next up previous
Next: About this document ... Up: Comparative protein structure modeling Previous: Example 3: Modeling the

Bibliography

1
W. J. Browne, A. C. T. North, D. C. Phillips, K. Brew, T. C. Vanaman, and R. C. Hill, J. Mol. Biol., 42, 65-86, 1969.

2
T. L. Blundell, M. J. E. Sternberg, B. L. Sibanda, and J. M. Thornton, Nature, 326, 347-352, 1987.

3
J. Bajorath, R. Stenkamp, and A. Aruffo, Protein Sci., 2, 1798-1810, 1994.

4
M. S. Johnson, N. Srinivasan, R. Sowdhamini, and T. L. Blundell, CRC Crit. Rev. Biochem. Mol. Biol., 29, 1-68, 1994.

5
R. Sánchez and A. Sali, Curr. Opin. Struct. Biol., 7, 206-214, 1997.

6
M. A. Martí-Renom, A. Stuart, A. Fiser, R. Sánchez, F. Melo, and A. Sali, Ann. Rev. Biophys. Biomolec. Struct., 29, 291-325, 2000.

7
A. Fiser, R. Sánchez, F. Melo, and A. Sali.
Comparative protein structure modeling.
In M. Watanabe, B. Roux, A. MacKerell, and O. Becker, editors, Computational Biochemistry and Biophysics, in press, pages 275-312. Marcel Dekker, 2000.

8
D. Baker, Nature, 405, 39-42, 2000.

9
A. M. Lesk and C. Chothia, J. Mol. Biol., 136, 225-270, 1980.

10
R. Sánchez, U. Pieper, F. Melo, N. Eswar, M.A. Martí-Renom, M.S. Madhusudhan, N. Mirkovic, and A. Sali, Nat. Struct. Biol., 7, 986-990, 2000.

11
A. J. Jennings and M. J. Sternberg, Prot. Eng., 14, 227-231, 2001.

12
D. A. Benson, M. S. Boguski, D. J. Lipman, J. Ostell, B. F. F. Ouellette, B. A. Rapp, and D. L. Wheeler, Nucl. Acids Res., 27, 12-17, 1999.

13
A. Bairoch and R. Apweiler, Nucl. Acids Res., 27, 49-54, 1999.

14
H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne, Nucleic Acids Res., 28, 235-242, 2000.

15
C. Chothia, Nature, 360, 543-544, 1992.

16
T. J. P. Hubbard, B. Ailey, S. E. Brenner, A. G. Murzin, and C. Chothia, Nucl. Acids Res., 27, 254-256, 1999.

17
L. Holm and C. Sander, Nucl. Acids Res., 27, 244-247, 1999.

18
J.E. Bray, A.E. Todd, F.M. Pearl, J.M. Thornton, and C.A. Orengo, Protein Eng, 13, 153-65, 2000.

19
L. Holm and C. Sander, Science, 273, 595-602, 1996.

20
S. K. Burley, S. C. Almo, J. B. Bonanno, , M. Capel, M. R. Chance, T. Gaasterland, D. Lin, A. Sali, F. W. Studier, and S. Swaminathan, Nat. Genet., 23, 151-157, 1999.

21
Nat. Str. Biol.
Suppl., 2000.

22
A. Sali and T. L. Blundell, J. Mol. Biol., 234, 779-815, 1993.

23
A. Sali and J.P Overington, Protein Sci., 3, 1582-1596, 1994.

24
A. Fiser, R. K. G. Do, and A. Sali, Protein Science, 9, 1753-1773, 2000.

25
S. F. Altschul, M. S. Boguski, W. Gish, and J. C. Wootton, Nature Genetics, 6, 119-129, 1994.

26
W. R. Pearson, Methods Enzymol., 266, 227-258, 1996.

27
G.D. Schuler, Methods Biochem. Anal., 39, 145-171, 1998.

28
G. J. Barton.
Protein sequence alignment and database scanning.
In M. J. E. Sternberg, editor, Protein Structure Prediction: A Practical Approach. IRL Press at Oxford University Press, 1998.

29
M. Levitt and M. Gerstein, Proc. Natl. Acad. Sci. USA, 95, 5913-5920, 1998.

30
M. Gribskov, Meth. Mol. Biol., 25, 247-266, 1994.

31
A. Krogh, M. Brown, I. S. Mian, K. Sjolander, and D. Haussler, J. Mol. Biol., 235, 1501-1531, 1994.

32
S. R. Eddy, Curr. Opin. Struct. Biol., 6, 361-365, 1996.

33
K. Karplus, C. Barrett, and R. Hughey, Bioinformatics, 14, 846-856, 1998.

34
J. Park, K. Karplus, C. Barrett, R. Hughey, D. Haussler, T. Hubbard, and Chothia C., J. Mol. Biol., 284, 201-210, 1998.

