A novel exhaustive search algorithm for predicting the conformation of polypeptide segments in proteins

Proteins: Structure, Function and Genetics

Volumn 40, Issue 1, 2000, Pages 135-144

  Deane, Charlotte M ^a   Blundell, Tom L ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

Hornology modelling; Polypeptide conformations; Protein folding; Protein loops; Structure prediction

Indexed keywords

POLYPEPTIDE; PROTEIN;

ALGORITHM; ARTICLE; CALCULATION; DATA BASE; PREDICTION; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY;

ALGORITHMS; DATABASES, FACTUAL; MODELS, MOLECULAR; PEPTIDE FRAGMENTS; PEPTIDES; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEINS; SOFTWARE;

EID: 0034237227     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(20000701)40:1<135::AID-PROT150>3.0.CO;2-1     Document Type: Article

References (58)

1. Johnson MS, Srinivasan N, Sowdhamini R, Blundell TL. Knowledge-based protein modeling. Crit Rev Biochem Mol Biol 1994;29: 1-68.
2. Moult J, Hubbard T, Bryant SH, Fidelis K, Pedersen JT. Critical assessment of methods of protein structure prediction (CASP): round II. Proteins 1997;Suppl: 2-6.
3. Blundell T, et al. 18th Sir Hans Krebs lecture. Knowledge-based protein modelling and design. Eur J Biochem 1988;172:513-20.
4. Chothia C, Lesk AM. The relation between the divergence of sequence and structure in proteins. EMBO 1986;5:823-826.
5. Sali A, Blundell TL. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol 1993;234:779-815.
6. Greer J. Model for haptoglobin heavy chain based upon structural homology. Proc Natl Acad Sci USA 1980;77:3393-3397.
7. Sibanda BL, Thornton JM. Beta-hairpin families in globular proteins. Nature 1985;316: 170-174.
8. Sibanda BL, Blundell TL, Thornton JM. Conformation of beta-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering. J Mol Biol 1989;206:759-777.
9. Jones TA, Thirup S. Using known substructures in protein model building and crystallography. EMBO 1986;5:819-822.
10. Abola EE, Bernstein FC, Bryant SH, Koetzle TF, Weng J. Data Commission of the International Union of Crystallography, 1987. p 107-132
11. Abola EE, Sussman JL, Prilusky J, Manning NO. Protein data bank archives of three-dimensional macromolecular structures. Methods Enzymol 1997;277:556-571.
12. Sutcliffe MJ, Haneef I, Carney D, Blundell TL. Knowledge based modelling of homologous proteins, Part I: Three-dimensional frameworks derived from the simultaneous superposition of multiple structures. Protein Eng 1987;1:377-384.
13. Fidelis K, Stern PS, Bacon D, Moult J. Comparison of systematic search and database methods for constructing segments of protein structure. Protein Eng 1994;7:953-960.
14. van Vlijmen HWT, Karplus M. PDB-based protein loop prediction: parameters for selection and methods for optimization. J Mol Biol 1997;267:975-1001.
15. Brooks BR, et al. A program for macromolecular energy minimisation and dynamics calculations. J Comp Chem 1983;4:187-217.
16. Sudarsanam S, DuBose RF, March CJ, Srinivasan S. Modeling protein loops using a phi i+1, psi i dimer database. Protein Sci 1995;4:1412-1420.
17. Tramontano A, Lesk AM. Common features of the conformations of antigen-binding loops in immunoglobulins and application to modeling loop conformations. Proteins 1992;13: 231-245.
18. Chothia C, Lesk AM. Canonical structures for the hypervariable regions of immunoglobulins. J Mol Biol 1987;196:901-917.
19. Topham CM, et al. Fragment ranking in modelling of protein structure. Conformationally constrained environmental amino acid substitution tables. J Mol Biol 1993;229:194-220.
20. Kwasigroch J-M, Chomilier J, Mornon J-P. A global taxonomy of loops in globular proteins. J Mol Biol 1996;259:855-872.
21. Sun Z, Jiang B. Patterns and conformations of commonly occurring supersecondary structures (basic motifs) in protein data bank. J Protein Chem 1996;15:675-690.
22. Baldomero O, Bates PA, Querol E, Aviles FX, Sternberg MJE. An automated classification of the structure of protein loops. J Mol Biol 1997;266:814-830.
23. Geetha V, Munson PJ. Linkers of secondary structures in proteins. Protein Sci 1997;6: 2538-2547.
24. Li W, Liu Z, Lai L. Protein loops on structurally similar scaffolds: database and conformational analysis. Biopolymers 1999;489:481-495.
25. Martin ACR, Thornton JM. Structural families in loops of monologous proteins: automatic classification, modeling and application to antibodies. J Mol Biol 1996;263:800-815.
