Similarity search profiling reveals effects of fingerprint scaling in virtual screening

Fingerprint scaling is a method to increase the performance of similarity search calculations. It is based on the detection of bit patterns in keyed fingerprints that are signatures of specific compound classes. Application of scaling factors to consensus bits that are mostly set on emphasizes signature bit patterns during similarity searching and has been shown to improve search results for different fingerprints. Similarity search profiling has recently been introduced as a method to analyze similarity search calculations. Profiles separately monitor correctly identified hits and other detected database compounds as a function of similarity threshold values and make it possible to estimate whether virtual screening calculations can be successful or to evaluate why they fail. This similarity search profile technique has been applied here to study fingerprint scaling in detail and better understand effects that are responsible for its performance. In particular, we have focused on the qualitative and quantitative analysis of similarity search profiles under scaling conditions. Therefore, we have carried out systematic similarity search calculations for 23 biological activity classes under scaling conditions over a wide range of scaling factors in a compound database containing approximately 1.3 million molecules and monitored these calculations in similarity search profiles. Analysis of these profiles confirmed increases in hit rates as a consequence of scaling and revealed that scaling influences similarity search calculations in different ways. Based on scaled similarity search profiles, compound sets could be divided into different categories. In a number of cases, increases in search performance under scaling conditions were due to a more significant relative increase in correctly identified hits than detected false-positives. This was also consistent with the finding that preferred similarity threshold values increased due to fingerprint scaling, which was well illustrated by similarity search profiling.     

Study of spectral analytical data using fingerprints and scaled similarity measurements

A new chemoinformatic model has been developed for enlarging the differences between spectra and applied to differentiation of wines according to the criteria grape origin and variety and ageing process. The model is based on generation of fingerprints from normalised spectra, using empirical parameters and a set of 120 samples. After generation of the fingerprints, similarity matrixes were built on the basis of the Tanimoto similarity index between the fingerprints of the samples. Calculation of the Tanimoto index was modified to adapt the index to the characteristics of the analytical measurements. Thus, scaling factors taking into account pattern fingerprints generated from a group of samples with common characteristics were used. In addition, a modified expression for calculating the Tanimoto index was employed. Principal-components analysis (PCA) and soft independent modelling of class analogy (SIMCA) were applied to the similarity matrixes. The results obtained are discussed as a function of the normalisation method employed, the empirical factor used in generation of the fingerprints, and selection of samples for building the pattern fingerprint, etc. Finally, results from differentiation of wines are compared with those obtained by applying PCA to the unprocessed spectra as stated by the proposed model.     

New approach on similarity analysis of chromatographic fingerprint of herbal medicine

A new approach to the construction and similarity analysis of chromatographic fingerprint for herbal medicine is presented in this paper. Samples of chuanxiong, a herbal medicine for headache, from three producing areas of China were used to evaluate the utility of this study. The samples were analyzed with high-performance liquid chromatography (HPLC) and the peak areas of the chromatograms were used to construct the fingerprints of the herbal medicines. A vector of differences was defined between the two fingerprints. The scalar mean of the difference vector was taken as a statistic and both the t-test and Bayesian hypothesis testing were implemented to provide a one-to-one comparison of the fingerprints. Compared with principal component analysis (PCA), correlation coefficient and vector cosine, the new method offers a better differentiation of the similarity or difference between the fingerprints from same sample of chuanxiong. When the new method was used in the similarity analysis of the fingerprints of chuanxiong from different production areas, a clear-cut signature was obtained that reveals the significant difference between them.     

基于信息融合的中药多元色谱指纹图谱相似性计算方法

摘要用信息融合算法合并多张色谱指纹图谱, 解决中药多元指纹图谱相似性评价难题, 提出一种多元色谱指纹图谱相似度计算方法. 用该方法先对各单元指纹图谱进行串行或并行象素级信息融合, 再对融合了各指纹峰信息的多元色谱指纹图谱进行相似度评价. 计算机仿真和复方丹参滴丸多元HPLC指纹图谱应用结果表明, 该法能够评价中药多元色谱指纹图谱相似度, 定量表征中成药产品批次间质量波动情况.     

