Biomedical subjects

Wensheng Cai

Publications and source records attributed to Wensheng Cai.

14 recordsLinked to original sources

PubMed2006

An adaptive strategy for selecting representative calibration samples in the continuous wavelet domain for near-infrared spectral analysis.

Sample selection is often used to improve the cost-effectiveness of near-infrared (NIR) spectral analysis. When raw NIR spectra are used, however, it is not easy to select appropriate samples, because of background interference and noise. In this paper, a novel adaptive strategy based on selection of representative NIR spectra in the continuous wavelet transform (CWT) domain is described. After pretreatment with the CWT, an extension of the Kennard-Stone (EKS) algorithm was used to adaptively select the most representative NIR spectra, which were then submitted to expensive chemical measurement and multivariate calibration. With the samples selected, a PLS model was finally built for prediction. It is of great interest to find that selection of representative samples in the CWT domain, rather than raw spectra, not only effectively eliminates background interference and noise but also further reduces the number of samples required for a good calibration, resulting in a high-quality regression model that is similar to the model obtained by use of all the samples. The results indicate that the proposed method can effectively enhance the cost-effectiveness of NIR spectral analysis. The strategy proposed here can also be applied to different analytical data for multivariate calibration.

Journal Article↗

PubMed2006

Prediction of low-energy isomers of large fullerenes from C132 to C160.

To predict energetically favored isomers, we used a topological scheme as a prescreening tool to select candidate isomers for each fullerene from C(106) to C(160). Comparison with the PM3 and tight-binding (TB) potential calculated results and few published data for the low-energy isomers of C(106) to C(130) indicates that the prescreening approach is feasible. For each fullerene from C(132) up to C(160), the selected 1000 candidate isomers were further optimized by PM3 and TB potential. The analysis of the semiempirical PM3 and TB results of C(106) to C(160) provides some qualitative features of the large fullerenes. Furthermore, calculations at the B3LYP/6-31G*//B3LYP/3-21G level of theory were carried out on the top ten PM3 and TB low-energy isomers of C(132) to C(160) to accurately predict the stable isomers, and the HOMO-LUMO gap, the ionization energy, and electron affinity of the lowest-energy isomers were also investigated at the same level.

Journal Article↗

PubMed2006

A fast surface-matching procedure for protein-ligand docking.

A very simple, fast, and efficient scheme is proposed for performing preliminary protein-ligand docking as the first step of intensive high-throughput virtual screening. The procedure acts as a surface-complementarity filter that first calculates the 2D-contour maps of both the protein cavity and of the ligands using a spherical harmonics description of the associated molecular surfaces. Next, the obtained 2D-fingerprint images are compared to detect their complementarity. This scheme was tested on three typical cases of protein cavities, namely, a well-closed pocket, a small open pocket, and a large open one. For that purpose, for each case, a sample of 101 ligand conformers was generated (the X-ray one and 100 different conformers generated using simulated annealing), and these conformational samples were ranked according to the complementarity with the protein cavity surface. Compared to traditional docking procedures such as FRED (considered as typical of a very fast rigid body docking algorithms) and GOLD (considered as typical of the more accurate flexible docking algorithms), our procedure was much faster and more successful in detecting the right X-ray conformation. We did, however, identify a certain weakness in the case of the very large pocket where results were not as expected. In general, our method could be used for incorporating indirectly flexibility in protein-ligand docking calculations as such a scheme can easily handle several conformational states of both the protein and the ligand.

Binding Sites↗

PubMed2006

Molecular dynamics study of the inclusion of cholesterol into cyclodextrins.

The interaction of three cyclodextrins (CDs), viz. beta-CD, heptakis (2,6-di-O-methyl)-beta-CD (DM-beta-CD), and 2-hydroxypropyl-beta-CD (HP-beta-CD), with cholesterol was investigated using molecular dynamics (MD) simulations. The free energy along the reaction pathway delineating the inclusion of cholesterol into each CD was computed using the adaptive biasing force method. The association constant and the corresponding association free energy were derived by integrating the potential of mean force (PMF) over a representative ordering parameter. The results show that the free energy profiles possess two local minima corresponding to roughly equally probable binding modes. Among the three CDs, DM-beta-CD exhibits the highest propensity to associate with cholesterol. Ranking for binding cholesterol, viz. DM-beta-CD > HP-beta-CD > beta-CD, agrees nicely with experiment. Partitioning of the PMF into free energy components illuminates that entering of cholesterol into the CD cavity is driven mainly by electrostatic interactions, whereas deeper inclusion results from van der Waals forces and solvation effects. Additional MD simulations were performed to investigate the structural stability of the host-guest complexes near the free energy minima. The present results demonstrate that association of cholesterol and CDs follows two possible binding modes. Although the latter are thermodynamically favorable for all CDs, one of the two inclusion complexes appears to be preferred kinetically in the case of DM-beta-CD.

