Improved modeling of side-chains in proteins with rotamer-based methods: A flexible rotamer model

Proteins: Structure, Function and Genetics

Volumn 37, Issue 4, 1999, Pages 530-543

  Mendes, Joaquim ^a   Baptista, António M ^a   Carrondo, Maria Arménia ^a   Soares, Cláudio M ^a,b  

^a UNIVERSIDADE NOVA DE LISBOA   (Portugal)

^b INSTITUTO DE TECNOLOGIA QUÍMICA E BIOLÓGICA   (Portugal)

Author keywords

Effective rotamer energy; Flexible rotamer model; Kirkwood superposition approximation; Protein design; Side chain modeling

Indexed keywords

AMINO ACID; PROTEIN;

ARTICLE; CRYSTALLOGRAPHY; MATHEMATICAL MODEL; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN CONFORMATION; PROTEIN TERTIARY STRUCTURE; THERMODYNAMICS;

AMINO ACIDS; ELECTROSTATICS; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; PROTEINS; THERMODYNAMICS;

EID: 0032732306     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19991201)37:4<530::AID-PROT4>3.0.CO;2-H     Document Type: Article

References (35)

1. Martin ACR, MacArthur MW, Thornton JM. Assessment of comparative modeling in CASP2. Proteins 1997;Suppl. 1:14-28.
2. Marchler-Bauer A, Bryant SH. Measures of threading specificity and accuracy. Proteins 1997;Suppl. 1:74-82.
3. Zemla A, Venclovas C, Reinhardt A, Fidelis K, Hubbard T. Numerical criteria for the evaluation of ab initio predictions of protein structure. Proteins 1997;Suppl. 1:140-150.
4. Kono H, Doi J. Energy minimization method using automata network for sequence and side-chain conformation prediction from given backbone geometry. Proteins 1994;19:244-255.
5. Dahiyat BI, Mayo SL. De novo protein design: fully automated sequence selection. Science 1997;278:82-87.
6. Kortemme T, Ramirez-Alvarado M, Serrano L. Design of a 20-amino acid, three-stranded beta-sheet protein. Science 1998;281: 253-256.
7. Kolinski A, Skolnick J. Monte Carlo simulations of protein folding. I. Lattice model and interaction scheme. Proteins 1994;18;338-352.
8. Vásquez M. Modeling side-chain conformation. Curr Opin Struct Biol 1996;6:217-221.
9. Janin J, Wodak S, Levitt M, Maigret B. Conformation of amino acid side-chains in proteins. J Mol Biol 1978:125:357-386.
10. Gelin BR, Karplus M. Side-chain torsional potentials: effect of dipeptide, protein and solvent environment. Biochemistry 1979;18: 1256-1268.
11. Schrauber H, Eisenhaber F, Argos P. Rotamers: to be or not to be? An analysis of amino acid side-chain conformations in globular proteins. J Mol Biol 1993;230:592-612.
12. Roitberg A, Elber R. Modeling side-chains in peptides and proteins: application of the locally enhanced sampling and simulated annealing methods to find minimum energy conformations. J Chem Phys 1991;95:9277-9287.
13. Lee C, Subbiah S. Prediction of protein side-chain conformation by packing optimization. J Mol Biol 1991;217:373-388.
14. Lee C. Predicting protein mutant energetics by self-consistent ensemble optimization. J Mol Biol 1994;236:918-939.
15. McCammon JA, Harvey SC. Dynamics of proteins and nucleic acids. Cambridge: Cambridge University Press; 1987.
16. Brook CLI, Karplus M, Pettit BM. Proteins: a theoretical perspective of dynamics, structure and thermodynamics. New York: John Wiley & Sons; 1987.
17. Levitt M. Accurate modelling of protein conformation by automatic segment matching. J Mol Biol 1992;226:507-533.
18. Holm L, Sander C. Fast and simple Monte Carlo algorithm for side-chain optimization in proteins: application to model building by homology. Proteins 1992;14:213-223.
19. Koehl P, Delarue M. Application of a self-consistent mean field theory to predict protein side-chains conformation and estimate their conformational entropy. J Mol Biol 1994;239:249-275.
20. Vásquez M. An evaluation of discrete and continuum search techniques for conformational analysis of side-chains in proteins. Biopolymers 1995;36:53-70.
21. Lazar GA, Desjarlais JR, Handel TM. De novo design of the hydrophobic core of ubiquitin. Prot Sci 1997;6:1167-1178.
22. Desmet J, de Maeyer M, Hazes B, Lasters I. The dead-end elimination theorem and its use in protein side-chain positioning. Nature 1992;356:539-542.
23. Mendes J, Soares CM, Carrondo MA. Improvement of side-chain modelling in proteins with the self-consistent mean field theory method based on an analysis of the factors influencing prediction. Biopolymers 1999;50:111-131.
24. Bower MJ, Cohen FE, Dunbrack RLJ. Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool. J Mol Biol 1997;267:1268-1282.
25. Hill TL. Statistical mechanics. New York: McGraw-Hill; 1956.
26. Tufféry P, Etchebest C, Hazout S. Prediction of protein side-chain conformations: a study on the influence of backbone accuracy on conformation stability in the rotamer space. Protein Eng 1997;10: 361-372.
27. van Gunsteren WF, Berendsen HJC. Groningen molecular simulation (GROMOS) library manual. Groningen, The Netherlands: Biomos B. V., Biomolecular Software; 1987.
28. Tufféry P, Etchebest C, Hazout S. http://condor.urbb.jussieu.fr/ rotamer-stdv.html; 1997.
29. Solmajer T, Mehler EL. Electrostatic screening in molecular dynamics simulations. Protein Eng 1991;4:911-917.
30. Solmajer T, Mehler EL. Modeling solvent effects on molecular dynamics simulations of proteins. Int J Quant Chem 1992;44:291-299.
31. Smith LJ, Mark AE, Dobson CM, van Gunsteren WF. Comparison of MD simulations and NMR experiments for hen lysozyme: analysis of local fluctuations, cooperative motions and global changes. Biochemistry 1995;34:10918-10931.
32. McRee DE. A visual protein crystallographic software system for X11/XView. J Mol Graph 1992;10:44-46.
33. Merritt EA, Bacon DJ. Raster3D: photorealistic molecular graphics. Meth Enzymol. 1997;277:505-524.
34. Burke DF, Deane CM, Nagarajaram HA, et al. An iterative structure-assisted approach to sequence alignment and comparative modelling. Proteins 1999; Suppl 3:55-60.
35. 3 terminal oxidase of the thermohalophilic bacterium Rhodothermus marinus: characterisation of a HiPIP:oxygen oxidoreductase lacking the key glutamate of the D-channel. BBA 1999;1413:1-3.