相似系统理论用于中药色谱指纹图谱的相似度评价

研究了中药色谱指纹图谱相似度的评价方法,提出了改良的程度相似度的计算方法。以模拟数据和实验数据研究了相关系数、夹角余弦和改良程度相似度的优劣,发现相关系数和夹角余弦对数据的差异不够敏感,经预处理之后仍然不灵敏;采用改良的程度相似度可以反映数据的差异,因此可以将其用于评价中药色谱指纹图谱共有峰的相似度。     

相似系统理论定量评价中药材色谱指纹图谱的相似度

研究相似系统理论定量评价中药材提取物液相色谱指纹图谱的相似度。以相似系统理论对栀子药材提取物高效液相色谱指纹图谱的相似度评价,发现相似系统理论对数据的差异比较敏感,而且相似度的计算结果能够反映样品的相对差异。相似系统理论可以作为一种评价中药色谱指纹图谱相似度的新方法。     

Assessment of quality consistency in traditional Chinese medicine using multi‐wavelength fusion profiling by integrated quantitative fingerprint method: Niuhuang Jiedu pill as an example

Under the wave of the revival of traditional Chinese medicine, there is a quite imperative duty to study an integrated and comprehensive method of fingerprint data processing and analysis on the quality consistency of traditional Chinese medicine. So, we proposed six parameters from two aspects (qualitative and quantitative), three levels (biased to strong peaks, biased to weak peaks, no obvious bias), to comprehensively evaluate the similarity of the two fingerprints. On this basis, another five parameters were proposed to evaluate the integrated effects (consistency, volatility, and similarity). This method was applied to 22 batches of Niuhuang Jiedu pill samples. Next, a practical and convenient multi‐wavelength fusion method was designed to provide more information, and the generated fusion profilings were used for subsequent evaluation. The characteristics of the parameters were confirmed by correlation analysis. The results of both hierarchical clustering analysis and principal component analysis for raw data and standardized data were consistent with integrated quantitative fingerprint method results. At the same time, this method gave a reasonable explanation for abnormal and dissimilar samples. This work illustrated that the proposed method was particularly suitable for similarity analysis of fingerprints and capable of ensuring the quality consistency in traditional Chinese medicine.     

Principle of nonlinear chemical fingerprint by using dissipative components in samples as well as calculation and evaluation of similarity

Under the conditions of constant temperature and pressure,different influences of samples with different chemical components on the mechanism of nonlinear chemical reaction will cause different changes of the potential-time relationship curve of the nonlinear chemical reaction system.Using it as the character,and using the B-Z nonlinear chemical system to use acetone and substrates in samples as main dissipative substances qua an example,the principle of nonlinear chemical fingerprint has been researched and discussed in detail.At the same time,the general method for calculating the system similarity about nonlinear chemical fingerprint was also put forward,and similarities of nonlinear chemistry fingerprints of different batches of Guhan Yangshengjing and 18 sorts of other samples were calculated by Euclidean distance,correlation coefficient,included angle cosine and system similarity,at the same time,the various similarities were analyzed.The results showed that,both of correlation coefficient and included angle cosine are unable to be used as the criterion for quantitatively evaluating the similarity of nonlinear chemistry fingerprint;as non-parametric similarity,Euclidean distance can accurately reflect the feature differences in the fingerprints,but as parametric similarity,sometimes,Euclidean distance can not accurately reflect the relative extent of characteristic difference in the nonlinear chemical fingerprints;system similarity can most truthfully reflect the characteristic difference in the nonlinear chemical fingerprints,and is the best evaluating method among the four ones.Therefore,system similarity can be used to quantitatively calculate the similar extent between the nonlinear chemical fingerprints.An economical,simple and convenient,easy pushing and effective method for identifying and evaluating complicated samples has successfully been put forward.     

