Order N algorithm for computation of electrostatic interactions in biomolecular systems

Proceedings of the National Academy of Sciences of the United States of America

Volumn 103, Issue 51, 2006, Pages 19314-19319

  Lu, Benzhuo ^a   Cheng, Xiaolin ^a   Huang, Jingfang ^b   McCammon, J Andrew ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b University of North Carolina at Chapel Hill   (United States)

Author keywords

Boundary integral equation; New version fast multipole method; Poisson Boltzmann electrostatics; Stress tensor and force

Indexed keywords

ACETYLCHOLINESTERASE; FASCICULIN; NICOTINIC RECEPTOR;

ALGORITHM; ARTICLE; BIOPHYSICS; COMPUTER MEMORY; ELECTRIC POTENTIAL; MATHEMATICAL MODEL; POISSON BOLTZMANN ELECTROSTATICS; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; SOLVATION;

ACETYLCHOLINESTERASE; ALGORITHMS; ELAPID VENOMS; ELECTROSTATICS; MODELS, MOLECULAR; MODELS, THEORETICAL; PROTEIN INTERACTION MAPPING; PROTEINS;

EID: 33845868249     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0605166103     Document Type: Article

References (25)

1. Appel AA (1985) SIAM J Sci Stat Comput 6:85-103.
2. Barnes J, Hut P (1986) Nature 324:446-449.
3. Kuo SS, Altman MD, Bardhan JP, Tidor B, White JK (2002) Proc IEEE/ACM Int Conf Comput Aided Des, 466-473.
4. Darden T, York D, Pedersen L (1993) J Chem Phys 98:10089-10092.
5. Greengard L, Rokhlin V (1987) J Comput Phys 73:325-348.
6. Greengard L, Rokhlin V (1997) Acta Numerica 6:229-269.
7. Rokhlin V (1983) Wave Motion 5:257-272.
8. Juffer AH, Botta EFF, Keulen BAM Van, Van der Ploeg A, Berendsen HJC (1991) J Comput Phys 97:144-170.
9. Liang J, Subramaniam S (1997) Biophys J 73:1830-1841.
10. Boschitsch AH, Fenley MO, Zhou HX (2002) J Phys Chem B 106:2741-2754.
11. Greengard L, Huang JF (2002) J Comput Phys 180:642-658.
12. Lu B, Zhang D, McCammon JA (2005) J Chem Phys 122:214102.
13. Lu B, Cheng X, Hou T, McCammon JA (2005) J Chem Phys 123:84904.
14. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA (2001) Proc Natl Acad Sci USA 98:10037-10041.
15. Radic Z, Kirchhoff PD, Quinn DM, McCammon JA, Taylor P (1997) J Biol Chem 272:23265-23277.
16. Elcock AH, Gabdoulline RR, Wade RC, McCammon JA (1999) J Mol Biol 291:149-162.
17. Nicholls A, Sharp KA, Honig B (1991) Proteins 11:281-296.
18. Madura JD, Briggs JM, Wade RC, Davis ME, Lut B, Ilin A, Antosiewicz J, Gilson MK, Bagheri B, Scott LR, McCammon JA (1995) Comput Phys Commun 91:57-95.
19. Rudolphi TJ (1991) Math Comput Modelling 15:269-278.
20. Ingber MS, Rudolphi TJ (1990) Appl Math Modelling 14:536-543.
21. Tanaka M, Sladek V, Sladek J (1994) AMSE Appl Mech Rev 47:457-499.
22. Zhou HX (1993) Biophys J 65:955-963.
23. da Cunha RD, Hopkins T (1995) Appl Numer 19:33-50.
24. Sanner MF, Olson AJ, Spehner JC (1996) Biopolymers 38:305-320.
25. Gilson MK, Davis ME, Luty BA, McCammon JA (1993) J Phys Chem B 97:3591-3600.