Fast accurate evaluation of protein solvent exposure

Proteins: Structure, Function and Genetics

Volumn 57, Issue 3, 2004, Pages 565-576

  Zhang, Naigong ^a   Zeng, Chen ^a   Wingreen, Ned S ^b  

^a GEORGE WASHINGTON UNIVERSITY   (United States)

^b NEC LABORATORIES AMERICA   (United States)

Author keywords

Dead end elimination; Generic side chains; Pair wise surface area; Protein design; Solvent accessible surface area

Indexed keywords

PROTEIN; SOLVENT;

ACCURACY; ANALYTIC METHOD; ARTICLE; EVALUATION; MATHEMATICAL MODEL; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN STRUCTURE; SOLVATION; SOLVENT EFFECT;

COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; DRUG DESIGN; PROTEIN FOLDING; PROTEINS; RESEARCH DESIGN; SENSITIVITY AND SPECIFICITY; SOLVENTS; SURFACE PROPERTIES; THERMODYNAMICS; TIME FACTORS;

BIKINIA LE-TESTUI; JONES;

EID: 6344260488     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/prot.20191     Document Type: Article

References (18)

1. Street AG, Mayo SL. Pairwise calculation of protein solvent accessible surface areas. Fold Des 1998;3:253-258.
2. Dill KA. Dominant forces in protein folding. Biochemistry 1990;29: 7133-7155.
3. Gordon DB, Marshall SA, Mayo SL. Energy function for protein design. Curr Opin Struct Biol 1999;9:509-513.
4. Desmet J, Maeyer MD, Hazes B, Lasters I. The dead-end elimination theorem and its use in protein side-chain positioning. Nature 1992;356:539-542.
5. Moret BME, Shapiro HD. Algorithms from P to NP. Redwood City: Benjamin 1991. Nemhauser GL, Rinnooykan AHG, Todd MJ, eds. Optimization. Amsterdam: North-Holland 1989.
6. Bolon DN, Mayo S. Enzyme-like proteins by computational design. Proc Natl Acad Sci 2001;98:14272-14279.
7. Looger LL, Dwyer MA, Smith JJ, Hellinga HW. Computational design of receptor and sensor proteins with novel functions. Nature 2003;423:185-190.
8. Wodak SJ, Janin J. Location of structural domains in proteins. Biochemistry 1981;20:6544-6552.
9. Wernisch L, Hunting M, Wodak SJ. Indentification of structural domains in proteins by a graph heuristic. Proteins 1999;35:338-352.
10. Wodak SJ, Janin J. Analytical approximation to the accessible surface area of proteins. Proc Natl Acad Sci 1980;77:1736-1740.
11. Marshall SA, Mayo SL. Achieving stability and conformational specificity in designed proteins via binary patterning. J Mol Biol 2001;305:619-631.
12. Orengo CA, Michie AD, Jones S, Jones DT, Swindells MB, Thornton JM. CATH - A hierarchic classification of protein domain structures. Structure 1997;5:1093-1108.
13. Kurochkina N, Lee B. Hydrophobic potential by pairwise surface area sum. Prot Eng 1995;8:437-442.
14. Shrake A, Rupley JA. Environment and exposure to solvent of protein atoms. Lysozyme and insulin. J Mol Biol 1973;79:351-371.
15. LeGrand SM, Merz KM. A rapid analytic approximation to molecular surface area via the use of boolean logic and look-up tables. J Comp Chem 1993;14:349-352.
16. Wesson L, Eisenberg D. Atomic solvation parameters applied to molecular dynamics of proteins in solution. Protein Sci 1992;1:227-235.
17. Dahiyat, BI, Mayo SL. Protein design automation. Protein Sci 1996;5:895-903.
18. Gordon DB, Hom GK, Mayo SL, Pierce NA. Exact rotamer optimization for protein design. J Comput Chem 2003;24:232-243.