Cholesterol↗

PubMed2005

Structural transition from icosahedra to decahedra of large Lennard-Jones clusters.

The lowest icosahedral and decahedral energies of LJ1001-1610 clusters are obtained using a greedy search method (GSM) based on lattice construction. By comparing the lowest energies of icosahedral and decahedral clusters with the same atoms, the structural transition of LJ clusters is studied. Results show that the critical size from icosahedra to decahedra is located at N = 1034. When the cluster size is larger than 1034, the optimal structures are decahedra except the LJ1367-1422 clusters near the magic number, 1402, of icosahedra. However, the energies of icosahedra near the next magic number, 2044, are higher than that of decahedra, which implies that decahedra will be the optimal structure when the cluster size is larger than 1422, even for those clusters near the magic numbers of icosahedra.

Journal Article↗

PubMed2005

Chiral recognition of aromatic compounds by beta-cyclodextrin based on bimodal complexation.

The chiral recognition of the selected aromatic chiral compounds by native beta-cyclodextrin (beta-CD) based on bimodal complexation was studied using a flexible docking algorithm FDOCK. A quantitative empirical free energy relationship model was employed to predict the complex stability constants and the preferred binding modes. The results showed that the calculated complex stability constants are in good agreement with the experimental data. Furthermore, the main force responsible for host-guest complexation is the van der Waals force and the chiral molecules are completely included into the beta-CD cavity. The chiral recognition for the selected aromatic chiral compounds is the result of the van der Waals force counterbalancing with the other effects, such as the electrostatic interaction and the hydrophobic effect.

Algorithms↗

PubMed2005

An efficient approach for theoretical study on the low-energy isomers of large fullerenes C90-C140.

An approach that consists of a molecular mechanics method based on the second generation reactive empirical bond order (REBO) potential and the more accurate semiempirical method PM3 (Parametric Method No. 3) was proposed to predict the energetically favored isomers of the fullerenes from C90 to C140 at the semiempirical level. All the 578,701 isolated-pentagon-rule isomers of fullerenes from C90 to C140 were enumerated from topological structures and systematically searched using an energy minimization method to select the best 100 low-energy isomers based on the REBO potential for each fullerene. Then these candidate isomers were further optimized by PM3 and ranked again to determine the top low-energy isomers. This approach was applied to calculate the energetically favored isomers of C90-C140. The results of C90-C120 are in good agreement with the published results by quantum-chemical methods. Furthermore, the top five low-energy isomers of C90-C120, as well as C122-C140 which have scarcely been systematically studied before, are also predicted with the approach. The analysis of the structures showed that the hexagon-neighbor rule is an important factor to the stability of C90-C140. The time cost for the systematical search based on the REBO potential was also discussed. It indicates that the approach proposed is efficient for predicting the energetically favored isomers of large fullerenes at the semiempirical level.

Journal Article↗

PubMed2005

Geometry optimization and conformational analysis of (C60)N clusters using a dynamic lattice-searching method.

A newly developed unbiased global optimization method, named dynamic lattice searching (DLS), is used to locate putative global minima for all (C6O)N clusters with Girifalco potential up to N=150. A simple greedy strategy is adopted for the basic frame, so DLS has a very high convergence speed and may converge at various configurations. As most structures are packed by basic tetrahedra, some sequences are defined by both configurations and the size of the basic tetrahedra. A sequence-based conformational analysis is carried out with the defined sequences by counting the hit number over 10,000 independent DLS runs for all the cases up to N = 5. It was found that the hit rate of a sequence is related to the size of the basic tetrahedra. U.e of this method proved that the Leary tetrahedral sequence is dominant in a certain range of cluster sizes, although the sequence has no potential energy advantage. The calculation results are also consistent with those of annealing experiments at high temperature, both in magic numbers and height of the peaks in the mass spectrum.

Journal Article↗

PubMed2004

A dynamic lattice searching method for fast optimization of Lennard-Jones clusters.

A highly efficient unbiased global optimization method called dynamic lattice searching (DLS) was proposed. The method starts with a randomly generated local minimum, and finds better solution by a circulation of construction and searching of the dynamic lattice (DL) until the better solution approaches the best solution. The DL is constructed adaptively based on the starting local minimum by searching the possible location sites for an added atom, and the DL searching is implemented by iteratively moving the atom located at the occupied lattice site with the highest energy to the vacant lattice site with the lowest energy. Because the DL can greatly reduce the searching space and the number of the time-consuming local minimization procedures, the proposed DLS method runs at a very high efficiency, especially for the clusters of larger size. The performance of the DLS is investigated in the optimization of Lennard-Jones (LJ) clusters up to 309 atoms, and the structure of the LJ(500) is also predicted. Furthermore, the idea of dynamic lattice can be easily adopted in the optimization of other molecular or atomic clusters. It may be a promising approach to be universally used for structural optimizations in the chemistry field.