矿物元素指纹图谱的建立及在西洋参产地鉴别中的应用研究

采用电感耦合等离子体质谱法测定了山东、吉林、美国和加拿大4个产地西洋参中50种矿物元素的含量,研究了不同产地西洋参矿物元素的差别和转换系数,构建了西洋参的矿物元素指纹图谱。以各产地矿物元素含量的平均值构建了山东、吉林、美国和加拿大产西洋参的矿物元素标准指纹图谱。采用SPSS 20.0计算了各西洋参矿物元素指纹图谱与其矿物元素标准指纹图谱的相似度,确定了山东、吉林、美国和加拿大产西洋参矿物元素指纹图谱的相似度阈值分别为0.93、0.91、0.98和0.93。通过比较未知产地西洋参矿物元素指纹图谱与矿物元素标准指纹图谱的相似度,进行西洋参的产地判别。采用20批未知产地西洋参样品验证模型的准确性,正确率为85%。此外,研究表明,不同生长年限和不同部位西洋参样品对所建立的西洋参产地鉴别方法无影响。     

利用样本成分耗散物的非线性化学指纹图谱原理及相似度计算与评价

在恒温恒压条件下,以丙酮和样本中底物作为主要耗散物的不同成分的样本对非线性化学反应机理产生不同影响,从而引起反应体系电位-时间曲线形状不同变化为特征的B-Z化学振荡体系为例,就非线性化学指纹图谱原理进行了详细研究和讨论,并提出了计算非线性化学指纹图谱系统相似度的通用方法.利用系统相似度和欧氏距离、相关系数及夹角余弦对不同生产批次古汉养生精和18种其他样本的非线性化学指纹图谱的相似度进行了计算与分析.结果表明,相关系数和夹角余弦都不能用来作为评价非线性化指纹图谱相似度的指标.利用欧氏距离公式计算指纹图谱的非参数型相似度时,能正确反映指纹图谱的特征差异,但用其计算参数型相似度时,则有时不能正确反映样本非线性化学指纹图谱特征差异的相对程度.系统相似度能最真实反映样本指纹图谱之间差异程度,是4种相似度计算方法中最好的,可用于非线性化学指纹图谱相似度计算与评价.成功提出了一种经济、简便、易行和有效的鉴别样本真伪与评价其质量的科学方法.     

Qualitative and quantitative assessment of the HPLC fingerprints of Ginkgo biloba extract by the involution similarity method.

In this paper, we develop a new method for evaluating chromatographic fingerprints of traditional Chinese medicine (TCM) by the average involution similarity and the quantitative involution similarity. To validate this novel approach, we studied the chromatographic fingerprints of Ginkgo biloba extract by the new similarity parameters. The results were compared with those of the cosine of vectorial angle (S(F)), the correlative coefficient (r) and some other quantitative parameters, such as the apparent quantitative similarity of fingerprint R% and the average mass percentage M%. The approach represented in this paper was proved to well reflect the similarity alteration of each batch of Ginkgo biloba extract and the quantitative differences of the extracted constituents. The S(gxq) and S(gxsq) are the best qualitive and quantitative similarity parameters of all those mentioned in this paper; they can be profitably used for the qualitative and quantitative assessments of TCM chromatographic fingerprints. Through this study, the quality evaluation of TCM can be simplified by using only one parameter of with the qualitive and quantitative functions proposed in this paper.     

HPLC指纹图谱相似度研究

将HPLC指纹图谱看作多维空间内的向量,利用向量夹角余弦的基本公式计算两个指纹图谱间的相似度。用7个不同品种的金银花提取物的HPLC指纹图谱对计算方法进行了检验,结果表明相似度能较好地定量评价指纹图谱间的相似性,可应用于中药质量控制。     

Multifingerprint based similarity searches for targeted class compound selection

Molecular fingerprints are widely used for similarity-based virtual screening in drug discovery projects. In this paper we discuss the performance and the complementarity of nine two-dimensional fingerprints (Daylight, Unity, AlFi, Hologram, CATS, TRUST, Molprint 2D, ChemGPS, and ALOGP) in retrieving active molecules by similarity searching against a set of query compounds. For this purpose, we used biological data from HTS screening campaigns of four protein families (GPCRs, kinases, ion channels, and proteases). We have established threshold values for the similarity index (Tanimoto index) to be used as starting points for similarity searches. Based on the complementarities between the selections made by using different fingerprints we propose a multifingerprint approach as an efficient tool to balance the strengths and weaknesses of various fingerprints.     

