Adaptation of a fast Fourier transform-based docking algorithm for protein design

Designing proteins with novel protein/protein binding properties can be achieved by combining the tools that have been developed independently for protein docking and protein design. We describe here the sequence-independent generation of protein dimer orientations by protein docking for use as scaffolds in protein sequence design algorithms. To dock monomers into sequence-independent dimer conformations, we use a reduced representation in which the side chains are approximated by spheres with atomic radii derived from known C2 symmetry-related homodimers. The interfaces of C2-related homodimers are usually more hydrophobic and protein core-like than the interfaces of heterodimers; we parameterize the radii for docking against this feature to capture and recreate the spatial characteristics of a hydrophobic interface. A fast Fourier transform-based geometric recognition algorithm is used for docking the reduced representation protein models. The resulting docking algorithm successfully predicted the wild-type homodimer orientations in 65 out of 121 dimer test cases. The success rate increases to approximately 70% for the subset of molecules with large surface area burial in the interface relative to their chain length. Forty-five of the predictions exhibited less than 1 A C(alpha) RMSD compared to the native X-ray structures. The reduced protein representation therefore appears to be a reasonable approximation and can be used to position protein backbones in plausible orientations for homodimer design.     

Application of algebraic method to the high overtones of C6H6 and C6D6

Both the spectra and infrared transition strengths of C₆H₆ and C₆D₆ for the C? H stretching overtones up to as high as v = 10 are described in high precision with few parameters (six for the spectra and four for the transition strengths) by the Iachello–Oss algebraic model. The Hamiltonian model is solved in the symmetry adapted bases, which are constructed by the symmetrized boson representation (SBR) technique. The results show that the combination of the algebraic method and SBR technique is a powerful method for describing vibrations of large molecules and high overtones. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Hermiticity of Hamiltonian Matrix using the Fourier Basis Sets in Bond-Bond-Angle and Radau Coordinates

In quantum calculations a transformed Hamiltonian is often used to avoid singularities in a certain basis set or to reduce computation time. We demonstrate for the Fourier basis set that the Hamiltonian can not be arbitrarily transformed. Otherwise, the Hamiltonian matrix becomes non-hermitian, which may lead to numerical problems. Methods for correctly constructing the Hamiltonian operators are discussed. Specific examples involving the Fourier basis functions for a triatomic molecular Hamiltonian (J=0) in bond-bond angle and Radau coordinates are presented. For illustration, absorption spectra are calculated for the OClO molecule using the time-dependent wavepacket method. Numerical results indicate that the non-hermiticity of the Hamiltonian matrix may also result from integration errors. The conclusion drawn here is generally useful for quantum calculation using basis expansion method using quadrature scheme.     

结构相角二阶代数式的应用：Ⅱ.正交空间群二阶式及其应用

以作者在前文中提出的单相角二阶代数式的推导方法为依据,在完成三斜、单斜空间群推导结果的基础上,进而又完成了正交晶系59个空间群二阶式的推导,从而提供了低级晶系(三斜、单斜和正交)全部74个空间群的简明、完备的二阶代数式运算用表。对三个晶体结构进行了相角估算,结果较好。文中提出了代数法应用的新特点,即“一种类型相角可用多种二阶式求得,多种类型相角也可用一种二阶式求算”。     

Bi-Sobolev mappings with differential matrices in Orlicz Zygmund classes

Bi-Sobolev mappings have been defined as those homeomorphisms such that f and f−1 belong to . We deduce regularity properties of the distortion of f from the regularity of the differential matrix Df−1 and conversely.     

四元数矩阵方程的复转化及保结构算法

给出四元数矩阵复表示运算定义及其相关性质,并运用复表示运算的保结构特性,讨论了四元数矩阵Moore-Penrose逆计算以及两类四元数矩阵方程AXB=C和AX-XB=C的数值求解方法.数值算例检验了所给算法的可行性.     

特征函数的性质

得到了特征函数、条件特征函数的一致可微性和条件特征函数的反演公式.