Ye Mei

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In this paper, we proposed a new affine invariant region-based shape descriptor, the ICA Zernike Moment Shape Descriptor (ICAZMSD). Independent Component Analysis (ICA) is first used to turn the original shape into a canonical form, in which the effects of scaling and skewing are eliminated. Next, the properties of the Zernike transform is used to further(More)
Recently, Baugh et al. discovered that a distal point mutation (F130L) in streptavidin causes no distinct variation to the structure of the binding pocket but a 1000-fold reduction in biotin binding affinity. In this work, we carry out molecular dynamics simulations and apply an end-state free energy method to calculate the binding free energies of biotin(More)
Multiple single-trajectory molecular dynamics (MD) simulation at room temperature (300 K) in explicit water was carried out to study the folding dynamics of an α-helix (PDB 2I9M ) using a polarized charge scheme that includes electronic polarization of backbone hydrogen bonds. Starting from an extended conformation, the 17-residue peptide was successfully(More)
The reliability of the linear interaction energy (LIE) depends on the atomic charge model used to delineate the Coulomb interaction between the ligand and its environment. In this work, the polarized protein-specific charge (PPC) implementing a recently proposed fitting scheme has been examined in the LIE calculations of the binding affinities for avidin(More)
Inspired by the idea of charge decomposition in calculation of the dipole preserving and polarization consistent charges (Zhang et al., J. Comput. Chem. 2011, 32, 2127), we have proposed a numerically stable restrained electrostatic potential (ESP)-based charge fitting method for protein. The atomic charge is composed of two parts. The dominant part is(More)
The origin of strong affinity of biotin and its analogs binding to (strept)avidin is still the subject of an ongoing controversy. In this work, thermodynamic integration is carried out to study of the difference of binding free energies between biotin and iminobiotin to streptavidin. Three atomic charge schemes are implemented and compared. One is the(More)
Systematic study has been carried out to investigate the accuracy of mid-bond functions in describing pi-pi interactions in benzene dimer. Potential energy curves are calculated for the sandwich, T-shaped, and parallel-displaced configurations of benzene dimer by adding bond functions in MP2 (second-order Møller-Plesset perturbation theory) calculations(More)
In this paper, we propose two new affine invariant shape descriptors, the ICA-Fourier descriptor and the PCA-Fourier descriptor. We tested the descriptors by using them as features for shape based silhouette image retrieval. Experiments on a 1000 silhouette image database show promising retrieval rates of 95.41% and 93.63%, using the ICA-Fourier descriptor(More)