化学指纹图谱的相似性测度及其评价方法

提出化学指纹图谱相似性测度概念,并以峰数弹性、峰比例同态性和峰面积同 态性为评价指标,用于多角度评价化学指纹图谱相似性测试优劣,根据这些评价指 标,用计算机仿真方法研究比较了6种相似性测度,结果表明夹角余弦测试用于度 量指纹图谱间谱峰比例的波动较适宜,峰匹配测度可较灵敏地检测小峰个数波动, 而欧氏距离测试则具有较好的综合评价能力。最后,采用实测的参麦注射液色谱分 析谱图。研究考察了上述计算机仿真实验结果,证明仿真结果符合实际情况,这表 明本研究方法可用于评价化学指纹图谱相似性测度。     

Selection and fingerprints of the control substances for plant drug Eucommia ulmodies Oliver by HPLC and LC-MS

Eucommia ulmodies Oliver (E. ulmodies) has been used as herbal medicine for thousands years in China. The selection of the control substances and their fingerprints of this plant medicine were investigated by using high performance liquid chromatography (HPLC) and liquid chromatography-mass spectrometry (LC-MS). The gradient elution mode was applied in chromatographic separation, and the data was analyzed by "Computer Aided Similarity Evaluation" software to compare the similarity of the E. ulmodies from different habitats. Low similarity was found in the samples from nonadjacent provinces, while high similarity was obtained in those from the adjacent provinces. The LC-MS fingerprints of E. ulmodies showed the main active constituents and could be used for its original identification and quality evaluation.     

Virtual screening and library enumeration of new hydroxycinnamates based antioxidant compounds: A complete framework

Designing of molecules for drugs is important topic from many decades. The search of new drugs is very hard, and it is expensive process. Computer assisted framework can provide the fastest way to design and screen drug-like compounds. In present work, a multidimensional approach is introduced for the designing and screening of antioxidant compounds. Antioxidants play a crucial role in ensuring that the body's oxidizing and reducing species are kept in the proper balance, minimizing oxidative stress. Machine learning models are used to predict antioxidant activity. Three hydroxycinnamates are selected as standard antioxidants. Similar compounds are searched from ChEMBL database using chemical structural similarity method. The libraries of new compounds are generated using evolutionary method. New compounds are also designed using automatic decomposition and construction building blocks. The antioxidant activity of all designed and searched compounds is predicted using machine learning models. The chemical space of searched and generated compounds is envisioned using t-distributed stochastic neighbor embedding (t-SNE) method. Best compounds are shortlisted, and their synthetic accessibility is predicted to further facilitate the experimental chemists. The chemical similarity between standard and selected compounds is also studied using fingerprints and heatmap.     

Mathematical correction for fingerprint similarity measures to improve chemical retrieval

In many modern chemoinformatics systems, molecules are represented by long binary fingerprint vectors recording the presence or absence of particular features or substructures, such as labeled paths or trees, in the molecular graphs. These long fingerprints are often compressed to much shorter fingerprints using a simple modulo operation. As the length of the fingerprints decreases, their typical density and overlap tend to increase, and so does any similarity measure based on overlap, such as the widely used Tanimoto similarity. Here we show that this correlation between shorter fingerprints and higher similarity can be thought of as a systematic error introduced by the fingerprint folding algorithm and that this systematic error can be corrected mathematically. More precisely, given two molecules and their compressed fingerprints of a given length, we show how a better estimate of their uncompressed overlap, hence of their similarity, can be derived to correct for this bias. We show how the correction can be implemented not only for the Tanimoto measure but also for all other commonly used measures. Experiments on various data sets and fingerprint sizes demonstrate how, with a negligible computational overhead, the correction noticeably improves the sensitivity and specificity of chemical retrieval.