35
J. U. Bowie, R. Lüthy, and D. Eisenberg, Science, 253, 164-170, 1991.

36
D. T. Jones, W. R. Taylor, and J. M. Thornton, Nature, 358, 86-89, 1992.

37
A. Godzik, A. Kolinski, and J. Skolnick, J. Mol. Biol., 227, 227-238, 1992.

38
M. J. Sippl and H. Flöckner, Structure, 4, 15-19, 1996.

39
A. E. Torda, Curr. Opin. Struct. Biol., 7, 200-205, 1997.

40
H. Lu and J. Skolnick, Proteins, 44, 223-232, 2001.

41
R. L. Dunbrack Jr., D. L. Gerloff, M. Bower, X. Chen, O. Lichtarge, and F. E. Cohen, Folding & Design, 2, R27-R42, 1997.

42
J. Felsenstein, Evolution, 39, 783-791, 1985.

43
A. Sali, L. Potterton, F. Yuan, H. van Vlijmen, and M. Karplus, Proteins, 23, 318-326, 1995.

44
R. Sánchez and A. Sali, Proteins, Suppl. 1, 50-58, 1997.

45
M. J. Sippl, Proteins, 17, 355-362, 1993.

46
G. Wu, H. G. Morrison, A. Fiser, A. G. McArthur, A. Sali, M. L. Sogin, and M. Müller, Mol. Biol. Evol., 17, 1156-1163, 2000.

47
R. Sánchez and A. Sali, Proc. Natl. Acad. Sci. USA, 95, 13597-13602, 1998.

48
TG. Dewey, J Comput Biol, 8, 177-90, 2001.

49
J. Shi, T. L. Blundell, and Mizuguchi K., J. Mol. Biol., 310, 243-257, 2001.

50
J.D. Blake and F.E. Cohen, J. Mol. Biol., 307, 721-35, 2001.

51
L. Jaroszewski, L. Rychlewski, and A. Godzik, Protein Sci, 9, 1487-96, 2000.

52
J.M. Sauder, J.W. Arthur, and R.L. Dunbrack, Proteins, 40, 6-22, 2000.

53
J. Greer, J. Mol. Biol., 153, 1027-1042, 1981.

54
T. L. Blundell, B. L. Sibanda, M. J. E. Sternberg, and J. M. Thornton, Nature, 326, 347-352, 1987.

55
T. H. Jones and S. Thirup, EMBO J., 5, 819-822, 1986.

56
R. Unger, D. Harel, S. Wherland, and J. L. Sussman, Proteins, 5, 355-373, 1989.

57
M. Claessens, E. V. Cutsem, I. Lasters, and S. Wodak, Protein Eng., 4, 335-345, 1989.

58
M. Levitt, J. Mol. Biol., 226, 507-533, 1992.

59
T. F. Havel and M. E. Snow, J. Mol. Biol., 217, 1-7, 1991.

60
S. Srinivasan, C. J. March, and S. Sudarsanam, Protein Sci., 2, 227-289, 1993.

61
S. M. Brocklehurst and R. N. Perham, Protein Sci., 2, 626-639, 1993.

62
A. Aszódi and W. R. Taylor, Folding and Design, 1, 325-334, 1996.

63
A. D. MacKerell, Jr., D. Bashford, M. Bellott, R.L. Dunbrack Jr., J.D. Evanseck, M.J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F.T.K. Lau, C. Mattos, S. Michnick, T. Ngo, D.T. Nguyen, B. Prodhom, W.E. Reiher, III, M. Roux, B.and Schlenkrich, J.C. Smith, J. Stote, R.and Straub, M. Watanabe, J. Wiorkiewicz-Kuczera, D. Yin, and M. Karplus, J. Phys. Chem. B, 102, 3586-3616, 1998.

