chemoinformatics
After the domain name appeared, there was no suitable name. Chemists active in this field always say that they work in the field of "chemical information". However, due to this name, it is difficult to separate the work of processing chemical literature from the research of developing computer methods to process chemical information. Therefore, some chemists call it "computer chemistry" to emphasize the importance of using computer technology to process chemical information. But this name is easily confused with theoretical chemical calculation, which is "computational chemistry".
1973, a seminar held by the summer school of NATO Institute of Advanced Studies in Nordweckhaut, the Netherlands, brought together scientists engaged in research in different chemical fields for the first time, but they all used computer methods to process chemical information or used computer technology to obtain knowledge from chemical data. The name of this seminar is "Computer Representation and Processing in chemoinformatics". Scientists attending this conference are mainly engaged in the research of chemical structure database, computer-aided organic synthesis design, spectral information analysis and chemometrics, or developing molecular simulation software. During the seminar, these chemists realized that a new research field had been formed, which was implicit in various branches of chemistry.
Since then, computer science and informatics methods applied to solving chemical problems have quietly entered various fields of chemistry.
The appearance of the term "chemoinformatics" is a recent thing. The following is the earliest definition: "The application of information technology and information processing methods has become a very important part in the process of drug discovery. Chemoinformatics is actually a mixture of information sources. It can turn data into information, and then turn information into knowledge, thus making our decision-making in the identification and organization of drug lead compounds more effective. " -brown medicinal, chemical,1998,33,375-384. "chemoinformatics-a new term for an old problem" -M. Hane, R. Green. Chemical biology,1999,33,375-384. Chemoinformatics is a broad term, which includes the design, manufacture, organization, processing, retrieval, analysis, dissemination and use of chemical information. -g. Paris (meeting of American Chemical Society1August 1999).
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1, compound registration. This includes dynamically combining the stereochemical parameters, related spectral data (such as NMR), purity data (such as HPLC), various biological activity measurement data and other related data of each compound in the database.
2. Research tools and techniques of structure-activity relationship. This includes the application of various softwares to establish various structure-activity relationship models, in which various chemometrics methods (such as multivariate statistical regression analysis) are used. The structure-activity relationship model is the correlation between the molecular structure and its biological activity characterized by numerical values. The traditional QSAR research is to connect the independent variables freely, that is, to measure the similarity with simple values. However, the similarity measurement between chemical structures is relatively complex, and chemical structures can only be measured and compared in a certain description space. How to describe chemical molecules is a very active research field. Only in the correct and effective description space, it is possible to objectively measure the similarities and differences between molecules, so as to carry out purposeful screening and get the ideal target molecular library. At present, many people are studying the characterization of molecules by two-dimensional, three-dimensional or even higher-dimensional pharmacophore fingerprints. It is completely different from the traditional expression of free energy, and the effect is more intuitive. New description methods such as feature tree are also widely used.
3. Virtual database assembly technology. It combines the chemical molecular structures and fragments of various elements by computational chemistry to virtually synthesize a large number of candidate compounds, and then screens targets in such a virtual compound library.
chemoinformatics
Drug molecules. The above work includes using appropriate description factors and corresponding algorithms to design the computing library. It is worth pointing out that an effective computing library often plays a key role in molecular design. Genetic algorithm has become an important tool for designing computational library, which can optimize the characteristics of each computational chemistry property in virtual library, thus approaching the target optimally. Clem and others expounded the background and extension of library design, while Drewry and Yang comprehensively summarized various methods of library design. Methods based on known active fragments (targeting the target receptor) were applied to monomer selection. Experience shows that the design of library should be based on the computational chemistry characteristics of product space, not in monomer space. This requires effective virtual synthesis technology of compounds, including: 1. Fragment marking, 2. Simulation technology of synthetic reaction. Synthetic chemists usually prefer the latter, but it is faster to use the former when all the fragments of the molecule have been determined. Hybrid systems are also used in library design. These methods all need to calculate the physical and chemical properties of compounds through models. James F Blake [18] commented on the prediction models of various performance values of drugs, such as adsorption, permeation and water solubility.
