Improving (Q)SAR predictions by examining bias in the selection of compounds for experimental testing

ABSTRACT

Existing data on structures and biological activities are limited and distributed unevenly across distinct molecular targets and chemical compounds. The question arises if these data represent an unbiased sample of the general population of chemical-biological interactions. To answer this question, we analyzed ChEMBL data for 87,583 molecules tested against 919 protein targets using supervised and unsupervised approaches. Hierarchical clustering of the Murcko frameworks generated using Chemistry Development Toolkit showed that the available data form a big diffuse cloud without apparent structure. In contrast hereto, PASS-based classifiers allowed prediction whether the compound had been tested against the particular molecular target, despite whether it was active or not. Thus, one may conclude that the selection of chemical compounds for testing against specific targets is biased, probably due to the influence of prior knowledge. We assessed the possibility to improve (Q)SAR predictions using this fact: PASS prediction of the interaction with the particular target for compounds predicted as tested against the target has significantly higher accuracy than for those predicted as untested (average ROC AUC are about 0.87 and 0.75, respectively). Thus, considering the existing bias in the data of the training set may increase the performance of virtual screening.     

SARS-CoV protease inhibitors design using virtual screening method from natural products libraries

Two natural products databases, the marine natural products database (MNPD) and the traditional Chinese medicines database (TCMD), were used to find novel structures of potent SARS-CoV protease inhibitors through virtual screening. Before the procedure, the databases were filtered by Lipinski's ROF and Xu's extension rules. The results were analyzed by statistic methods to eliminate the bias in target-based database screening toward higher molecular weight compounds for enhancing the hit rate. Eighteen lead compounds were recommended by the screening procedure. They were useful for experimental scientists in prioritizing drug candidates and studying the interaction mechanism. The binding mechanism was also analyzed between the best screening compound and the SARS protein.     

The investigation of the (p,ρ,T) and (ps,ρs,Ts) properties of {(1−x)CH3OH + xLiBr} for the application in absorption refrigeration machines and heat pumps

The (p,ρ,T) and (p_s,ρ_s,T_s) properties of {(1−x)CH₃OH + xLiBr} over a wide range of state parameters are reported for the first time. The experiments were carried out in a constant volume piezometer over a temperature range from 298.15 K to 398.15 K, at 0.08421, 0.13617, 0.19692, 0.23133 and 0.26891 mole fractions and from atmospheric pressure up to 60 MPa. The experimental uncertainties are ΔT=±3 mK for temperature, Δp=±5·10⁻² MPa for high pressure and Δp=±5·10⁻⁴ MPa for atmospheric pressure, Δρ=±3·10⁻² kg · m⁻³ for density. An equation of state was derived for correlation of the experimental data of the solutions.     

Validation of an empirical RNA-ligand scoring function for fast flexible docking using RiboDock®

We report the design and validation of a fast empirical function for scoring RNA-ligand interactions, and describe its implementation within RiboDock, a virtual screening system for automated flexible docking. Building on well-known protein-ligand scoring function foundations, features were added to describe the interactions of common RNA-binding functional groups that were not handled adequately by conventional terms, to disfavour non-complementary polar contacts, and to control non-specific charged interactions. The results of validation experiments against known structures of RNA-ligand complexes compare favourably with previously reported methods. Binding modes were well predicted in most cases and good discrimination was achieved between native and non-native ligands for each binding site, and between native and non-native binding sites for each ligand. Further evidence of the ability of the method to identify true RNA binders is provided by compound selection ('enrichment factor') experiments based around a series of HIV-1 TAR RNA-binding ligands. Significant enrichment in true binders was achieved amongst high scoring docking hits, even when selection was from a library of structurally related, positively charged molecules. Coupled with a semi-automated cavity detection algorithm for identification of putative ligand binding sites, also described here, the method is suitable for the screening of very large databases of molecules against RNA and RNA-protein interfaces, such as those presented by the bacterial ribosome.     

基于支持向量机的凝血功能诊断模型

使用凝血四项指标诊断凝血功能是临床的常规检查,但根据经验进行诊断正确率不高.剔除临床上最重要的指标FIB后,建立支持向量机模型诊断的正确率和根据凝血四项指标诊断的正确率没有显著差异,100次模拟的平均正确率分别达到了95.4496%和95.5039%.     

基于PLC的三维调整机同步控制系统设计与实现

针对三维调整机难以实现多台同步工作，设计了基于PLC的同步控制方案。在同步控制系统方案中，采用西门子PLC通过工业无线以太网进行同步控制，由各维度油缸的位移传感器来保证同步控制的精确性。经实验，证实了此系统的精度满足设计要求，实现了同步控制的效果。     

Divergent Synthesis of Molecular Winch Prototypes

We report the synthesis of conceptually new prototypes of molecular winches with the ultimate aim to investigate the work performed by a single ruthenium-based molecular motor anchored on a surface by probing its ability to pull a load upon electrically-driven directional rotation. According to a technomimetic design, the motor was embedded in a winch structure, with a long flexible polyethylene glycol chain terminated by an azide hook to connect a variety of molecular loads. The structure of the motor was first derivatized by means of two sequential cross-coupling reactions involving a penta(4-halogenophenyl)cyclopentadienyl hydrotris(indazolyl)borate ruthenium(II) precursor and the resulting benzylamine derivative was next exploited as key intermediate in the divergent synthesis of a family of nanowinch prototypes. A one-pot method involving sequential peptide coupling and Cu-catalyzed azide-alkyne cycloaddition was developed to yield four loaded nanowinches, with load fragments encompassing triptycene, fullerene and porphyrin moieties.     

基于LabVIEW机器视觉的迈克耳孙干涉仪实验

基于机器视觉设计了迈克耳孙干涉仪实验,采用机器视觉技术替代人眼对目标(干涉圆环)进行分析与测量,可有效避免因视觉疲劳而造成的测量错误.