.¹ Samudrala, R.²

95
- 33749618171
- Interrogating the druggable genome with structural informatics
- DOI 10.1007/s11030-006-9035-3
- K Hambly J Danzer S Muskal, et al. 2006 Mol Divers 10 273 10.1007/s11030-006-9035-3 1:CAS:528:DC%2BD28Xht1GrtLrE (Pubitemid 44546682)
- (2006) Molecular Diversity , vol.10 , Issue.3 , pp. 273-281
- Hambly, K.¹ Danzer, J.² Muskal, S.³ Debe, D.A.⁴

96
- 72849126206
- WIPO patent
- Xie L (2004) WIPO patent http://www.wipo.int/pctdb/en/wo.jsp?WO= 2005045424
- (2004)
- Xie, L.¹

97
- 44449139387
- Detecting evolutionary relationships across existing fold space, using sequence order-independent profile-profile alignments
- DOI 10.1073/pnas.0704422105
- L Xie P Bourne 2008 Proc Natl Acad Sci USA 105 5441 10.1073/pnas. 0704422105 1:CAS:528:DC%2BD1cXkslSnsLY%3D (Pubitemid 351753882)
- (2008) Proceedings of the National Academy of Sciences of the United States of America , vol.105 , Issue.14 , pp. 5441-5446
- Xie, L.¹ Bourne, P.E.²

98
- 6944227836
- Automated prediction of protein function and detection of functional sites from structure
- DOI 10.1073/pnas.0404569101
- F Pazos MJ Sternberg 2004 Proc Natl Acad Sci USA 101 14754 10.1073/pnas.0404569101 1:CAS:528:DC%2BD2cXovVyjurg%3D (Pubitemid 39410747)
- (2004) Proceedings of the National Academy of Sciences of the United States of America , vol.101 , Issue.41 , pp. 14754-14759
- Pazos, F.¹ Sternberg, M.J.E.²

99
- 11844292002
- Inference of protein function from protein structure
- DOI 10.1016/j.str.2004.10.015, PII S0969212604003892
- D Pal D Eisenberg 2005 Structure (Camb) 13 121 10.1016/j.str.2004.10.015 1:CAS:528:DC%2BD2MXitVegtw%3D%3D (Pubitemid 40092480)
- (2005) Structure , vol.13 , Issue.1 , pp. 121-130
- Pal, D.¹ Eisenberg, D.²

100
- 0033613813
- Recognition of spatial motifs in protein structures
- DOI 10.1006/jmbi.1998.2393
- GJ Kleywegt 1999 J Mol Biol 285 4 1887 10.1006/jmbi.1998.2393 1:CAS:528:DyaK1MXhtV2ht78%3D (Pubitemid 29060478)
- (1999) Journal of Molecular Biology , vol.285 , Issue.4 , pp. 1887-1897
- Kleywegt, G.J.¹

* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.