4. Database mining technology. This is mainly to find the required drug molecules from a large number of candidate drug molecules, generally through substructure, 2D or 3D similarity measurement, molecular shape, framework, pharmacophore and so on. Or screening drugs in three-dimensional space according to the three-dimensional structure between receptor and ligand. The effect of mining technology depends on the understanding of target molecules, such as the three-dimensional structure and chemical characteristics of molecules; It also depends on mining tools, such as calculating speed. Selecting a subset from the multidimensional feature description space as a representative set is the so-called molecular virtual screening. Through the study of data sets, Bayada and others come to the conclusion that Ward's two-dimensional fingerprint has the greatest improvement on random selection; However, in another study, it is found that the divided chemical descriptor space is suitable for different subset screening, which solves the problem related to.
chemoinformatics
Clustering technology. Deborah K. et al. used recursive partition method to screen drugs and applied it to 14g- protein double receptor test.
5. Statistical methods and techniques. Statistical methods such as principal component analysis and factor analysis are widely used to reduce the dimension of molecular descriptors, which makes the expression of molecular information simpler and more effective and reduces the complexity of calculation.
Degree.
6. Visualization of large-scale data. In chemoinformatics's research, it is necessary to express the structure-activity relationship model of thousands of molecules. If the data is filtered and automatically expressed by computer programs in the form of charts, it will be beneficial to analysis.
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The latest development of modern science makes the chemical substance system faced by various disciplines more and more complex, and the task of identification research is more and more arduous, including both qualitative and quantitative analysis of complex components and uncertain chemical pattern recognition. There are not only large-scale database management problems, but also data law discovery problems and so on. Chemoinformatics is a new discipline formed by combining with other related disciplines to solve a large number of data processing and information extraction tasks in the field of chemistry. This new discipline evolved on the basis of chemometrics and computational chemistry [3], and absorbed and integrated the essence of many disciplines.
With the development of chemometrics and the introduction of computer technology, chemists can easily obtain a large number of chemical data. For example, people can get a series of data such as peak height, peak position and peak area from the computer data acquisition system of analytical instrument without knowing anything about the sample. However, data is not the same as information, especially valuable information. Therefore, how to use modern computing tools and information processing methods to quickly process and analyze chemical measurement data has become a very urgent demand. In this case, chemometrics, which applies mathematics, statistics and computer technology to chemistry, came into being. As a booming new technology in the 1980s, it used mathematics.
chemoinformatics
, statistics, computer technology and other tools to design or choose the best chemical measurement method, process and analyze the chemical measurement data, and extract the chemical related information of the substance system to be measured as much as possible.
In the research of analytical chemistry, Gao Hong predicted that the era of combining analytical chemistry with statistics and mathematics would come. As a chemometrics science, analytical chemistry involves the statistical and mathematical methods of sampling, experimental design, data processing and analysis of analytical signals, as well as the extraction and utilization of chemical information. Chemometrics has made an important contribution to the development of the basic theory of modern analytical chemistry, and basically formed analytical information theory, analytical sampling theory, analytical experiment design and optimization theory, analytical detection theory, analytical correction theory, analytical instrument signal processing technology, chemical database and expert system technology, which greatly enriched the theoretical and technical tools of modern analytical chemistry.
In addition, chemometrics has been widely used in industrial production. For example, multivariate calibration method has become a routine monitoring method in beer production and drug manufacturing; Also used for process monitoring); In papermaking, chemical industry, food, beverage, cosmetics and other industries. Recently, these methods have also been used to monitor batch production processes, such as biochemical fermentation and semiconductor wafers. Up to now, the most successful applications of chemometrics are multivariate calibration, quantitative structure-activity relationship modeling, chemical pattern recognition, multivariate process simulation and monitoring. However, with the expansion of its application scope, the research object is becoming more and more complex, and the amount of data to be processed is getting higher and higher, and the amount of data is also increasing. For example, in the virtual screening of lead compounds in the field of drug design, the number of compounds to be treated reaches 1040. Obviously, the traditional chemometrics is no longer competent for the calculation and analysis of complex chemical problems in pharmacology, life science, environmental science, material science and other fields, and it is urgent to derive and develop a new discipline including chemometrics itself. This is an important reason for the rapid rise of chemoinformatics.
