The Fourier-Green's function and the rapid evaluation of molecular potentials.
Two tasks must be accomplished when calculating the binding modalities and binding energies of two molecules in solution: the calculation of the interaction energy and the calculation of the effects of solvation. It is the competition between the energy of binding and the energy of remaining solvation which determines the binding properties. It is necessary to calculate (or at least approximate in some manner) the partition function in order to make a theoretical estimate of these effects. An efficient algorithm for performing the energy evaluations necessary for this calculation is presented in this paper. The fast Fourier transform (FFT) is used in combination with a polar factorization of the potentials to calculate the interaction energy at all relative translations between two molecules of fixed orientation. Thermodynamic quantities, including the partition function, internal and free energies can then be estimated from a set of these calculations covering the orientation space.
Harrison
R W
RW
Department of Pharmacology, Jefferson Cancer Institute, Thomas Jefferson University, Philadelphia, PA 19107.
Kourinov
I V
IV
Andrews
L C
LC
D000465:Algorithms; D000596:Amino Acids / Q000737:chemistry; D001483:Base Sequence; D055598:Chemical Phenomena; D002627:Chemistry, Physical; D003460:Crystallization; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D004563:Electrochemistry; D005583:Fourier Analysis; D008969:Molecular Sequence Data; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D013816:Thermodynamics; D014357:Trypsin / Q000737:chemistry / Q000378:metabolism
D000596:Amino Acids; D011506:Proteins; D004247:DNA; D014357:Trypsin