| Chinese Materia Medica (CMM) are characterized as the diversity and pluralism on their species, richness and complexity on their ingredients, flexibility and variability on their compatibility. Information resources of CMM are sharply rising nowadays, and the accumulative data need to mine and abstract. But the methodologies and technologies are limited in the studies of CMM at present. All of these make the CMM study a tough mission with tremendous difficulty and complexity. In order to understand the complexity of CMM and the relationship between CMM and their ingredients, it is necessary to change our thinking mode, and apply computational sciences to solve the key problems of CMM based on the current experimental methodologies. Therefore, a new concept, Computational Chinese Materia Medica (CCMM), was proposed in this dissertation. CCMM applies the methodologies and technologies of computing and information sciences to the field of CMM study, and supplies fresh ideas and reasonable solutions on the problems that failed by conventional experiments, and offers quantitative and scientific evidences for the abstract concepts and theories in the field of Traditional Chinese Medicine (TCM).The concept, theory and methodology of CCMM were introduced in detail in this dissertation firstly. And then, the application studies of CCMM on CMM Properties and TCM Prescriptions were shown in different sections. The research programs in this dissertation were listed as follow.1) Construction of CMM chemical database. We used ISIS/Base, a piece of software for database creation and administration, to create a CMM chemical database, which contains 374 common CMM and 15000 chemicals in CMM. All the chemicals have their 2D and 3D structures stored in the database.2) Creation of prediction system for CMM hot/cold properties. A prediction system for CMM hot/cold properties was created by using CMM chemical database, descriptor calculation, weight center treatment (original method) and support vector machine classification. The prediction accuracy of this system is over 80%, which ensures its application to the hot/cold properties prediction of folk and foreign herbs. Besides, the descriptors derived from this system have given the help on interpretation the relationship between hot/cold properties of CMM and their chemical ingredients.3) The study of interaction between pungent CMM and olfactory receptors. The three-dimensional structures of three typical olfactory receptors were constructed for the first time by using homology modeling and molecular dynamics simulation method. The interaction between pungent CMM and these olfactory receptors has been researched by molecular docking. It's inferred that the action of pungent CMM is probably involved with the activation of olfactory receptors as the first step.4) The study of incompatibility property of CMM through TCM formula network and chemical space. A TCM formula network was built by using complex network methodologies. Topology analysis was preformed based on this network. Meanwhile, we built a TCM chemical space and performed some analyses. "Eighteen antagonisms and nineteen mutual inhibitions", the ancient theory of TCM prescription incompatibility, was interpreted in modern scientific language through the network pathway distance analysis and the chemical space distance measurement based on the theory of complex networks and chemical space, respectively.5) Studies on the effective materials of Xuebijing towards Sepsis treatment. We drew maps on the network effects of sepsis, and selected a series of key protein targets involved. The effective materials of Xuebijing, a TCM prescription, were searched by virtual screening. Several compounds have been found at last, and they will be tested by bio-experiments in the future.This dissertation gives the concept of the CCMM and its application studies through theory demonstration and case researches. We believe CCMM will be widely used in all aspects of CMM researches as methodology improving and study deepening, and make a contribution to the progress of modernization of TCM...
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