Development of Computational Chemistry Computational chemistry came into being in response to the demand of quantitative analysis of chemical data, which provided chemoinformatics with tools for data calculation and information analysis. With the deepening of understanding, most objects in the field of chemistry can be abstracted and characterized by certain mathematical models; The solution of the model needs the help of various mathematical means. Therefore, the requirements of chemistry for scientific calculation are getting higher and higher. For example, all kinds of chemical reactions can be modeled by certain differential equations, and their reaction, transfer and other processes can be simulated by mathematical models. However, solving differential equations brings higher computational requirements. Usually, a large number of differential equations cannot be solved by theoretical derivation, and approximate solutions need to be found by numerical calculation. Similarly, in the microscopic world, with the deepening understanding of molecular structure, we can simulate the state of molecules through various mathematical models, such as Schrodinger equation, which can simulate the motion state of electron clouds; Molecular simulation can be accurately accomplished by quantum mechanics, molecular dynamics, statistical mechanics and other methods. This means that modern chemical research needs to establish more models and solve more scientific calculation problems.
With the development of science and technology, people have gradually deepened their understanding of the objective world, and constantly summed up the regular knowledge in various research fields, thus making it possible to establish various models. With the development of science today, people have become more and more inclined to look at, understand and solve problems from the perspective of mathematics. Therefore, the advent of computational chemistry has greatly promoted the modern development of chemistry and its related disciplines, and has become a technical support and powerful tool to solve complex problems in the chemical field. Generally speaking, computational chemistry needs to meet two basic requirements: 1. Solve problems accurately; 2. Solve the problem quickly. So computational chemistry has been developing in these two directions. On the one hand, it includes multivariate statistical analysis methods (such as PLS, PCA, discriminant analysis, cluster analysis, factor analysis, regression analysis, etc. ) and artificial intelligence methods (such as pattern recognition, ANN, genetic algorithm, expert system, etc. ) to complete the accurate modeling task of chemical objects; On the other hand, it includes database technology, fast search algorithm, parallel computing technology and other methods to improve the computing speed.
chemoinformatics
Come in, complete the task of fast database search, and realize the application goal of virtual drug screening. Because the extended molecular system needs quantitative description in surface science, pharmacy and materials science, and there is little experimental information about this kind of chemical system, it needs to be solved by means of computational chemistry. Usually, this kind of scientific calculation has a large amount of calculation, so it is difficult to give the calculation results quickly according to the general algorithm with the calculation ability of the existing computer, and it is also impossible to realize human-computer interaction. The introduction of parallel computer and its parallel algorithm greatly improves the calculation speed and makes it possible to solve many problems. It can be seen that the main task of computational chemistry is to provide a method to solve problems in the chemical field by using high-performance scientific computing tools.
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With the development of drug discovery and manufacturing technology, chemoinformatics was first defined by Frank Brown in the following concise language: integrating information resources, transforming data into information, transforming information into knowledge, and applying it to the identification and optimization of specific drug lead compounds. As we all know, the emergence of combinatorial chemistry has brought a revolution to pharmacology. Modern drug design can use computational chemistry to virtually synthesize various compounds through molecular modeling and simulation. However, the compound library obtained by this method is very large, and more than 1040 drug-like molecules can be synthesized theoretically. Obviously, it is impossible to screen every drug without actual synthesis. Therefore, it is necessary to summarize the rules from a large number of data and apply these rules to virtual Qualcomm screening (HTS), so as to reduce the number of compounds that need to be actually synthesized and approach the target compounds as close as possible. Faced with such a large amount of data, it is necessary to integrate the original independent disciplines such as chemistry, mathematics and computer, and build a series of computing technology tools to complete the whole chemical information processing process from data to information and from information to knowledge. These technical tools include not only the analysis and processing of experimental data, but also the calculation of various properties of molecules, the establishment of compound database, the virtual synthesis of molecules, the research of QSAR, the establishment of chemical structure and properties database, the design of molecules based on three-dimensional structure, the research of statistical methods and so on. Chemoinformatics is an interdisciplinary subject developed on the basis of the above requirements. It combines the knowledge of mathematics, chemistry, biology, informatics, computer application, pharmacology and other disciplines, and mainly studies how to properly select the diversity of compound libraries, how to characterize the molecular characteristics of drugs, how to measure the differences between different molecules, how to identify the relationship between drug-like molecules, molecular structures and biological activities, and how to develop corresponding computer software and hardware.