26. Morea V, Tramontano A, Rustici M, Chothia C, Lesk AM. Conformations of the third hypervariable region in the VH domain of immunoglobulins. J Mol Biol 1998;275:269-294.
27. Wintjens RT, Rooman MJ, Wodak S. Automatic classification and analysis of aa-turn motifs in proteins. J Mol Biol 1996;255:235-253.
28. Rufino SD, Donate LE, Canard LHJ, Blundell TL. Predicting the conformational class of short and medium size loops connecting regular secondary structures: application to comparative modelling. J Mol Biol 1997;267:352-367.
29. Donate LE, Rufino SD, Canard LHJ, Blundell TL. Conformational analysis and clustering of short and medium size loops connecting regular secondary structures: a database for modeling and prediction. Protein Sci 1996;5:2600-2616.
30. Go N, Scheraga HA. Ring closure and local conformational deformations of chain molecules. Macromolecules 1970;3:178-187.
31. Moult J, James MNG. An algorithm for determining the conformation of polypeptide segments in proteins by systematic search. Proteins 1986;1:146-163.
32. Pedersen J, Moult J. Ab initio structure prediction for small polypeptides and protein fragments using genetic algorithms. Proteins 1995;23:454-460.
33. Collura V, Higo J, Garnier J. Modeling of protein loops by simulated annealing. Protein Sci 1993;2:1502-1510.
34. Zhang H, Lai L, Wang L, Han Y, Tang Y. A fast and efficient program for modeling protein loops. Biopolymers 1997;41:61-72.
35. Rapp CS, Friesner RA. Prediction of loop geometries using a generalized Born model of solvation effects. Proteins 1999;35:173-183.
36. Zheng Q, Kyle DJ. Accuracy and reliability of the scaling-relaxation method for loop closure: an evaluation based on extensive and multiple copy conformational samplings. Proteins 1996; 24:209-217.
37. Zheng Q, Rosenfeld R, Vajda S, DeLisi C. Determining protein loop conformation using scaling-relaxation techniques. Protein Sci 1993;2:1242-1248.
38. Bruccoleri RE, Karplus M. Prediction of the folding of short polypeptide segments by uniform conformational sampling. Bioplymers 1987;26:137-168.
39. Hobohm U, Scharf M, Schneider R, Sander C. Selection of a representative set of structures from the Brookhaven Protein Data Bank. Protein Sci 1992;1:409-417.
40. Hobohm U, Sander C. Enlarged representative set of protein structures. Protein Sci 1994;3:552.
41. Morris AL, Macarthur MW, Hutchinson EG, Thornton JM. Stereochemical quality of protein-structure coordinates. Proteins 1992; 12:345-364.
42. Ramachandran GN, Sasisekharan V. Conformation of polypeptides and proteins. Adv Protein Chem 1968;28:283-437.
43. Kabsch W, Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983;22:2577-2637.
44. Efimov AV. Standard confomations of polypeptide chans in irregular regions of proteins. Mol Biol (MOSCOW) 1980;20:208-216.
45. Swindells MB, MacArthur MW, Thornton JM. Intrinsic phi,psi propensities of amino acids, derived from the coil regions of known structures. Nature Struct Biol 1995;2:596-603.
46. Richardson JS. The anatomy and taxonomy of protein structure. Adv Protein Chem 1981;34:167-339.
47. Kearsley SK. Structural comparisons using restrained inhomogeneous transformations. Acta Crystallogr 1989;A45:628-635.
48. Kearsley SK. On the orthogonal transformation used for structural comparisons. Acta Crystallogr 1989;A45:208-210.
49. Samudrala R, Moult J. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction. J Mol Biol 1998;275:895-916.
50. Lee B, Richards FM. The interpretation of protein structures: estimation of static accessibility. J Mol Biol 1971;55:379-400.
51. Martin AC, Cheetham JC, Rees AR. Modeling antibody hypervariable loops: a combined algorithm. Proc Natl Acad Sci USA 1989;86:9268-9272.
52. Wojcik J, Mornon JP, Chomilier J. New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification. J Mol Biol 1999;289:1469-1490.
53. Sanchez R, Sali A. Advances in comparative protein-structure modelling. Curr Opin Struct Biol 1997;7:206-214.
54. Bower MJ, Cohen FE, Dunbrack RL, Jr. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool. J Mol Biol 1997;267: 1268-1282.
55. Oliva B, Bates PA, Querol E, Aviles FX, Sternberg MJ. An automated classification of the structure of protein loops. J Mol Biol 1997;266:814-830.
56. Martin AC, Toda K, Stirk HJ, Thornton JM. Long loops in proteins. Protein Eng 1995;8: 1093-1101.
57. Kraulis PJ. MOLSCRIPT: a program to produce both detailed and schematic plots of protein structure. J Applied Crystallogr 1991;24: 946-950.
58. Merritt EA, Murphy MEP. Raster 3D Version 2.0- A program for photorealistic molecular graphics. Acta Crystallogr 1994;D50:869-873.