Journal Article↗

PubMed2004

An adaptive immune optimization algorithm for energy minimization problems.

Based on the immune theory of biology, a novel evolutionary algorithm, adaptive immune optimization algorithm (AIOA), is proposed. In AIOA, density regulation and immune selection is adopted to control the individual diversity and the convergence adaptively. By an application of the algorithm to the optimization of test functions, it is shown that the algorithm is a highly efficient optimization method compared with other stochastic optimization methods. The algorithm was also applied to the optimization of Lennard-Jones clusters, and the results show that the method can find the optimal structure of N</=80 with a very high efficiency. The proposed algorithm may be a good tool for fast global optimization in chemical or biological molecular simulations.

Journal Article↗

PubMed2002

A fast annealing evolutionary algorithm for global optimization.

By combining the aspect of population in genetic algorithms (GAs) and the simulated annealing algorithm (SAA), a novel algorithm, called fast annealing evolutionary algorithm (FAEA), is proposed. The algorithm is similar to the annealing evolutionary algorithm (AEA), and a very fast annealing technique is adopted for the annealing procedure. By an application of the algorithm to the optimization of test functions and a comparison of the algorithm with other stochastic optimization methods, it is shown that the algorithm is a highly efficient optimization method. It was also applied in optimization of Lennard-Jones clusters and compared with other methods in this study. The results indicate that the algorithm is a good tool for the energy minimization problem.

Journal Article↗

PubMed2002

Protein-ligand recognition using spherical harmonic molecular surfaces: towards a fast and efficient filter for large virtual throughput screening.

Molecular surfaces are important because surface-shape complementarity is often a necessary condition in protein-ligand interactions and docking studies. We have previously described a fast and efficient method to obtain triangulated surface-meshes by topologically mapping ellipsoids on molecular surfaces. In this paper, we present an extension of our work to spherical harmonic surfaces in order to approximate molecular surfaces of both ligands and receptor-cavities and to easily check the surface-shape complementarity. The method consists of (1) finding lobes and holes on both ligand and cavity surfaces using contour maps of radius functions with spherical harmonic expansions, (2) superposing the surfaces around a given binding site by minimizing the distance between their respective expansion coefficients. This docking procedure capabilities was demonstrated by application to 35 protein-ligand complexes of known crystal structures. The method can also be easily and efficiently used as a filter to detect in a large conformational sampling the possible conformations presenting good complementarity with the receptor site, and being, therefore, good candidates for further more elaborate docking studies. This "virtual screening" was demonstrated on the platelet thrombin receptor.

HIV Protease↗

PubMedDate not supplied

Global optimization of Lennard-Jones clusters by a parallel fast annealing evolutionary algorithm.

A parallel fast annealing evolutionary algorithm (PFAEA) was presented and applied to optimize Lennard-Jones (LJ) clusters. All the lowest known minima up to LJ(116) with both icosahedral and nonicosahedral structure, including the truncated octahedron of LJ(38), central fcc tetrahedron of LJ(98), the Marks' decahedron of LJ(75)(-)(77), and LJ(102)(-)(104), were located successfully by the unbiased algorithm. PFAEA is a parallel version of fast annealing evolutionary algorithm (FAEA) that combines the aspect of population in genetic algorithm and annealing algorithm with a very fast annealing schedule. A master-slave paradigm is used to parallelize FAEA to improve the efficiency. The performance of PFAEA is studied, and the scaling of execution time with the cluster size is approximately cubic, which is important for larger scale energy minimization systems.

Journal Article↗

PubMedDate not supplied

Parallel random tunneling algorithm for structural optimization of Lennard-Jones clusters up to N=330.

A random tunneling algorithm (RTA) is derived from the terminal repeller unconstrained subenergy tunneling (TRUST) algorithm, and the parallelization of the RTA is implemented with an island parallel paradigm. Combined with the techniques of angular moving, the parallel random tunneling algorithm (PRTA) is applied to the optimization of Lennard-Jones (LJ) atomic clusters, and all the global minima of LJ clusters with size up to 200 are successfully located. For the optimization of larger cluster, a PRTA with an improved seeding technique is developed and successfully applied to the optimization of LJ151-LJ309. Furthermore, the optimized structures of LJ309-330 with the PRTA, which have not been studied before, are also provided.

Journal Article↗