64
A. Kolinski, M. R. Betancourt, D. Kihara, P. Rotkiewicz, and J. Skolnick, Proteins, 44, 133-149, 2001.

65
K. Fidelis, P. S. Stern, D. Bacon, and J. Moult, Protein Eng., 7, 953-960, 1994.

66
M. J. Sippl, J. Mol. Biol., 213, 859-883, 1990.

67
B. Cheng, A. Nayeem, and H. A. Scheraga, J. Comp. Chem., 17, 1453-1480, 1996.

68
R. Lüthy, J. U. Bowie, and D. Eisenberg, Nature, 356, 83-85, 1992.

69
R. A. Laskowski, M. W. McArthur, D. S. Moss, and J. M. Thornton, J. Appl. Cryst., 26, 283-291, 1993.

70
R.W.W Hooft, G. Vriend, C. Sander, and E.E. Abola, Nature, 381, 272, 1996.

71
B. Guenther, R. Onrust, A. Sali, M. O'Donnell, and J. Kuriyan, Cell, 91, 335-345, 1997.

72
A. Sali, R. Sánchez, A. Y. Badretdinov, A. Fiser, F. Melo, J. P. Overington, E. Feyfant, and M. A. Martí-Renom.
MODELLER, A Protein Structure Modeling Program, Release 6.
URL http://guitar.rockefeller.edu/, 2000.

73
G. Wu, A. Fiser, B. ter Kuile, A. Sali, and M. Müller, Proc. Natl. Acad. Sci. USA, 96, 6285-6290, 1999.

74
W.C. Barker, J.S. Garavelli, D.H. Haft, L.T. Hunt, C.R. Marzec, B.C. Orcutt, G.Y. Srinivasarao, L.S.L. Yeh, R.S. Ledley, H.W. Mewes, F. Pfeiffer, and A. Tsugita, Nucl. Acids Res., 26, 27-32, 1998.

75
S. B. Needleman and C. D. Wunsch, J. Mol. Biol., 48, 443-453, 1970.

76
L. G. Barrientos, R. Campos-Olivas, J. M. Louis, A. Fiser, A. Sali, and A. M. Gronenborn, J. Biomol. NMR, 19, 289-290, 2001.

77
R. Sánchez and A. Sali.
Comparative protein structure modeling: Introduction and practical examples with MODELLER.
In D. M. Webster, editor, Protein Structure Prediction: Methods and Protocols, pages 97-129. Humana Press, 2000.


 
Table 1: Common uses of comparative protein structure models. A list of our papers using MODELLER to address practical problems in collaboration with experimentalists can be obtained at URL http://guitar.rockefeller.edu/publications/ref/ref.html.
Designing (site-directed) mutants to test hypotheses about function
Identifying active and binding sites
Searching for ligands of a given binding site
Designing and improving ligands of a given binding site
Modeling substrate specificity
Predicting antigenic epitopes
Protein-protein docking simulations
Inferring function from calculated electrostatic potential around the protein
Molecular replacement in X-ray structure refinement
Refining models against NMR dipolar coupling data
Testing a given sequence - structure alignment
Rationalizing known experimental observations
Planning new experiments
 


 
Table 2: Web sites useful for comparative modeling.
Databases
NCBI www.ncbi.nlm.nih.gov/
PDB www.rcsb.org/
MSD www.rcsb.org/databases.html
CATH www.biochem.ucl.ac.uk/bsm/cath/
TrEMBL srs.ebi.ac.uk/
SCOP scop.mrc-lmb.cam.ac.uk/scop/
PRESAGE presage.stanford.edu
MODBASE guitar.rockefeller.edu/modbase/
GeneCensus bioinfo.mbb.yale.edu/genome
GeneBank www.ncbi.nlm.nih.gov/Genbank/GenbankSearch.html
PSI www.structuralgenomics.org
Template search, fold assignment
PDB-Blast bioinformatics.burnham-inst.orgpdb_blast
BLAST www.ncbi.nlm.nih.gov/BLAST/
FastA www.dna.affrc.go.jp/htdocs/Blast/fasta.html
DALI www2.ebi.ac.uk/dali/
PhD, TOPITS www.embl-heidelberg.de/predictprotein/predictprotein.html
THREADER insulin.brunel.ac.uk/
123D genomic.sanger.ac.uk/123D/run123D.html
UCLA-DOE www.doe-mbi.ucla.edu/people/frsvr/frsvr.html
PROFIT lore.came.sbg.ac.at/
MATCHMAKER www.tripos.com/software/mm.html
3D-PSSM www.bmm.icnet.uk/ 3dpssm/html/ffrecog.html
BIOINGBGU www.cs.bgu.ac.il/ bioinbgu/
FUGUE www-cryst.bioc.cam.ac.uk/ fugue
LOOPP ser-loopp.tc.cornell.edu/loopp.html
FASS bioinformatics.burnham-inst.org/FFAS/index.html
SAM-T99/T98 www.cse.ucsc.edu/research/compbio/sam.html


