Wensheng Cai - Academia.edu (original) (raw)

Papers by Wensheng Cai

Frontiers in Molecular Biosciences

The emergence of drug resistance may increase the death rates in advanced non-small cell lung can... more The emergence of drug resistance may increase the death rates in advanced non-small cell lung cancer (NSCLC) patients. The resistance of erlotinib, the effective first-line antitumor drug for NSCLC with the L858R mutation of epidermal growth factor receptor (EGFR), happens after the T790M mutation of EGFR, because this mutation causes the binding of adenosine triphosphate (ATP) to EGFR more favorable than erlotinib. However, the mechanism of the enhancement of the binding affinity of ATP to EGFR, which is of paramount importance for the development of new inhibitors, is still unclear. In this work, to explore the detailed mechanism of the drug resistance due to the T790M mutation, molecular dynamics simulations and absolute binding free energy calculations have been performed. The results show that the binding affinity of ATP with respect to the L858R/T790M mutant is higher compared with the L858R mutant, in good agreement with experiments. Further analysis demonstrates that the T79...

Chinese Science Bulletin (Chinese Version), 2015

Updating a near-infrared multivariate calibration model formed with lab-prepared pharmaceutical t... more Updating a near-infrared multivariate calibration model formed with lab-prepared pharmaceutical tablet types to new tablet types in full production.

The Journal of Physical Chemistry Letters, 2019

Content 1. Molecular dynamics details 1.1 Interaction between Chlorin-e6 and a solvated membrane ... more Content 1. Molecular dynamics details 1.1 Interaction between Chlorin-e6 and a solvated membrane or rhodopsin embedded in a solvated membrane 1.2 Singlet-oxygen penetration to the retinal pocket 2. Quantum chemistry computations 3. Details on the probability of a Förster resonance energy transfer (FRET) mechanism on the singlet manifold 4. Dark photochemistry details 5. Cartesian coordinates (in Ångström) of representative structures along the dark photochemistry pathway 6. References

The Journal of Physical Chemistry C, 2013

The Journal of Physical Chemistry B, 2009

Journal of Molecular Modeling, 2006

A very simple, fast, and efficient scheme is proposed for performing preliminary protein-ligand d... more 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 wellclosed 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 Xray 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.

Journal of Inclusion Phenomena and Macrocyclic Chemistry, 2005

A flexible docking algorithm was developed for studying the inclusion complexes of cyclodextrins ... more A flexible docking algorithm was developed for studying the inclusion complexes of cyclodextrins with steroids in aqueous solution by an optimization method and an empirical function. The function is used to estimate the binding free energy including intermolecular interaction energy, the conformational energy change, and the solvation energy. The bimodal complexations of twelve steroids in β-and γ-CD cavities were studied by the algorithm. For the two orientations of the guests in the cavity, the possible binding regions were investigated, and the lowest energies for the inclusion complexes in the binding regions were obtained. The stability constant for each orientation was estimated from the optimized energy components by a quantitative model. Therefore, the preferential orientations of the guests were found out from the results finally.

Journal of Computational Chemistry, 2004

A highly efficient unbiased global optimization method called dynamic lattice searching (DLS) was... more 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 LJ500 i...

The Journal of Chemical Physics, 2004

Based on the immune theory of biology, a novel evolutionary algorithm, adaptive immune optimizati... more 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.

Chemical Physics Letters, 2005

An energy-based perturbation and a new idea of taboo strategy are proposed for structural optimiz... more An energy-based perturbation and a new idea of taboo strategy are proposed for structural optimization and applied in a benchmark problem, i.e., the optimization of Lennard-Jones (LJ) clusters. It is proved that the energy-based perturbation is much better than the traditional random perturbation both in convergence speed and searching ability when it is combined with a simple greedy method. By tabooing the most widespread funnel instead of the visited solutions, the hit rate of other funnels can be significantly improved. Global minima of (LJ) clusters up to 200 atoms are found with high efficiency.