Compared with traditional chemometrics methods, chemoinformatics method pays more attention to the extraction of useful information and the improvement of calculation speed. In order to meet the needs of information extraction, it adopts a large number of advanced methods and tools in the fields of artificial intelligence and information science. For example, using data mining technology to find hidden rules in a large number of original data; Using feature extraction technology and coding technology to express patterns; Using database technology to complete the storage and retrieval of big data; Computer simulation technology is used to simulate the synthesis of molecules and the matching of receptors and ligands. In order to meet the requirements of computing speed, on the one hand, we use higher-performance computer hardware, such as parallel computers; On the other hand, research and design more efficient algorithms to maximize the computing power provided by computer hardware. Obviously, chemoinformatics's research has gone beyond the scope of traditional chemometrics, and the existing chemometrics methods are difficult to solve a large number of new problems in the field of molecular design research. In this sense, the establishment and development of chemoinformatics is the historical necessity of chemical development. Chemoinformatics has been widely used in chemistry, chemical engineering, drug design, material science and many other fields. For example, in the field of chemistry, chemoinformatics is used to optimize the reaction conditions and screen catalysts, mainly to model the experimental data, and then use the prediction model to guide the experimental work; In the field of drug design, it is mainly used in molecular simulation, virtual synthesis, structure-activity relationship analysis, virtual screening and so on. In the field of materials science, chemoinformatics is used in molecular simulation and molecular design. On the basis of molecular performance prediction, the actually synthesized molecules are screened from the designed molecules, so as to obtain materials with optimized performance.
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The new task of current curriculum construction
In recent years, some foreign universities are trying to systematically add chemoinformatics courses to chemistry education. The development of chemoinformatics will promote the reform of traditional chemistry education mode. In 2003, Johann Gasteiger published A Textbook for chemoinformatics, which systematically, comprehensively and simply introduced various research fields in chemoinformatics, its research status and future development trend. In China, the Steering Committee of Science Chemistry Teaching of the Ministry of Education has listed chemoinformatics as the basic content of chemistry teaching for chemistry majors and applied chemistry majors in colleges and universities. At present, chemoinformatics is a new teaching course, and its curriculum requirements, contents, teaching methods and teaching materials have become a new topic in curriculum construction. The teaching in chemoinformatics abroad is mainly professional teaching, which is cross-cutting and involves a wide range. However, due to the limitation of class hours, the teaching content of chemoinformatics in China is mainly chemical philology. This traditional method of obtaining information seriously hinders students' development vision, fetters students' hands and feet to obtain new information, and is not conducive to students' personality development and long-term development. This is a short-sighted behavior of putting the cart before the horse. Even in the chemistry major of higher vocational colleges, chemoinformatics is considered as a dispensable course. They think that as long as students are taught basic skills, it is most important for them to find projects in a short time, while their long-term personal development is seriously ignored. This educational concept is incompatible with the original intention of higher education and should be changed and corrected in time.
Higher vocational students provide solutions to problems.
There are three main research objects in chemical research: structure determination, molecular design and synthetic design. Chemoinformatics's research will focus on culture. Three scientific research objects carry out related computer simulation methods and their application research: computer-aided structural determination, computer-aided molecular design and computer-aided synthetic design. It has its own unique methods to solve chemical problems, which can be divided into three categories: data-based, logic-based and principle-based. The first category mainly refers to the establishment of various database management systems and databases, using the data in them; The second is to use the data in the existing database, and on this basis, use the methods of induction, reasoning and classification to transform the data into knowledge, and manage the knowledge effectively, so that the knowledge can be widely used. Finally, it can be used to solve practical chemical problems; The third category mainly uses the existing quantum chemistry theory to study related chemical problems. Among them, the first two methods focus on the analysis and processing of a large number of chemical information (whole), and their core lies in the analysis and comparison of chemical structures, the analysis and processing methods of related physical and chemical properties and application research. The third method mainly focuses on the accurate analysis of the related properties of a single compound and its application research. The reasonable combination of these three methods will promote the continuous innovation of research methods in chemistry and production methods in industry. At the same time, it is the foundation of green chemistry and green chemical industry, a bridge connecting chemistry and chemical industry to serve the sustainable development of national economy, and one of the effective methods to realize chemical innovation. From the three methods, it can be seen that the application of the first two aspects of higher vocational students will be very important.