Comparative modeling
3D-JIGSAW www.bmm.icnet.uk/servers/3djigsaw/
CPH-Models www.cbs.dtu.dk/services/CPHmodels/
COMPOSER www-cryst.bioc.cam.ac.uk/
FAMS physchem.pharm.kitasato-u.ac.jp/FAMS/fams.html
MODELLER guitar.rockefeller.edu/modeller/modeller.html
PrISM honiglab.cpmc.columbia.edu/
SWISS-MODEL www.expasy.ch/swissmod/SWISS-MODEL.html
SDSC1 cl.sdsc.edu/hm.html
WHAT IF www.cmbi.kun.nl/bioinf/predictprotein/
ICM www.molsoft.com/
SCWRL www.fccc.edu/research/labs/dunbrack/scwrl/
InsightII www.accelrys.com
SYBYL www.tripos.com
Model evaluation
PROCHECK www.biochem.ucl.ac.uk/~roman/procheck/procheck.html
WHATCHECK www.cmbi.kun.nl/swift/whatcheck/
ProsaII www.came.sbg.ac.at
BIOTECH biotech.embl-ebi.ac.uk:8400/
VERIFY3D www.doe-mbi.ucla.edu/Services/Verify_3D/
ERRAT www.doe-mbi.ucla.edu/Services/Errat.html
ANOLEA guitar.rockefeller.edu/ fmelo/anolea/anolea.html
AQUA urchin.bmrb.wisc.edu/ jurgen/Aqua/server/
SQUID www.yorvic.york.ac.uk/~oldfield/squid
PROVE www.ucmb.ulb.ac.be/UCMB/PROVE/
 Table 2 continued.


  
Figure 1: Steps in comparative protein structure modeling. See text for description of each step.


  
Figure 2: Comparative model building by program MODELLER. First, homology-derived spatial restraints on many atom-atom distances and dihedral angles are extracted from the template structure(s). The alignment is used to determine equivalent residues between the target and the template. The homology-derived and stereochemical restraints are combined into an objective function. Finally, the model of the target is optimized until a model that best satisfies the spatial restraints is obtained. This procedure is similar to the one used in structure determination by NMR spectroscopy.


  
Figure 3: Average model accuracy as a function of sequence identity. As the sequence identity between the target sequence and the template structure decreases, the average structural similarity between the template and the target also decreases (dotted line, open circles). (continued on the next page)

(Figure 3: continued from the previous page)

Structural overlap is defined as the fraction of equivalent $\mbox{C}_\alpha$ atoms. For the comparison of the model with the actual structure (filled circles), two $\mbox{C}_\alpha$ atoms were considered equivalent if they belonged to the same residue and were within 3.5Å of each other after least-squares superposition of all $\mbox{C}_\alpha$ atoms by the ALIGN3D command in MODELLER. For comparison of the template structure with the actual target structure (open circles), two $\mbox{C}_\alpha$ atoms were considered equivalent if they were within 3.5Å of each other after alignment and rigid-body superposition. At high sequence identities, the models are close to the templates and therefore also close to the experimental target structure (solid line, filled circles). At low sequence identities, errors in the target-template alignment become more frequent and the structural similarity of the model with the experimental target structure falls below the target-template structural similarity. The difference between the model and the actual target structure is a combination of the target-template differences (light area) and the alignment errors (dark area). The figure was constructed by calculating 3993 comparative models based on single templates of varying similarity to the targets. All targets had known (experimentally determined) structures and therefore the comparison of the models and templates with the experimental structures was possible [47]. The top part of the figure shows three models (solid line) compared with their corresponding experimental structures (dotted line). The models were calculated with MODELLER in a completely automated fashion before the experimental structures were available [43]. The arrows indicate the target-template similarity in each case.


  
Figure 4: PROSAII [45] energy profile for the raw TvLDH model (dashed line), refined TvLDH model (thin line), and the 4mdhA template structure (heavy line) (Examples 1 and 2). The extended peak above the zero line in the region 90-100 and 220-250 of the raw model highlights a possible error in the raw model, significantly improved in the refined model.


  
Figure 5: Superposition of models for six linker segments with lengths from 6 to 9 residues. Towards the C-terminus of the loop, a larger structural variation can be observed, but the dominant conformation is well defined by a cluster of four loops.


next up previous
Next: About this document ... Up: Comparative protein structure modeling Previous: Example 3: Modeling the
Andras Fiser
2001-08-09