Acta Chimica Sinica, 2016

Effect of temperature on near-infrared (NIR) spectra has been studied and applied to structural a... more Effect of temperature on near-infrared (NIR) spectra has been studied and applied to structural and quantitative analyses. To investigate the effect of temperature on NIR spectra of alkyl organic system, n-alkanes were studied in this work. NIR spectra of pure n-alkanes (hexane to decane), binary (hexane and octane) and ternary (octane, nonane and decane) mixtures were measured. In the experiments, temperature was controlled to change from 60 to 20 ℃ with a step of ca. 5 ℃. Comparing the spectra at different temperatures, only a little difference in peak intensity of some bands can be found. Therefore, alternating trilinear decomposition (ATLD) algorithm was adopted to analyze the three-order data matrix. The results show that two spectral loadings are obtained because the influence of temperature on the spectra of terminal ethyl (C 2 H 5) groups differs from that of mid-chain methylene (CH 2) groups. Furthermore, the temperature scores of CH 2 and C 2 H 5 groups decrease linearly with temperature, implying that the temperature effect can be quantitatively described by a quantitative spectra-temperature relationship (QSTR) model. The QSTR model provides an efficient way to predict the temperature of n-alkane solutions. Good linearity also exists between sample scores and carbon number or the relative content of CH 2 and C 2 H 5 groups in the molecules of the n-alkanes. Linear models between the two scores and the relative content of CH 2 and C 2 H 5 groups are obtained, respectively, using the least square fitting of the score and the relative contents. The model can be used for prediction of the relative content of CH 2 and C 2 H 5 groups in mixtures, which can further be used to estimate the composition of the mixtures. Furthermore, the relationship between the scores and the carbon atom numbers is modeled using multivariate linear regression (MLR). The composition of n-alkane mixtures can also be estimated through the predicted carbon number using the MLR model. These models are validated by binary and ternary mixtures of the n-alkanes. It was indicated that the relative contents of CH 2 and C 2 H 5 groups or the carbon atom number can be predicted using the models. Therefore, a new way for quantitative estimation of the composition in n-alkane mixtures was developed using the temperature effect of the near-infrared spectra.

Physical Chemistry Chemical Physics, 2022

Hyperactive AFPs can promote ice growth on the basal plane but not on the prismatic plane.

Acta Chimica Sinica, 2013

The main thrust of this contribution is to review applications of numerical simulations to biolog... more The main thrust of this contribution is to review applications of numerical simulations to biological systems over the past 35 years-specifically classical molecular-dynamics simulations and related preferential sampling approaches aimed at exploring selected degrees of freedom of the molecular assembly. Arguably enough, structural biology and biophysics represent one of the greatest challenges for molecular dynamics, owing to the size of the biological objects of interest and the time scales spanned by the molecular processes of the cell machinery in which these objects are prominent actors. The reader is assumed to be fully familiarized with the basic theoretical underpinnings of molecular-dynamics simulations, which will be discussed here from a biological standpoint, emphasizing how the enterprise of modeling increasingly larger molecular assemblies over physiologically relevant times has shaped the field. This review article will further show how the unbridled race to dilate both the spatial and the temporal scales, in an effort to bridge the gap between the latter, has greatly benefitted from groundbreaking advances on the hardware, computational front-notably through the development of massively parallel and dedicated architectures, as well as on the methodological, algorithmic front. The current trends in this research field, boosted by recent, cutting-edge achievements, wherein molecular dynamics has reached new frontiers, provide the basis for an introspective reflection and a prospective outlook into the future of biologically-oriented, high-performance numerical simulations. Furthermore, alternatives to brute-force molecular dynamics towards connecting time and size scales will be discussed, in particular a class of approaches relying upon the preferential sampling of judiciously chosen, important degrees of freedom of the biological object at hand. These methods, targeted primarily at providing a detailed thermodynamic picture of the molecular process at hand, can be viewed as computational tweezers designed to dissect the latter by means of a reduced set of collective variables. Keywords molecular dynamics simulations; biological systems; theory and algorithms; high-performance and large-scale calculations; time and size scales

Journal of Molecular Structure: THEOCHEM, 2006

This article appeared in a journal published by Elsevier. The attached copy is furnished to the a... more This article appeared in a journal published by Elsevier. The attached copy is furnished to the author for internal non-commercial research and education use, including for instruction at the authors institution and sharing with colleagues. Other uses, including reproduction and distribution, or selling or licensing copies, or posting to personal, institutional or third party websites are prohibited. In most cases authors are permitted to post their version of the article (e.g. in Word or Tex form) to their personal website or institutional repository. Authors requiring further information regarding Elsevier's archiving and manuscript policies are

Science China Chemistry, 2011

ABSTRACT

Science in China Series B: Chemistry, 2007

Independent component analysis (ICA) has demonstrated its power to extract mass spectra from over... more Independent component analysis (ICA) has demonstrated its power to extract mass spectra from overlapping GC/MS signal. However, there is still a problem that mass spectra with negative peaks at some m/z will be obtained in the resolved results when there are overlapping peaks in the mass spectra of a mixture. Based on a detail theoretical analysis of the preconditions for ICA and the non-negative property of GC/MS signals, a post-modification based on chemical knowledge (PMBK) strategy is proposed to solve this problem. By both simulated and experimental GC/MS signals, it was proved that the PMBK strategy can improve the resolution effectively. independent component analysis (ICA), post modification, immune algorithm (IA), GC/MS

Physical Chemistry Chemical Physics, 2011