Improve students' integration of information content
The current information has four characteristics: large amount of information, wide extension, fast propagation speed and strong cross-performance. The recording, organization and exchange of these information play an increasingly important role in promoting the development of chemistry and become an important part of chemistry. Chemical information can be divided into two parts, namely, chemical information of chemical substances and chemical information in the form of media. The former refers to the related information of chemical components measured by scientific principles and methods, such as physical and chemical properties of substances, qualitative and quantitative information of each component in substances, structural information, etc. The latter is the record form of chemical information, such as books, periodicals and patents. The spread of chemical information enables chemists to enjoy the principles, methods and results of measurement. If students want to make full use of useful measurement data and results, they must first learn to integrate information content and improve their comprehensive ability to integrate information. You can neither throw away useful information nor use false information. Secondly, we should learn to express, manage, transform and use chemical information. At present, the most advanced means is to represent and manage chemical information with computers, because computers can conveniently store, read, calculate and output digital symbols of data information. At the same time, the computer can also express the structural information in chemical information through linear coding. And can ensure the uniqueness and ambiguity of structural information. Chemoinformatics made a detailed introduction and elaboration from the basis of computer and Internet, to online literature retrieval, to the resources and use of database, to information expression and wavelet analysis, which is no longer the original narrow sense of information retrieval. This interdisciplinary subject will certainly enable students to have the perfect ability to analyze, process, transform and use information. That is, the ability to comprehensively integrate information.
Cultivate students' information literacy
Information literacy is a comprehensive ability involving information content, dissemination, analysis, information retrieval and evaluation. 1In June 1999, the Central Committee of the Communist Party of China and the State Council issued the Decision on Deepening Education Reform and Promoting Quality Education in an All-round Way, which clearly pointed out that "students should feel and understand the process of knowledge generation and development, cultivate their scientific spirit and innovative thinking habits, and attach importance to cultivating their ability to collect and process information, acquire new knowledge, analyze and solve problems". This shows that the government of China has realized the importance of information literacy education. Only by improving the basic information literacy of the whole people, especially college students, such as information consciousness with scientific spirit as the core and information ability with innovative thinking as the core, can the national potential be transformed into national intelligence and the national competitiveness be comprehensively improved. For students in higher vocational colleges, chemoinformatics can improve their ability of consciously screening and absorbing information, develop innovative thinking habits, consciously have novelty retrieval consciousness, have a desire for knowledge, master the necessary information processing ability, improve the competitiveness of future jobs, and adapt to the objective requirements of future further study and social lifelong learning.
Cultivate innovative personality
Chemoinformatics can first cultivate students' good information literacy. Good information literacy will make students have better independence, persistence, cooperation, self-confidence and sense of responsibility after entering the society, and these five elements are the concrete embodiment of students' innovative personality. Students are independent and can find and solve problems independently in intellectual activities and practical activities. With good persistence, students can calmly face and wisely think about all the difficulties they face in innovation activities. I will find a glimmer of light in many difficulties and find ways and means to achieve my innovative goals for myself. Based on computer and network technology, chemoinformatics emphasizes cooperation in a wide range of fields. Students with good information literacy will not give up cooperation for independent personality. On the contrary, I will be more willing to meet more people and share my ideas and practices with my collaborators. Good information literacy certainly strengthens students' sense of responsibility and self-confidence. Confidence is half the battle. On the other hand, with more knowledge and information, students will certainly find effective ways to solve problems on the basis of wide-area cooperation or extensive access to useful information. This will not only kill their will to overcome difficulties, but also enhance their self-confidence and sense of responsibility, so that they can perform more perfectly in their work and creatively complete innovative tasks.
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